]> Semantic Publishing of Knowledge about Amino Acids version 1.2, copyright The University of Manchester, Nick Drummond, Georgina Moulton, Robert Stevens, Phil Lord Amino acids and their properties We semantically publish knowledge about the amino acids commonly described within biochemistry. The classification of amino acids is based on taylor's article (PMID:3461222) from 1986 published in the Journal of Theoretical Biology. The ontology goes further than the static paper version; it combines many aspects of the physicochemical properties taylor uses to classify amino acids to give a rich, multi axial classification of amino acids. taylor's original description of the amino acid's physicochemical properties are captured with value partitions and restrictions on the amino acid classes themselves. A series of defined classes then establishes the multi-axial classification. by publishing this knowledge about amino acids as a semantic document in the form of an ontology we persue an agenda of disruptive technology in publishing. Blogs about the published semantics of amino acids may be found at http://robertdavidstevens.wordpress.com/2010/12/18/an-update-to-the-amino-acids-ontology/ and links following. version 1.3, Annotated by Lin Zhang, Bethune International Peace Hospital, Hebei, China.1 Robert Stevens and Phillip Lord version 2.0 robert Stevens see http://robertdavidstevens.wordpress.com/2010/12/18/an-update-to-the-amino-acids-ontology/ 氨基酸及其性质 http://purl.obolibrary.org/obo/IAO_0000115 definition http://purl.obolibrary.org/obo/IAO_0000412 imported from http://purl.obolibrary.org/obo/SO_0000417 A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution. http://purl.obolibrary.org/obo/SO_0000417 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0000417 polypeptide_domain http://purl.obolibrary.org/obo/SO_0000912 A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). http://purl.obolibrary.org/obo/SO_0000912 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0000912 asx_turn http://purl.obolibrary.org/obo/SO_0001070 Region of polypeptide with a given structural property. http://purl.obolibrary.org/obo/SO_0001070 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001070 polypeptide_structural_region http://purl.obolibrary.org/obo/SO_0001071 Arrangement of the polypeptide with respect to the lipid bilayer. http://purl.obolibrary.org/obo/SO_0001071 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001071 membrane_structure http://purl.obolibrary.org/obo/SO_0001072 Polypeptide region that is localized outside of a lipid bilayer. http://purl.obolibrary.org/obo/SO_0001072 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001072 extramembrane_polypeptide_region http://purl.obolibrary.org/obo/SO_0001073 Polypeptide region that is localized inside the cytoplasm. http://purl.obolibrary.org/obo/SO_0001073 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001073 cytoplasmic_polypeptide_region http://purl.obolibrary.org/obo/SO_0001074 Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm. http://purl.obolibrary.org/obo/SO_0001074 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001074 non_cytoplasmic_polypeptide_region http://purl.obolibrary.org/obo/SO_0001075 Polypeptide region present in the lipid bilayer. http://purl.obolibrary.org/obo/SO_0001075 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001075 intramembrane_polypeptide_region http://purl.obolibrary.org/obo/SO_0001076 Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane. http://purl.obolibrary.org/obo/SO_0001076 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001076 membrane_peptide_loop http://purl.obolibrary.org/obo/SO_0001077 Polypeptide region traversing the lipid bilayer. http://purl.obolibrary.org/obo/SO_0001077 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001077 transmembrane_polypeptide_region http://purl.obolibrary.org/obo/SO_0001078 A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain. http://purl.obolibrary.org/obo/SO_0001078 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure http://purl.obolibrary.org/obo/SO_0001079 Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit. http://purl.obolibrary.org/obo/SO_0001079 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001079 polypeptide_structural_motif http://purl.obolibrary.org/obo/SO_0001080 A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope. http://purl.obolibrary.org/obo/SO_0001080 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001080 coiled_coil http://purl.obolibrary.org/obo/SO_0001081 A motif comprising two helices separated by a turn. http://purl.obolibrary.org/obo/SO_0001081 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001081 helix_turn_helix http://purl.obolibrary.org/obo/SO_0001106 A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). http://purl.obolibrary.org/obo/SO_0001106 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001106 asx_motif http://purl.obolibrary.org/obo/SO_0001107 A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees. http://purl.obolibrary.org/obo/SO_0001107 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001107 beta_bulge http://purl.obolibrary.org/obo/SO_0001108 A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins. http://purl.obolibrary.org/obo/SO_0001108 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001108 beta_bulge_loop http://purl.obolibrary.org/obo/SO_0001109 A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3. http://purl.obolibrary.org/obo/SO_0001109 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001109 beta_bulge_loop_five http://purl.obolibrary.org/obo/SO_0001110 A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4. http://purl.obolibrary.org/obo/SO_0001110 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001110 beta_bulge_loop_six http://purl.obolibrary.org/obo/SO_0001111 A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array. http://purl.obolibrary.org/obo/SO_0001111 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001111 beta_strand http://purl.obolibrary.org/obo/SO_0001112 A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets. http://purl.obolibrary.org/obo/SO_0001112 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001112 antiparallel_beta_strand http://purl.obolibrary.org/obo/SO_0001113 A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets. http://purl.obolibrary.org/obo/SO_0001113 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001113 parallel_beta_strand http://purl.obolibrary.org/obo/SO_0001114 A helix is a secondary_structure conformation where the peptide backbone forms a coil. http://purl.obolibrary.org/obo/SO_0001114 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001114 peptide_helix http://purl.obolibrary.org/obo/SO_0001115 A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw. http://purl.obolibrary.org/obo/SO_0001115 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001115 left_handed_peptide_helix http://purl.obolibrary.org/obo/SO_0001116 A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw. http://purl.obolibrary.org/obo/SO_0001116 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001116 right_handed_peptide_helix http://purl.obolibrary.org/obo/SO_0001117 The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. http://purl.obolibrary.org/obo/SO_0001117 