Contacts of the helix formed by residues 1110 - 1130 (chain A) in PDB entry 2OOQ
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 ALA1110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943A ILE* 3.9 23.1 - - + -
1106A CYS* 3.6 2.2 - - - -
1108A ALA* 3.5 4.5 - - + +
1109A GLY* 1.3 79.7 - - - +
1111A GLY* 1.3 60.5 + - - +
1112A ARG 3.8 0.4 - - - -
1113A THR 4.2 0.2 - - - -
1114A GLY 2.8 23.0 + - - -
1146A VAL 3.9 14.1 - - - +
1147A ASN* 3.6 17.0 - - + +
1148A LEU* 3.2 9.5 - - - -
1149A VAL 3.0 13.2 + - - -
1150A GLN* 4.8 5.4 - - + -
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Residues in contact with GLY1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074A ASP* 6.2 0.2 - - - -
1106A CYS* 4.2 2.0 - - - -
1110A ALA* 1.3 78.5 - - - +
1112A ARG* 1.3 61.5 + - - +
1114A GLY* 3.7 0.3 - - - -
1115A CYS* 2.9 31.4 + - - -
1149A VAL 3.9 2.1 + - - -
1150A GLN* 3.7 18.7 - - - +
1154A GLN* 3.3 24.1 - - - +
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Residues in contact with ARG1112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008A VAL* 3.2 37.5 + - + +
1009A THR* 2.9 22.2 + - - +
1013A GLU* 3.0 15.8 + - - -
1018A LYS* 4.8 0.8 - - - +
1072A TRP* 2.8 76.7 + - + +
1073A PRO 3.9 4.0 - - - -
1074A ASP* 2.9 46.9 + - - +
1075A HIS 5.0 0.4 - - - +
1106A CYS* 3.9 9.2 - - + +
1107A SER* 3.9 15.2 - - - +
1111A GLY* 1.3 70.6 - - - +
1113A THR* 1.3 66.6 + - - +
1115A CYS* 3.2 2.1 + - - +
1116A PHE* 3.0 23.6 + - - +
1154A GLN* 4.3 8.5 - - - +
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Residues in contact with THR1113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981A ALA* 3.7 31.0 - - + -
1008A VAL* 3.9 2.4 - - - +
1104A VAL* 3.6 29.2 - - + +
1105A HIS* 3.2 6.6 - - - -
1106A CYS* 3.0 38.5 + - - -
1109A GLY* 3.6 14.3 - - - +
1111A GLY 3.3 0.2 - - - -
1112A ARG* 1.3 78.9 - - - +
1114A GLY* 1.3 64.0 + - - +
1116A PHE* 3.2 2.4 + - - +
1117A ILE* 3.1 26.9 + - + +
1148A LEU* 4.3 1.3 - - + -
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Residues in contact with GLY1114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110A ALA 2.8 24.8 + - - -
1111A GLY 3.7 0.2 - - - -
1113A THR* 1.3 74.6 - - - +
1115A CYS* 1.3 55.6 + - - +
1117A ILE* 3.4 3.2 + - - -
1118A ALA* 2.9 31.2 + - - +
1141A LEU* 3.8 2.9 - - - +
1148A LEU* 3.9 19.5 - - - -
1149A VAL* 3.6 16.0 - - - +
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Residues in contact with CYS1115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A TRP* 3.2 34.8 - - + -
1111A GLY 2.9 20.1 + - - -
1112A ARG 3.2 2.2 + - - +
1114A GLY* 1.3 74.0 - - - +
1116A PHE* 1.3 64.1 + - - +
1118A ALA* 3.3 1.0 + - - +
1119A ILE* 3.0 30.5 + - + +
1149A VAL* 3.9 5.8 - - - +
1154A GLN* 3.5 33.7 - - - -
1157A PHE* 5.0 1.3 - - + -
1158A VAL* 3.8 24.7 - - + -
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Residues in contact with PHE1116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979A TYR* 4.4 9.9 - + - -
1006A VAL* 3.8 28.5 - - + -
1008A VAL* 4.7 10.3 - - + -
1072A TRP* 4.3 6.2 - - + -
1084A LEU* 4.8 3.8 - - + -
1087A PHE* 3.7 28.3 - + - -
