Contacts of the helix formed by residues 1113 - 1132 (chain B) in PDB entry 4BHW
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 GLU1113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1049B PHE* 4.2 9.9 - - + -
1054B LEU* 4.6 4.9 - - - -
1111B TYR* 4.9 2.4 - - - +
1112B GLN* 1.3 81.7 - - + +
1114B PRO* 1.3 67.0 - - + +
1115B TRP* 2.8 58.3 + - - +
1116B GLN* 3.0 45.7 + - - +
1117B TYR 4.2 0.9 + - - -
1162B TYR* 4.4 3.7 + - - +
1253B LYS* 4.3 19.9 + - - +
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Residues in contact with PRO1114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049B PHE* 3.8 12.1 - - + -
1054B LEU* 4.0 13.2 - - + -
1058B LEU* 4.6 13.8 - - + +
1111B TYR* 6.2 0.2 - - + -
1113B GLU* 1.3 83.9 - - + +
1115B TRP* 1.3 61.0 + - - +
1116B GLN 3.2 0.2 - - - -
1117B TYR* 3.3 17.3 + - + +
1118B VAL* 3.3 15.7 + - - +
1157B MET* 3.7 27.8 - - + +
1160B LEU* 3.9 19.3 - - + -
1162B TYR* 3.3 36.6 - - + +
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Residues in contact with TRP1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113B GLU* 2.8 29.7 + - - +
1114B PRO* 1.3 71.8 - - - +
1116B GLN* 1.3 59.9 + - - +
1118B VAL* 3.3 28.6 + - + +
1119B ASP* 2.9 38.5 + - - +
1157B MET* 3.9 10.1 - - + -
1162B TYR* 3.4 20.2 - + + -
1163B CYS* 5.0 4.3 - - - -
1164B CYS 3.5 25.6 - - - -
1165B GLY* 4.0 7.6 - - - -
1166B ARG 3.6 16.4 - - - -
1167B LYS* 5.2 2.9 - - + -
1244B PHE* 3.7 27.1 - + + -
1253B LYS* 2.8 44.9 + - + +
1255B HIS* 3.6 24.2 - + - -
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Residues in contact with GLN1116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105B LYS* 5.7 1.0 - - - +
1110B GLN 3.8 5.1 + - - -
1111B TYR* 3.3 25.1 - - + +
1112B GLN* 2.9 47.6 - - - +
1113B GLU* 3.0 27.7 + - - +
1115B TRP* 1.3 77.2 - - - +
1117B TYR* 1.3 58.4 + - - +
1119B ASP* 3.2 9.6 + - - +
1120B ASP* 3.0 30.3 + - - +
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Residues in contact with TYR1117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058B LEU* 3.3 36.3 + - + -
1061B THR* 2.9 27.7 + - - -
1062B LEU* 3.2 25.1 + - + +
1102B ILE* 3.6 31.0 - - + -
1106B LEU* 4.0 17.7 - - + -
1111B TYR* 3.7 26.0 - + + -
1113B GLU 4.2 0.4 + - - -
1114B PRO* 3.3 12.4 + - + +
1116B GLN* 1.3 79.1 - - - +
1118B VAL* 1.3 64.3 + - + +
1120B ASP* 3.5 2.6 + - - +
1121B ILE* 3.1 45.2 + - + +
1149B PHE* 3.8 17.7 - + - -
1153B ILE* 4.3 4.0 - - + -
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Residues in contact with VAL1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114B PRO 3.3 11.9 + - - +
1115B TRP* 3.7 33.7 - - + +
1116B GLN 3.3 0.2 - - - -
1117B TYR* 1.3 76.5 - - + +
1119B ASP* 1.3 66.7 + - - +
1121B ILE* 3.4 5.0 + - - +
1122B TRP* 3.1 42.3 + - + +
1149B PHE* 4.3 4.0 - - + -
1153B ILE* 4.2 30.3 - - + -
1157B MET* 4.7 7.6 - - - -
1165B GLY 4.1 14.1 - - - +
1167B LYS* 4.5 10.8 - - + -