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001117 alpha_helix http://purl.obolibrary.org/obo/SO_0001118 The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier. http://purl.obolibrary.org/obo/SO_0001118 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001118 pi_helix http://purl.obolibrary.org/obo/SO_0001119 The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier. http://purl.obolibrary.org/obo/SO_0001119 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001119 three_ten_helix http://purl.obolibrary.org/obo/SO_0001120 A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops. http://purl.obolibrary.org/obo/SO_0001120 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001120 polypeptide_nest_motif http://purl.obolibrary.org/obo/SO_0001121 A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001121 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001121 polypeptide_nest_left_right_motif http://purl.obolibrary.org/obo/SO_0001122 A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001122 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001122 polypeptide_nest_right_left_motif http://purl.obolibrary.org/obo/SO_0001123 A motif of six or seven consecutive residues that contains two H-bonds. http://purl.obolibrary.org/obo/SO_0001123 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001123 schellmann_loop http://purl.obolibrary.org/obo/SO_0001124 Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5). http://purl.obolibrary.org/obo/SO_0001124 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001124 schellmann_loop_seven http://purl.obolibrary.org/obo/SO_0001125 Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4). http://purl.obolibrary.org/obo/SO_0001125 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001125 schellmann_loop_six http://purl.obolibrary.org/obo/SO_0001126 A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). http://purl.obolibrary.org/obo/SO_0001126 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001126 serine_threonine_motif http://purl.obolibrary.org/obo/SO_0001127 A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative. http://purl.obolibrary.org/obo/SO_0001127 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001127 serine_threonine_staple_motif http://purl.obolibrary.org/obo/SO_0001128 A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues. http://purl.obolibrary.org/obo/SO_0001128 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001128 polypeptide_turn_motif http://purl.obolibrary.org/obo/SO_0001129 Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001129 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001129 asx_turn_left_handed_type_one http://purl.obolibrary.org/obo/SO_0001130 Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001130 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001130 asx_turn_left_handed_type_two http://purl.obolibrary.org/obo/SO_0001131 Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001131 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001131 asx_turn_right_handed_type_two http://purl.obolibrary.org/obo/SO_0001132 Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001132 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001132 asx_turn_right_handed_type_one http://purl.obolibrary.org/obo/SO_0001133 A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization. http://purl.obolibrary.org/obo/SO_0001133 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001133 beta_turn http://purl.obolibrary.org/obo/SO_0001134 Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. http://purl.obolibrary.org/obo/SO_0001134 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001134 beta_turn_left_handed_type_one http://purl.obolibrary.org/obo/SO_0001135 Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees. http://purl.obolibrary.org/obo/SO_0001135 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001135 beta_turn_left_handed_type_two http://purl.obolibrary.org/obo/SO_0001136 Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001136 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001136 beta_turn_right_handed_type_one http://purl.obolibrary.org/obo/SO_0001137 Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001137 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001137 beta_turn_right_handed_type_two http://purl.obolibrary.org/obo/SO_0001138 Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees. http://purl.obolibrary.org/obo/SO_0001138 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001138 gamma_turn http://purl.obolibrary.org/obo/SO_0001139 Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0. http://purl.obolibrary.org/obo/SO_0001139 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001139 gamma_turn_classic http://purl.obolibrary.org/obo/SO_0001140 Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0. http://purl.obolibrary.org/obo/SO_0001140 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001140 gamma_turn_inverse http://purl.obolibrary.org/obo/SO_0001141 A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). http://purl.obolibrary.org/obo/SO_0001141 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001141 serine_threonine_turn http://purl.obolibrary.org/obo/SO_0001142 The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001142 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001142 st_turn_left_handed_type_one http://purl.obolibrary.org/obo/SO_0001143 The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001143 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001143 st_turn_left_handed_type_two http://purl.obolibrary.org/obo/SO_0001144 The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001144 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001144 st_turn_right_handed_type_one http://purl.obolibrary.org/obo/SO_0001145 The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001145 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001145 st_turn_right_handed_type_two http://purl.obolibrary.org/obo/SO_0001150 A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline. http://purl.obolibrary.org/obo/SO_0001150 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001150 beta_turn_type_six http://purl.obolibrary.org/obo/SO_0001151 A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees. http://purl.obolibrary.org/obo/SO_0001151 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001151 beta_turn_type_six_a http://purl.obolibrary.org/obo/SO_0001152 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001152 beta_turn_type_six_a_one http://purl.obolibrary.org/obo/SO_0001153 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001153 beta_turn_type_six_a_two http://purl.obolibrary.org/obo/SO_0001154 A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees. http://purl.obolibrary.org/obo/SO_0001154 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001154 beta_turn_type_six_b http://purl.obolibrary.org/obo/SO_0001155 A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees. http://purl.obolibrary.org/obo/SO_0001155 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001155 beta_turn_type_eight http://purl.obolibrary.org/obo/SO_0001812 A region that traverses the lipid bilayer and adopts a helical secondary structure. http://purl.obolibrary.org/obo/SO_0001812 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0001812 transmembrane_helix