1088A VAL* 3.8 29.1 - - + +
1091A VAL* 4.3 17.5 - - + -
1102A ILE* 5.3 0.7 - - + -
1104A VAL* 4.0 30.1 - - + -
1112A ARG 3.0 12.4 + - - +
1113A THR 3.7 6.3 - - - +
1115A CYS* 1.3 76.1 - - - +
1117A ILE* 1.3 62.6 + - + +
1119A ILE* 3.9 5.9 - - - +
1120A ASP* 2.9 44.8 + - + +
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Residues in contact with ILE1117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970A ILE* 4.1 18.8 - - + -
971A ASP 5.1 0.4 - - - +
979A TYR* 3.5 53.4 - - + -
981A ALA* 4.2 4.3 - - + -
1104A VAL* 4.2 11.7 - - + -
1113A THR* 3.1 33.6 + - + +
1114A GLY* 3.9 3.4 - - - +
1116A PHE* 1.3 79.1 - - + +
1118A ALA* 1.3 62.2 + - - +
1120A ASP* 3.8 3.2 - - - +
1121A THR* 2.8 33.3 + - - +
1141A LEU* 3.7 25.8 - - + -
1148A LEU* 4.7 4.5 - - + -
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Residues in contact with ALA1118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114A GLY 2.9 18.3 + - - +
1115A CYS 3.7 3.6 - - - +
1117A ILE* 1.3 77.6 - - - +
1119A ILE* 1.3 56.3 + - - +
1121A THR* 3.8 0.5 - - - -
1122A MET* 2.9 38.2 + - + +
1134A ILE* 5.5 0.2 - - + -
1137A CYS* 4.1 12.1 - - - -
1138A VAL* 4.4 10.8 - - + -
1141A LEU* 3.9 18.1 - - + +
1149A VAL* 4.5 1.1 - - + -
1158A VAL* 3.9 23.1 - - + -
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Residues in contact with ILE1119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A LEU* 3.8 25.6 - - + -
1085A LEU* 4.0 25.6 - - + -
1088A VAL* 4.5 10.8 - - + -
1115A CYS 3.0 25.2 + - - +
1116A PHE* 3.9 3.8 - - - +
1118A ALA* 1.3 73.2 - - - +
1120A ASP* 1.3 65.9 + - - +
1122A MET* 3.2 2.1 + - - +
1123A LEU* 2.9 40.0 + - + +
1157A PHE* 4.0 9.4 - - + -
1158A VAL* 4.1 23.1 - - + +
1161A ALA* 3.7 26.5 - - + -
1162A ILE* 4.3 10.3 - - + +
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Residues in contact with ASP1120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978A HIS* 4.5 7.4 - - - -
979A TYR* 2.5 34.8 + - + +
1088A VAL* 3.6 14.1 - - + +
1091A VAL* 5.9 1.9 - - - +
1092A LYS* 2.7 65.4 + - - +
1102A ILE* 5.2 2.9 - - - +
1116A PHE* 2.9 32.4 + - + +
1117A ILE 3.8 1.1 - - - +
1119A ILE* 1.3 78.9 - - - +
1121A THR* 1.3 61.8 + - - +
1123A LEU 3.6 0.5 + - - -
1124A ASP* 3.4 10.6 + - - +
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Residues in contact with THR1121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971A ASP 4.8 1.8 + - - +
972A GLY* 4.4 5.9 - - - -
973A TYR* 3.8 25.6 - - + +
979A TYR* 3.2 22.2 + - - -
1117A ILE* 2.8 21.8 + - - +
1118A ALA 3.8 3.4 - - - -
1120A ASP* 1.3 76.7 - - - +
1122A MET* 1.3 76.6 + - + +
1124A ASP* 3.2 11.0 + - - +
1125A MET* 3.0 24.5 + - + +
1137A CYS* 4.2 10.1 - - - -
1141A LEU* 5.6 1.1 - - + +
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Residues in contact with MET1122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118A ALA 2.9 22.2 + - - +
1119A ILE 3.9 0.2 - - - +
1121A THR* 1.3 89.1 - - + +
1123A LEU* 1.3 63.0 + - - +
1125A MET* 3.3 35.9 - - + +
1126A ALA* 2.8 31.2 + - - +
1132A VAL* 3.7 11.7 - - + +
1133A ASP 3.8 34.1 - - - +
1134A ILE* 4.0 7.6 - - + -
1137A CYS* 3.7 26.9 - - + -