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Residues in contact with ASP1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115B TRP* 2.9 25.8 + - - +
1116B GLN* 3.2 8.7 + - - +
1118B VAL* 1.3 77.6 - - - +
1120B ASP* 1.3 51.0 + - - +
1122B TRP* 3.0 5.9 + - - +
1123B LEU* 2.4 37.9 + - - +
1167B LYS* 2.5 39.2 + - - +
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Residues in contact with ASP1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097B MET* 3.5 32.0 - - + +
1102B ILE* 3.7 11.9 - - + -
1105B LYS* 3.2 22.6 + - - +
1111B TYR* 2.7 29.3 + - - +
1116B GLN 3.0 12.9 + - - +
1117B TYR 3.9 2.0 - - - +
1119B ASP* 1.3 76.9 - - - +
1121B ILE* 1.3 62.4 + - - +
1123B LEU* 3.2 23.5 - - - +
1124B MET* 3.0 20.8 + - - +
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Residues in contact with ILE1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B LEU* 4.2 7.2 - - + -
1065B LEU* 3.9 19.5 - - + -
1102B ILE* 3.6 22.2 - - + -
1117B TYR* 3.1 44.0 + - + +
1118B VAL 3.7 4.7 - - - +
1119B ASP 3.2 0.2 - - - -
1120B ASP* 1.3 76.0 - - - +
1122B TRP* 1.3 58.5 + - + +
1124B MET* 3.6 6.9 + - + +
1125B PHE* 3.3 54.9 + - + -
1149B PHE* 3.9 37.0 - - + -
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Residues in contact with TRP1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118B VAL* 3.1 38.8 + - + +
1119B ASP* 3.0 4.7 + - - +
1121B ILE* 1.3 74.0 - - + +
1123B LEU* 1.3 64.8 + - - +
1125B PHE* 3.8 21.8 - + + +
1126B ASN* 2.6 44.2 + - - +
1129B TRP* 3.4 34.1 - + - -
1146B SER* 4.2 11.4 - - - -
1149B PHE* 4.0 22.1 - + - -
1150B GLU* 3.9 32.8 - - + -
1165B GLY 5.1 1.4 + - - -
1167B LYS* 3.8 44.5 - - + +
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Residues in contact with LEU1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095B SER* 4.1 24.5 - - - +
1096B PRO 4.8 0.4 - - - +
1097B MET* 3.6 28.9 - - + -
1119B ASP 2.4 26.5 + - - +
1120B ASP* 3.2 29.6 - - - +
1122B TRP* 1.3 73.1 - - - +
1124B MET* 1.3 60.4 + - - +
1126B ASN* 3.4 2.6 + - - +
1127B ASN* 2.7 41.6 + - - +
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Residues in contact with MET1124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065B LEU* 4.5 0.9 - - + -
1075B PHE* 4.0 26.0 - - + -
1097B MET* 3.6 29.9 - - + +
1098B ASP* 3.9 17.7 - - - -
1099B LEU* 3.5 37.7 - - + -
1102B ILE* 4.6 1.8 - - + -
1120B ASP 3.0 9.3 + - - +
1121B ILE* 3.6 17.9 - - + +
1123B LEU* 1.3 81.5 - - - +
1125B PHE* 1.3 92.4 + - + +
1127B ASN* 3.6 5.9 + - - +
1128B ALA* 3.3 21.1 + - - +
1145B LEU* 5.5 1.1 - - + -
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Residues in contact with PHE1125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065B LEU* 4.4 7.9 - - + -
1075B PHE* 5.5 0.7 - + - -
1121B ILE* 3.3 36.1 + - + +
1122B TRP* 3.8 26.0 - + + +
1123B LEU 3.3 0.4 + - - -
1124B MET* 1.3 103.0 - - + +
1126B ASN* 1.3 58.4 + - - +
1128B ALA 3.4 0.2 + - - -
1129B TRP* 2.9 42.1 + - + +
1142B CYS* 3.2 28.2 - - - -
1145B LEU* 4.0 25.8 - - + -
1146B SER* 3.4 38.8 - - - -
1149B PHE* 4.3 6.1 - - + -
