Contacts of the helix formed by residues 1117 - 1136 (chain B) in PDB entry 3GIL
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 ASP1117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002B ILE* 3.8 12.5 - - - +
1115B VAL 4.5 0.5 - - - +
1116B ARG* 1.3 83.6 - - - +
1118B TYR* 1.3 72.4 + - - +
1119B ARG* 3.0 26.8 + - - +
1120B GLU* 3.4 14.9 + - + +
1121B ALA* 3.3 19.2 + - - +
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Residues in contact with TYR1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B GLY 4.3 2.5 + - - -
1002B ILE* 3.8 25.6 - - + -
1117B ASP* 1.3 73.0 + - - +
1119B ARG* 1.3 58.7 + - - +
1120B GLU 3.3 0.2 - - - -
1121B ALA* 3.7 3.6 - - - +
1122B TYR* 3.0 30.0 + - - +
1144B ILE* 3.7 29.6 - - + -
1145B SER* 3.7 9.2 + - - -
1146B LYS* 3.5 30.3 + - - +
1165B VAL* 3.6 21.3 - - + +
1166B ILE 4.0 8.1 + - - -
1167B ASP* 3.8 31.9 - - + -
1168B ASP* 4.2 14.4 + - - -
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Residues in contact with ARG1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117B ASP* 3.0 16.6 + - - +
1118B TYR* 1.3 76.5 - - - +
1120B GLU* 1.3 65.8 + - + +
1122B TYR* 3.7 5.5 + - - +
1123B ASN* 3.6 28.7 + - - +
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Residues in contact with GLU1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115B VAL* 3.9 31.0 + - - +
1116B ARG 4.0 5.6 - - - +
1117B ASP* 3.5 26.0 - - + +
1118B TYR 3.3 0.2 - - - -
1119B ARG* 1.3 75.6 - - + +
1121B ALA* 1.3 64.4 + - - +
1123B ASN* 3.2 10.8 + - - +
1124B LEU* 3.1 22.2 + - - +
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Residues in contact with ALA1121 (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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1002B ILE* 4.4 12.8 - - + -
1004B LEU* 4.6 1.2 - - - +
1111B ILE* 4.8 9.0 - - + -
1115B VAL 5.2 1.1 + - - +
1117B ASP 3.3 10.8 + - - +
1118B TYR* 3.7 9.9 - - - +
1119B ARG 3.4 0.2 - - - -
1120B GLU* 1.3 79.0 - - - +
1122B TYR* 1.3 58.5 + - - +
1124B LEU* 3.2 13.8 + - - +
1125B GLY 2.8 25.3 + - - -
1144B ILE* 3.5 35.3 - - + +
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Residues in contact with TYR1122 (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 TYR 3.0 18.3 + - - +
1119B ARG* 3.9 6.1 - - - +
1121B ALA* 1.3 74.9 - - - +
1123B ASN* 1.3 68.2 + - - +
1126B LEU* 3.1 42.1 + - + +
1144B ILE* 3.7 8.9 - - - +
1163B ILE* 3.2 61.0 + - + +
1164B LYS* 5.3 0.9 - - - -
1165B VAL* 3.8 22.0 - - + -
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Residues in contact with ASN1123 (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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1119B ARG* 3.6 18.8 + - - +
1120B GLU* 3.2 10.0 + - - +
1122B TYR* 1.3 84.4 - - - +
1124B LEU* 1.3 55.9 + - - +
1125B GLY 3.1 1.3 - - - -
1126B LEU* 3.0 17.2 + - - +
1127B GLU* 2.8 34.8 + - - +
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Residues in contact with LEU1124 (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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1004B LEU* 4.8 7.6 - - + -
1095B TYR* 3.6 40.2 - - + -
1111B ILE* 4.0 30.3 - - + -
1114B LYS* 5.0 14.6 - - + -
1120B GLU 3.1 9.8 + - - +
1121B ALA* 3.5 9.6 - - - +
1123B ASN* 1.3 77.9 - - - +
1125B GLY* 1.3 57.4 + - - +
1127B GLU* 3.3 18.4 + - - +
1128B ILE* 2.9 32.1 + - + +
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Residues in contact with GLY1125 (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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1004B LEU* 4.2 16.3 - - - +
1121B ALA 2.8 12.6 + - - -
1122B TYR 3.6 5.6 - - - -
1123B ASN 3.1 0.4 - - - -
1124B LEU* 1.3 74.6 - - - +
1126B LEU* 1.3 58.7 + - - +
1128B ILE* 3.0 6.2 + - - +
1129B LYS* 2.9 31.9 + - - +
1142B VAL* 4.4 6.5 - - - +
1163B ILE* 3.7 15.7 - - - -
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Residues in contact with LEU1126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122B TYR* 3.1 40.7 + - + +
1123B ASN* 3.0 16.2 + - - +
1125B GLY* 1.3 74.2 - - - +
1127B GLU* 1.3 56.7 + - - +
1129B LYS* 3.6 24.4 + - + +
1130B ASN* 3.1 37.5 + - - +
1163B ILE* 3.8 12.0 - - + +
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Residues in contact with GLU1127 (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 TYR* 3.6 33.5 + - - +
1123B ASN 2.8 12.6 + - - +
1124B LEU* 3.3 25.0 + - + +
1125B GLY 3.2 0.2 - - - -