1162A ILE* 3.3 30.5 - - + -
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Residues in contact with LEU1123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085A LEU* 4.4 6.1 - - + +
1088A VAL* 4.2 24.5 - - + -
1092A LYS* 4.2 10.5 - - + -
1119A ILE* 2.9 30.0 + - + +
1120A ASP 3.9 4.9 - - - +
1122A MET* 1.3 77.4 - - - +
1124A ASP* 1.3 58.0 + - - +
1126A ALA* 3.5 4.6 + - + +
1127A GLU* 2.9 30.7 + - - +
1162A ILE* 4.2 24.9 - - + +
1165A ALA* 3.4 34.3 - - + -
1166A CYS* 5.1 4.7 - - - -
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Residues in contact with ASP1124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A TYR* 3.7 28.4 + - + +
974A HIS* 5.3 3.6 + - - +
978A HIS* 5.6 5.2 - - - -
979A TYR* 5.2 1.6 + - - -
1092A LYS* 2.6 33.5 + - - +
1120A ASP* 3.4 9.4 + - - +
1121A THR* 3.2 11.0 + - - +
1122A MET 3.2 0.4 - - - -
1123A LEU* 1.3 76.5 - - - +
1125A MET* 1.3 60.9 + - - +
1127A GLU* 3.2 7.3 + - - +
1128A ASN* 3.1 24.9 + - - +
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Residues in contact with MET1125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890A ALA* 6.2 0.2 - - - -
973A TYR* 3.6 39.7 - - + -
1121A THR* 3.0 11.5 + - + +
1122A MET* 3.3 34.7 + - + +
1124A ASP* 1.3 75.7 - - - +
1126A ALA* 1.3 53.8 + - - +
1128A ASN 3.3 0.2 + - - -
1129A GLU* 2.8 46.9 + - - +
1131A VAL* 3.4 15.5 - - - +
1132A VAL* 3.9 5.6 - - - -
1133A ASP* 3.7 27.8 - - + +
1137A CYS* 6.4 0.2 - - - -
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Residues in contact with ALA1126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A VAL* 3.9 17.3 - - + +
1122A MET 2.8 21.6 + - - +
1123A LEU* 3.8 6.5 - - - +
1125A MET* 1.3 72.0 - - - +
1127A GLU* 1.3 64.8 + - - +
1130A GLY* 3.0 23.0 + - - -
1131A VAL 3.5 11.1 + - - -
1132A VAL* 3.7 14.4 - - + -
1166A CYS* 4.0 15.9 - - - -
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Residues in contact with GLU1127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123A LEU 2.9 18.9 + - - +
1124A ASP* 3.6 7.0 - - - +
1126A ALA* 1.3 77.3 - - - +
1128A ASN* 1.3 59.5 + - - +
1130A GLY 4.9 0.3 + - - -
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Residues in contact with ASN1128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A TYR* 3.8 24.2 - - + +
1124A ASP 3.1 16.4 + - - +
1127A GLU* 1.3 79.9 - - + +
1129A GLU* 1.3 60.4 + - + +
1130A GLY 3.7 0.2 - - - -
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Residues in contact with GLU1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A TYR* 2.5 39.9 + - - +
1125A MET* 2.8 27.5 + - - +
1128A ASN* 1.3 76.4 - - + +
1130A GLY* 1.3 63.1 + - - +
1131A VAL* 3.0 30.4 + - + +
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Residues in contact with GLY1130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892A ARG* 3.6 4.0 - - - +
893A VAL* 3.0 32.2 + - - +
1126A ALA 3.0 18.0 + - - -
1127A GLU 4.8 0.6 + - - -
1128A ASN 3.7 0.8 - - - -
1129A GLU* 1.3 76.8 - - - +
1131A VAL* 1.3 62.5 + - - +
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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