Contacts of the helix formed by residues 1096 - 1116 (chain C) in PDB entry 5Y3R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL1096 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1049C GLN* 4.6 9.6 - - + +
1050C GLU* 5.4 0.9 - - + -
1056C THR* 3.9 42.2 - - + +
1057C LYS* 3.7 27.6 - - + +
1060C PHE* 4.5 3.6 - - + -
1093C GLU 4.4 2.8 + - - +
1094C SER* 3.7 1.5 - - - -
1095C LEU* 1.3 95.2 - - + +
1097C GLU* 1.3 61.7 + - - +
1098C GLN 3.1 0.2 - - - -
1099C PHE* 3.2 7.3 + - + +
1100C VAL* 2.9 37.7 + - + +
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Residues in contact with GLU1097 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089C PHE 2.6 15.6 - - - +
1090C ARG* 3.5 28.5 - - - +
1091C GLU 3.1 6.6 - - - +
1092C GLU* 2.7 23.6 - - - +
1093C GLU* 2.2 44.7 + - - +
1094C SER 3.3 5.0 - - - +
1095C LEU 2.6 4.8 + - - +
1096C VAL* 1.3 72.9 - - - +
1098C GLN* 1.3 64.8 + - - +
1100C VAL 3.0 1.0 + - - -
1101C PHE* 2.8 49.8 + - + -
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Residues in contact with GLN1098 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095C LEU* 2.3 38.7 + - + +
1097C GLU* 1.3 68.7 - - - +
1099C PHE* 1.3 70.1 + - + +
1101C PHE* 3.2 21.8 - - + +
1102C GLU* 2.7 31.7 - - - +
1149C LYS* 4.7 22.2 - - + +
1150C LYS* 6.5 0.2 - - + -
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Residues in contact with PHE1099 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057C LYS* 3.3 45.3 - - + -
1095C LEU* 5.0 7.0 - - + -
1096C VAL* 3.2 8.9 + - + +
1098C GLN* 1.3 88.2 - - + +
1100C VAL* 1.3 58.7 + - + +
1101C PHE 2.8 15.5 + - - -
1102C GLU* 3.0 8.0 + - - +
1103C ALA* 3.0 28.1 + - + +
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Residues in contact with VAL1100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060C PHE* 3.4 41.7 - - + -
1064C TYR* 2.9 23.1 - - - +
1090C ARG* 3.1 37.2 - - - +
1096C VAL* 2.9 25.8 + - + +
1097C GLU 3.7 0.2 - - - +
1099C PHE* 1.3 76.0 - - + +
1101C PHE* 1.3 51.8 + - - +
1103C ALA* 4.4 3.8 - - - -
1104C LEU* 2.2 48.1 - - + +
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Residues in contact with PHE1101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090C ARG* 3.7 29.4 - - - -
1091C GLU 5.2 1.6 - - - -
1097C GLU* 2.8 60.2 + - + -
1098C GLN* 3.2 21.3 - - + +
1099C PHE 2.8 0.8 + - - -
1100C VAL* 1.3 83.7 - - - +
1102C GLU* 1.3 61.6 + - - +
1104C LEU* 3.1 5.1 - - + +
1105C VAL* 2.9 30.4 + - + +
1138C ILE* 4.7 24.7 - - + -
1150C LYS* 4.0 28.9 - - + -
1153C LEU* 5.1 0.4 - - - -
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Residues in contact with GLU1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098C GLN* 2.7 26.8 - - - +
1099C PHE* 3.0 4.6 + - - +
1101C PHE* 1.3 72.3 - - - +
1103C ALA* 1.3 57.8 + - - +
1105C VAL* 2.5 22.5 + - - +
1106C ILE* 2.9 21.1 + - + +
1149C LYS* 3.8 21.4 - - + +
1150C LYS* 3.1 27.6 - - - +
1153C LEU* 3.5 40.4 - - + -
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Residues in contact with ALA1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060C PHE* 6.1 0.2 - - + -