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Residues in contact with ASN1126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122B TRP* 2.6 40.9 + - - +
1123B LEU* 4.0 3.1 - - - +
1125B PHE* 1.3 72.6 - - - +
1127B ASN* 1.3 62.8 + - - +
1129B TRP* 3.0 24.3 + - - +
1130B LEU* 2.8 34.8 + - - +
1167B LYS* 6.2 1.4 - - - +
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Residues in contact with ASN1127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B TYR* 4.3 8.5 - - - +
1093B VAL* 3.3 32.1 - - + +
1095B SER 2.7 29.9 + - - -
1096B PRO* 3.8 6.5 - - - +
1097B MET 3.9 7.4 - - - +
1123B LEU* 2.7 35.2 + - - +
1124B MET* 3.7 8.0 - - - +
1125B PHE 3.4 0.2 - - - -
1126B ASN* 1.3 79.3 - - - +
1128B ALA* 1.3 61.3 + - - +
1130B LEU* 3.4 6.2 + - - +
1131B TYR* 3.3 22.2 + - - +
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Residues in contact with ALA1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075B PHE* 3.5 33.9 - - + -
1089B TYR* 5.1 4.2 + - - +
1124B MET 3.3 6.2 + - - +
1125B PHE 3.8 6.7 - - - +
1126B ASN 3.2 0.2 - - - -
1127B ASN* 1.3 80.1 - - - +
1129B TRP* 1.3 61.8 + - - +
1130B LEU 3.4 0.2 + - - -
1131B TYR* 5.0 1.6 - - - -
1132B ASN* 3.0 32.4 + - - +
1138B VAL* 4.5 10.8 - - + +
1139B TYR* 4.5 2.9 - - - -
1142B CYS* 4.3 5.4 - - + -
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Residues in contact with TRP1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122B TRP* 3.4 36.6 - + - -
1125B PHE* 2.9 28.0 + - + +
1126B ASN* 3.0 26.0 + - - +
1128B ALA* 1.3 76.0 - - - +
1130B LEU* 1.3 56.9 + - - +
1132B ASN 3.2 7.7 - - - +
1139B TYR* 3.0 62.0 + + + +
1142B CYS* 3.9 17.3 - - + -
1143B SER* 3.2 23.8 + - - -
1146B SER* 3.6 27.6 - - - -
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Residues in contact with LEU1130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092B ILE* 3.8 36.3 - - + +
1093B VAL* 5.7 2.9 - - + -
1126B ASN 2.8 15.5 + - - +
1127B ASN* 3.8 6.3 - - - +
1128B ALA 3.2 0.2 - - - -
1129B TRP* 1.3 77.1 - - - +
1131B TYR* 1.3 64.2 + - - +
1132B ASN 3.3 7.4 - - - +
1133B ARG* 5.6 2.1 - - - +
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Residues in contact with TYR1131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086B ILE* 3.2 51.0 - - + +
1087B PRO* 4.9 0.2 - - - +
1088B ASP* 2.4 40.2 + - - -
1089B TYR* 3.8 38.7 + + + -
1092B ILE* 4.5 20.6 - - + -
1093B VAL* 5.1 2.7 - - + -
1127B ASN 3.3 13.6 + - - +
1128B ALA* 3.7 1.1 + - - +
1130B LEU* 1.3 80.8 - - - +
1132B ASN* 1.3 72.7 + - - +
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Residues in contact with ASN1132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128B ALA* 3.0 21.4 + - - +
1129B TRP 3.2 20.8 - - - +
1130B LEU 3.3 6.8 - - - +
1131B TYR* 1.3 93.7 - - - +
1133B ARG* 1.3 65.2 + - - +
1136B SER* 3.2 23.3 + - - +
1138B VAL* 3.4 39.6 - - - +
1139B TYR* 3.7 6.6 - - + -
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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