Contacts of the helix formed by residues 1147 - 1158 (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 ASN1147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003B VAL* 3.6 12.7 - - - +
1145B SER 3.4 0.6 + - - -
1146B LYS* 1.3 93.6 - - - +
1148B LYS* 1.3 66.2 + - - +
1149B VAL* 3.3 3.5 + - - +
1150B PHE* 2.9 46.2 + - - -
1151B ALA* 3.0 22.9 + - - +
1231B ASP 6.1 0.6 - - - -
1233B TYR* 3.2 47.6 + - + +
1234B ASN* 3.9 8.3 - - - +
1235B GLU 5.4 1.8 - - - +
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Residues in contact with LYS1148 (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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1003B VAL* 3.8 4.9 - - - +
1100B GLU* 3.1 41.5 + - - +
1108B TYR* 3.3 45.3 - - + +
1147B ASN* 1.3 74.7 - - - +
1149B VAL* 1.3 64.2 + - + +
1151B ALA* 3.3 1.0 + - - +
1152B LYS* 3.1 18.9 + - - +
1233B TYR* 4.2 12.2 + - + +
1235B GLU* 3.6 40.0 + - - +
1236B PRO 4.1 5.3 + - - +
1237B ILE* 3.9 20.6 - - + -
1238B ARG* 5.4 1.6 - - - +
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Residues in contact with VAL1149 (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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1108B TYR* 5.5 0.9 - - - -
1147B ASN* 3.2 7.4 + - - +
1148B LYS* 1.3 76.5 - - + +
1150B PHE* 1.3 61.4 + - + +
1152B LYS* 3.3 8.8 + - - +
1153B ILE* 3.2 36.2 + - + +
1183B VAL* 5.0 0.4 - - + -
1184B PRO* 4.0 17.9 - - + +
1224B TYR* 3.4 28.7 - - + +
1228B LEU* 4.0 22.7 - - + -
1233B TYR* 3.5 31.2 - - + +
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Residues in contact with PHE1150 (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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1145B SER* 3.7 21.5 - - - +
1146B LYS* 4.9 2.5 - - + +
1147B ASN* 2.9 36.5 + - - +
1149B VAL* 1.3 75.5 - - + +
1151B ALA* 1.3 65.6 + - - +
1153B ILE* 3.4 21.7 + - + -
1154B ALA* 3.2 21.3 + - - +
1166B ILE* 3.7 11.1 - - + +
1171B VAL* 3.7 33.2 - - + -
1174B LEU* 4.3 29.6 - - + -
1175B ILE* 4.4 14.6 - - + -
1178B LEU* 5.4 1.8 - - + -
1202B LEU* 4.5 11.9 - - + -
1228B LEU* 3.5 33.2 - - + -
1231B ASP* 5.7 2.5 - - - -
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Residues in contact with ALA1151 (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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1003B VAL* 3.8 26.9 - - + +
1005B PHE* 3.7 22.2 - - + -
1143B GLY* 3.4 10.2 - - - +
1144B ILE 4.4 0.2 - - - -
1145B SER* 3.7 12.4 - - - +
1147B ASN 3.0 14.3 + - - +
1148B LYS 3.3 10.5 - - - +
1150B PHE* 1.3 75.8 - - - +
1152B LYS* 1.3 62.1 + - - +
1154B ALA* 3.1 18.9 + - - +
1155B ALA* 3.2 5.4 + - - +
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Residues in contact with LYS1152 (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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1005B PHE* 3.3 24.8 - - + -
1007B ASP* 4.2 3.4 + - - -
1106B GLU* 2.8 35.4 + - - -
1108B TYR* 3.5 18.8 - - + +
1148B LYS 3.1 9.8 + - - +
1149B VAL* 3.5 11.2 - - - +
1150B PHE 3.2 0.2 - - - -
1151B ALA* 1.3 76.3 - - - +
1153B ILE* 1.3 64.4 + - - +
1155B ALA* 3.5 2.9 + - - +
1156B ASP* 3.1 36.7 + - - +
1184B PRO* 4.5 21.5 - - + -
1813H G 5.8 1.3 - - - -
1814H 2DT 3.0 26.3 + - - -
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Residues in contact with ILE1153 (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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1149B VAL* 3.2 28.6 + - + +
1150B PHE* 3.7 34.5 - - + +
1151B ALA 3.3 0.2 - - - -
1152B LYS* 1.3 73.1 - - - +
1154B ALA* 1.3 66.4 + - - +
1156B ASP* 3.1 11.3 + - + +
1157B MET* 3.0 48.8 + - + +
1166B ILE* 4.3 7.6 - - + -
1174B LEU* 4.7 2.7 - - + -
1178B LEU* 4.2 25.8 - - + -
1182B ASP 4.8 3.8 - - - +
1183B VAL* 5.6 1.1 - - + -
1184B PRO* 4.1 18.8 - - + -
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Residues in contact with ALA1154 (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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1143B GLY* 3.6 3.8 - - - -
1144B ILE 3.8 5.8 - - - +
1150B PHE 3.2 11.9 + - - +
1151B ALA 3.1 11.6 + - - +
1153B ILE* 1.3 78.1 - - - +
1155B ALA* 1.3 64.2 + - - +
1157B MET* 3.2 2.2 + - - +
1158B ALA 3.0 17.2 + - - -
1164B LYS* 3.4 49.1 - - + +
1166B ILE* 3.7 15.9 - - + +
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Residues in contact with ALA1155 (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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1005B PHE* 3.8 27.6 - - + -
1007B ASP* 4.9 4.5 - - + -
1141B THR* 3.4 25.0 - - + +
1142B VAL 4.3 1.1 - - - -
1143B GLY* 3.6 14.2 - - - +
1151B ALA 3.2 2.6 + - - -
1152B LYS 3.6 9.2 - - - +
1154B ALA* 1.3 78.4 - - - +
1156B ASP* 1.3 66.0 + - - +
1158B ALA 2.9 10.9 + - - -
1159B LYS* 3.1 20.3 + - - +
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Residues in contact with ASP1156 (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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1005B PHE* 5.7 0.9 - - - -
1007B ASP* 5.4 0.5 - - - +
1152B LYS* 3.1 32.0 + - - +
1153B ILE* 3.1 15.1 + - + +
1155B ALA* 1.3 80.4 - - - +
1157B MET* 1.3 64.0 + - + +
1158B ALA 3.4 0.2 + - - -
1159B LYS* 3.6 38.7 + - - +
1182B ASP 5.4 3.5 - - - +
1184B PRO* 5.7 4.3 - - - +
1814H 2DT 5.7 0.7 + - - -
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Residues in contact with MET1157 (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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1153B ILE* 3.0 30.9 + - + +
1154B ALA* 3.7 7.0 - - - +
1156B ASP* 1.3 79.0 - - + +
1158B ALA* 1.3 59.8 + - - +
1159B LYS 3.4 1.3 + - - -
1164B LYS* 4.8 16.2 - - + -
1166B ILE* 4.8 10.3 - - - -
1173B ARG* 5.4 6.7 - - - +
1174B LEU* 3.3 34.3 - - + -
1178B LEU* 4.5 9.9 - - + -
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Residues in contact with ALA1158 (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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1141B THR* 3.5 5.3 - - + +
1154B ALA 3.0 5.2 + - - +
1155B ALA 2.9 6.2 + - - +
1157B MET* 1.3 76.2 - - - +
1159B LYS* 1.3 69.6 + - - +
1162B GLY* 3.1 19.1 + - - -
1163B ILE 4.0 15.9 - - - +
1164B LYS* 3.3 35.4 - - + -
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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