1064C TYR* 4.0 16.7 - - + -
1099C PHE* 3.0 21.7 + - + +
1100C VAL* 4.4 0.9 - - + -
1102C GLU* 1.3 76.8 - - - +
1104C LEU* 1.3 51.9 + - - +
1106C ILE* 4.2 9.5 - - - +
1107C TYR* 2.5 39.7 + - - +
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Residues in contact with LEU1104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064C TYR* 3.0 33.4 - - + +
1083C ASN* 3.2 28.9 - - + +
1090C ARG* 4.8 6.7 - - - +
1100C VAL* 2.2 38.7 + - + +
1101C PHE* 3.1 5.6 - - - +
1103C ALA* 1.3 77.2 - - - +
1105C VAL* 1.3 59.0 + - + +
1107C TYR* 2.9 8.7 - - + +
1108C MET* 2.8 59.3 + - + +
1134C LEU* 5.6 2.2 - - + -
1138C ILE* 4.3 22.4 - - + -
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Residues in contact with VAL1105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101C PHE 2.9 22.0 + - - +
1102C GLU* 2.5 15.2 + - - +
1104C LEU* 1.3 70.3 - - + +
1106C ILE* 1.3 58.1 + - - +
1107C TYR 2.8 3.1 - - - -
1108C MET* 2.3 44.4 + - + +
1109C GLU* 2.9 9.4 + - + +
1135C CYS* 5.3 13.0 - - - -
1138C ILE* 6.4 2.5 - - + -
1153C LEU* 4.1 15.0 - - + -
1157C PHE* 3.5 33.0 - - + -
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Residues in contact with ILE1106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102C GLU* 2.9 19.5 + - + +
1103C ALA* 4.2 9.0 - - - +
1105C VAL* 1.3 78.2 - - + +
1107C TYR* 1.3 58.5 + - - +
1109C GLU* 3.2 27.1 - - - +
1110C SER* 2.8 40.2 + - - +
1153C LEU* 4.6 9.9 - - + -
1157C PHE* 3.6 21.5 - - + -
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Residues in contact with TYR1107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063C LEU 4.7 0.3 + - - -
1064C TYR* 3.3 64.8 - + + -
1067C ALA* 3.6 10.2 - - + +
1068C LEU* 3.6 25.6 - - + -
1079C SER* 3.3 24.1 + - - -
1082C PHE* 5.0 3.1 - + - -
1083C ASN* 4.7 1.6 - - - -
1103C ALA 2.5 26.7 + - - +
1104C LEU* 2.9 16.6 - - + +
1106C ILE* 1.3 79.4 - - - +
1108C MET* 1.3 50.9 - - - -
1110C SER* 4.9 2.5 - - - -
1111C LEU* 2.2 69.6 + - + +
1131C ILE* 4.1 10.8 - - + -
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Residues in contact with MET1108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104C LEU* 2.8 50.1 + - + +
1105C VAL* 2.3 36.9 + - + +
1107C TYR* 1.3 66.5 - - - +
1109C GLU* 1.3 56.9 + - - +
1111C LEU* 2.9 11.9 - - + +
1112C ALA* 2.8 32.1 + - - +
1128C CYS* 5.2 3.2 - - - -
1131C ILE* 3.5 46.9 - - + +
1132C ASP* 3.5 22.0 - - - +
1134C LEU 4.0 10.3 - - - +
1135C CYS* 6.1 1.8 - - - -
1168C LEU* 5.2 5.3 - - + +
1171C TRP* 5.9 4.3 - - - -
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Residues in contact with GLU1109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105C VAL* 2.9 5.8 + - + +
1106C ILE* 3.2 38.1 - - - +
1108C MET* 1.3 78.4 - - - +
1110C SER* 1.3 70.8 + - - +
1113C LEU* 3.0 33.0 + - + +
1157C PHE* 3.3 22.7 - - + -
1160C SER* 3.3 27.5 + - - -
1162C SER* 5.6 1.1 - - - -
1165C LEU* 4.6 8.8 - - + +
1168C LEU* 4.4 20.9 - - + -