http://purl.obolibrary.org/obo/SO_0100003 A region of polypeptide chain with high conformational flexibility. http://purl.obolibrary.org/obo/SO_0100003 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0100003 intrinsically_unstructured_polypeptide_region http://purl.obolibrary.org/obo/SO_0100004 A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. http://purl.obolibrary.org/obo/SO_0100004 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0100004 catmat_left_handed_three http://purl.obolibrary.org/obo/SO_0100005 A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. http://purl.obolibrary.org/obo/SO_0100005 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0100005 catmat_left_handed_four http://purl.obolibrary.org/obo/SO_0100006 A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. http://purl.obolibrary.org/obo/SO_0100006 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0100006 catmat_right_handed_three http://purl.obolibrary.org/obo/SO_0100007 A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. http://purl.obolibrary.org/obo/SO_0100007 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0100007 catmat_right_handed_four http://purl.obolibrary.org/obo/SO_0100008 A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative. http://purl.obolibrary.org/obo/SO_0100008 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0100008 alpha_beta_motif http://purl.obolibrary.org/obo/SO_0100012 Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds). http://purl.obolibrary.org/obo/SO_0100012 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0100012 peptide_coil http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#A ala http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#A Alanine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#A A http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#A Alanine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#C Cys http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#C Cysteine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#C C http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#C Cysteine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#D Asp http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#D Aspartate http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#D D http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#D Aspartate http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#E glu http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#E Glutamate http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#E E http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#E Glutamate http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#F Phe http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#F Phenylalanine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#F F http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#F Phenylalanine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#G gly http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#G glycine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#G G http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#G glycine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#H His http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#H Histidine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#H H http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#H Histidine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#I Ile http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#I Isoleucine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#I I http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#I Isoleucine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#K Lys http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#K Lysine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#K K http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#K Lysine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#L Leu http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#L Leucine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#L L http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#L Leucine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#M Met http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#M Methionine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#M M http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#M Methionine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#N Asn http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#N Asparagine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#N N http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#N Asparagine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#P Pro http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#P Proline http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#P P http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#P Proline http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#Q Gln http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#Q Glutamine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#Q Q http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#Q Glutamine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#R Arg http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#R Arginine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#R R http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#R Arginine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#S Ser http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#S Serine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#S S http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#S Serine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#T Thr http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#T Threonine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#T T http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#T Threonine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#V Val http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#V Valine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#V V http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#V Valine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#W Trp http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#W Tryptophan http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#W W http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#W Tryptophan http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#Y Tyr http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#Y Tyrosine http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#Y Y http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#Y Tyrosine http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00001 entity http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00002 Feature of a residue-residue contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00002 contact_attribute http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00003 residue_attribute http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00004 contact_probability http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00005 The method used to uncover the contact site. It can be computational or experimental. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00005 discovery_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00006 interaction_type http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00007 location_in_structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00008 sequence_separation http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00009 A contact between amino acids from different polypeptide chains. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00009 inter_chain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00010 A contact between amino acid residues within a single polypeptide chain. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00010 In literature (e. g. [1]) contact are devided into three categories: short, medium, long. However definition of each group vary from paper to paper. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00010 intra_chain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00011 long_range http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00012 medium_range http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00013 short_range http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00014 Contact between two protein domains. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00014 interdomain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00015 A contact within the same protein domain. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00015 intradomain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00016 Contact between two different secondary structures. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00016 inter_secondary_structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00017 A contact within the same secondary structure. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00017 intra_secondary_structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00018 beta_beta http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00020 beta_helix http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00021 beta_turn http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00022 helix_helix http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00023 helix_coil http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00024 helix_turn http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00025 turn_turn http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00026 coil_coil http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00027 turn_coil http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00028 A real interaction resulting from physics and chemistry. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00028 physico_chemical_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00029 No actuall interaction was identified. Close proximity of residues does not mean that they actually interact. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00029 undefined_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00030 A chemical bond that results from sharing electron pairs between atoms. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00030 covalent_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00031 A weak interaction, which does not involve sharing electron pairs between atoms. The energy of typical non-covalent interactions is in the range 1-5 kcal/mol. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00031 non_covalent_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00032 An interaction between two hydrophobic amino acid residues. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00032 hydrophobic_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00033 polar_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00034 aliphatic_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00035 Interactions of aromatic amino acids resulting from the orientation of side chain aromatic rings. The distance between aromatic ring centers of mass is < 7.5 A or the minimal distance between rings is < 4.5 A http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00035 stacking_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00036 electrostatic_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00037 hydrogen_bond_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00038 saltbridge_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00039 Hydrogen bonds formed by backbone NH and CO groups. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00039 backbone_hbond http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00040 Hydrogen bonds formed by side chains. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00040 sidechain_hbond http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00041 The distance between aromatic ring centers of mass is < 7.5 A or the minimal distance between rings in < 4.5 A. The angle between vectors normal to ring planes is close to 0. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00041 displaced_parallel_stacking_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00042 The distance between aromatic ring centers of mass is < 7.5 A or the minimal distance between rings in < 4.5 A. The angle between vectors normal to ring planes is betweeen 20 and 70 degrees. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00042 oblique_stacking_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00043 The distance between aromatic ring centers of mass is < 7.5 A or the minimal distance between rings in < 4.5 A. The angle between vectors normal to ring planes equals approx. 90 degrees. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00043 T_shape_stacking_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00044 In silico prediction methods. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00044 computational_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00045 Wet lab experimental technique. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00045 experimental_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00046 machine_learning_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00047 The method uses evolutionary information and a machine learning approach. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00047 hybrid_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00048 Contacts are copied from structural homology templates. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00048 homology_modeling_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00049 The mehtod uses mutation covariance. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00049 correlated_mutation_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00050 in_solution_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00051 solid_state_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00052 NMR http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00053 crystal_structure_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00054 powder_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00055 high_probability http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00056 low_probability http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00057 unknown_probability http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00058 amino_acid_attribute http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00059 residue_location_in_structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00060 amino_acid_residue http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00061 contact_group http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00062 protein http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00063 structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00064 part_of http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00065 is_part_of_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00066 is_part_of_contact_cluster http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00067 is_part_of_secondary_structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00068 located_in http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00070 has_burial http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00071 has_contact_attribute http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00072 is_model_of http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00073 is_characterized_by http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00074 contains_residues_in_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00075 A sequence od amino acids conected with peptide bonds. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00075 polypeptide_chain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00076 globular_protein http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00077 membrane_protein http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00078 A pair of amino acids within a threshold range of each other in the 3D space. A contact group of cardinality equal 1. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00078 single_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00079 A cluster of contacts in protein. Contact cluster can be define according to Chen et al. [1] as a: "two contact (i,j) and (k,l) are taken to be in same cluster if they are close together on the contact map, according to the distance criterion |i-k| + |j-l| <=4" Clustering has sense only for medium and long contact. [1]: Chen P., Liu C., Mohammed M., Southerland B., Gloster C. "Prediction of Inter-residue Contact Cluster from Hydrophobic Cores" 7th International Conference on Machine Learing and Application, 2008, 703-708. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00079 contact_cluster http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00080 inter_domain_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00081 intra_domain_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00082 inter_secondary_structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00083 intra_secondary_structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00084 long_range_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00085 short_range_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00086 medium_range_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00087 phy_chem_interaction_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00088 undefined_interaction_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00089 single_technique_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00090 experimentally_detected_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00091 predicted_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00092 single_model_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00093 covalent_bond_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00094 non_covalent_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00095 disulphide_bridge http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00096 hydrophobic_interaction_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00097 polar_interaction_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00098 aliphatic_interaction_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00099 stacking_interaction_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00100 electrostatic_interaction_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00101 hydrogen_bond_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00102 salt_bridge http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00103 helix_beta_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00104 helix_helix_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00105 helix_turn_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00106 beta_beta_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00107 beta_turn_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00108 turn_turn_contact http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00109 buried_residue http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00110 exposed_resiude http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00111 A bond between carboxyl and amin groups of amino acids. Protein backbone is formed by peptide bonds between a sequence of amino acids. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00111 peptide_bond_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00112 A chemical bond between sulhur atoms in thiol grups. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00112 disulphide_bond_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00113 Covalent bond not classified elsewhere. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00113 specific_bond_interaction http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00114 beta_coil http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00115 has_discovery_technique http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00116 has_interaction_type http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00117 has_sequence_separation http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00118 has_probability http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00119 has_location http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00120 super_secondary_structure http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00121 all_alpha_domain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00122 all_beta_domain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00123 alpha_plus_beta_domain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00124 alpha_slash_beta_domain http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00125 A region inside the protein core not accessible to the solvent. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00125 buried_polypeptide_region http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00126 A region near protein surface. Residues in this region have a considerable solvent accessible area. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00126 exposed_polypeptide_region http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00128 polyproline_helix http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00129 peptide_sheet http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00130 initial_beta_strand http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00131 beta_bridge http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00133 Sequence separation is lower or equal to 5 amino acids. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00133 sequential http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00134 The contact results from closness in the amino acid sequence. http://www.semanticweb.org/bob/ontologies/2015/8/PCO_v16/PCO_00134 sequential_contact