1126B LEU* 1.3 77.2 - - - +
1128B ILE* 1.3 60.2 + - - +
1130B ASN* 3.4 8.1 + - + +
1131B LYS* 3.2 18.5 + - - +
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Residues in contact with ILE1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004B LEU* 4.1 22.7 - - + -
1006B VAL* 4.7 10.5 - - + -
1092B LEU* 4.1 22.4 - - + -
1095B TYR* 3.7 41.5 - - + -
1109B LEU* 4.1 24.0 - - + -
1124B LEU* 2.9 16.5 + - + +
1125B GLY* 3.0 8.9 + - - +
1127B GLU* 1.3 72.2 - - - +
1129B LYS* 1.3 68.1 + - - +
1130B ASN 3.1 2.3 + - - -
1131B LYS* 3.3 2.1 + - - +
1132B ILE* 3.2 34.0 + - + +
1140B VAL* 5.1 0.7 - - + -
1142B VAL* 4.8 5.8 - - + -
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Residues in contact with LYS1129 (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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1125B GLY 2.9 20.3 + - - +
1126B LEU* 3.8 21.1 - - + +
1128B ILE* 1.3 77.0 - - - +
1130B ASN* 1.3 60.0 + - - +
1132B ILE* 4.2 1.7 - - - +
1133B LEU* 3.0 31.1 + - - +
1138B ILE 4.6 1.6 - - - +
1139B THR* 5.8 1.2 - - - -
1140B VAL* 2.9 49.9 + - + +
1142B VAL* 4.2 7.4 - - + -
1161B ASN* 2.9 33.6 + - - +
1162B GLY* 2.9 25.3 + - - +
1163B ILE* 4.3 13.5 - - + -
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Residues in contact with ASN1130 (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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1126B LEU* 3.1 25.8 + - - +
1127B GLU* 3.6 8.1 - - - +
1128B ILE 3.1 0.2 - - - -
1129B LYS* 1.3 79.1 - - - +
1131B LYS* 1.3 59.9 + - - +
1133B LEU* 3.4 12.2 + - - +
1134B GLU* 2.9 30.2 + - - +
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Residues in contact with LYS1131 (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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1091B LEU* 4.8 20.2 - - + -
1094B GLU* 5.0 13.8 - - - +
1095B TYR* 3.2 48.1 + - + +
1127B GLU* 3.2 7.1 + - - +
1128B ILE 3.3 2.9 + - - +
1130B ASN* 1.3 74.3 - - - +
1132B ILE* 1.3 58.3 + - + +
1134B GLU* 3.1 7.1 + - + +
1135B LYS* 2.7 65.1 + - + +
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Residues in contact with ILE1132 (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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1006B VAL* 4.6 3.8 - - + -
1088B ILE* 3.5 36.1 - - + -
1091B LEU* 4.7 21.1 - - + -
1092B LEU* 4.3 11.9 - - + -
1128B ILE* 3.2 30.4 + - + +
1129B LYS* 4.2 2.7 - - - +
1131B LYS* 1.3 77.9 - - + +
1133B LEU* 1.3 56.8 + - - +
1135B LYS 4.6 0.2 - - - +
1136B GLU* 2.9 32.0 + - + +
1137B LYS 3.4 1.2 + - - -
1138B ILE* 3.3 31.2 - - + +
1140B VAL* 4.1 21.5 - - + -
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Residues in contact with LEU1133 (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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1129B LYS* 3.0 23.4 + - + +
1130B ASN* 3.7 14.1 - - - +
1132B ILE* 1.3 77.9 - - - +
1134B GLU* 1.3 58.1 + - - +
1137B LYS* 3.2 24.1 + - - +
1138B ILE 3.5 22.9 + - - +
1139B THR* 4.1 22.0 - - + -
1161B ASN* 5.7 3.1 - - - +
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Residues in contact with GLU1134 (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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1130B ASN 2.9 17.3 + - - +
1131B LYS* 3.1 7.0 + - + +
1133B LEU* 1.3 79.2 - - - +
1135B LYS* 1.3 77.0 + - + +
1136B GLU 3.6 0.3 + - - -
1137B LYS* 4.5 9.2 + - - +
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Residues in contact with LYS1135 (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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1091B LEU* 3.9 32.2 - - + +
1131B LYS* 2.7 42.9 + - + +
1134B GLU* 1.3 86.6 + - + +
1136B GLU* 1.3 67.6 + - + +
1137B LYS* 5.4 1.5 - - - +
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Residues in contact with GLU1136 (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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1018B VAL* 3.9 10.4 - - - +
1084B VAL* 3.7 14.1 - - - +
1087B ARG* 3.0 52.5 + - - +
1088B ILE* 3.7 24.9 - - + -
1091B LEU* 4.5 8.2 - - + +
1132B ILE* 2.9 13.6 + - + +
1135B LYS* 1.3 94.3 - - + +
1137B LYS* 1.3 74.3 + - - +
1138B ILE* 3.6 22.7 - - + +
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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
------------------------------------------------------------
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