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Residues in contact with SER1110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C LEU* 4.8 9.6 - - - -
1106C ILE* 2.8 20.5 + - - +
1107C TYR* 4.6 2.0 - - - -
1109C GLU* 1.3 79.5 + - - +
1111C LEU* 1.3 66.7 + - - +
1113C LEU* 4.7 4.3 - - - +
1114C ALA* 2.8 26.5 + - - +
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Residues in contact with LEU1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067C ALA* 5.3 2.9 - - + -
1068C LEU* 3.8 16.3 - - + +
1075C ARG* 5.7 3.8 - - + -
1079C SER* 5.0 6.1 - - - +
1107C TYR* 2.2 70.6 + - + +
1108C MET* 2.9 23.3 - - + +
1110C SER* 1.3 80.9 - - - +
1112C ALA* 1.3 58.5 + - - +
1114C ALA* 3.0 6.2 + - - +
1115C HIS* 2.6 37.0 + - + +
1128C CYS* 5.1 13.2 - - + -
1131C ILE* 3.8 15.7 - - + -
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Residues in contact with ALA1112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108C MET 2.8 14.7 + - - +
1109C GLU 3.5 2.5 - - - +
1111C LEU* 1.3 77.5 - - - +
1113C LEU* 1.3 76.8 + - + +
1114C ALA 2.8 1.7 + - - -
1115C HIS* 2.7 35.6 + - - +
1116C ALA* 3.0 6.7 + - - +
1125C GLN* 5.5 2.2 - - + +
1128C CYS* 4.4 20.4 - - - -
1164C CYS* 4.8 10.5 - - - -
1168C LEU* 4.7 8.3 - - + -
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Residues in contact with LEU1113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109C GLU* 3.0 26.1 + - + +
1110C SER* 4.3 3.6 - - - +
1112C ALA* 1.3 81.7 - - + +
1114C ALA* 1.3 66.4 + - - +
1116C ALA* 3.0 18.5 - - - +
1117C ASP* 4.8 2.1 + - - +
1162C SER* 3.1 39.9 - - - +
1163C LEU* 3.4 37.7 - - + +
1164C CYS* 3.6 21.3 - - + +
1165C LEU* 4.9 2.7 - - + -
1168C LEU* 3.8 20.9 - - + -
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Residues in contact with ALA1114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C LEU* 5.5 11.0 - - + +
1071C ASN* 5.1 13.0 - - - +
1110C SER 2.8 21.8 + - - +
1111C LEU* 3.1 7.2 - - - +
1112C ALA 2.8 1.6 + - - -
1113C LEU* 1.3 81.4 - - - +
1115C HIS* 1.3 62.0 + - - +
1116C ALA 2.9 2.4 + - - -
1117C ASP* 4.4 7.4 + - - +
3692C VAL* 6.3 4.5 - - + -
3695C LEU* 5.3 12.6 - - - +
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Residues in contact with HIS1115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071C ASN* 5.4 20.3 + - + +
1072C ALA 5.7 6.3 + - - +
1073C PHE* 6.0 1.1 - - - +
1076C LEU* 6.0 5.2 - - + -
1111C LEU* 2.6 51.5 + - + +
1112C ALA* 2.7 25.3 + - - -
1114C ALA* 1.3 75.1 - - - +
1116C ALA* 1.3 50.5 - - - +
1117C ASP* 2.2 25.3 + - - +
1118C GLU 3.4 4.9 + - - -
1119C LYS* 3.1 38.6 + - + +
1124C ILE* 5.0 13.1 - - + +
1125C GLN* 6.1 2.6 - - - +
1128C CYS* 6.0 3.3 - - + +
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Residues in contact with ALA1116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112C ALA 3.0 14.8 + - - +
1113C LEU* 3.0 24.7 - - - +
1114C ALA 2.9 4.6 + - - -
1115C HIS* 1.3 74.1 - - - +
1117C ASP* 1.3 54.7 + - - +
1119C LYS* 2.1 42.2 + - + -
1164C CYS* 4.7 2.5 - - + -
1256C TRP* 3.6 35.5 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il