Contacts of the helix formed by residues 1167 - 1178 (chain B) in PDB entry 3GIJ
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 ASP1167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1118B TYR* 3.6 20.9 - - + -
1165B VAL* 3.5 10.0 + - + +
1166B ILE* 1.3 76.6 - - - +
1168B ASP* 1.3 58.9 + - - +
1169B GLU* 2.9 14.8 + - - +
1170B GLU* 2.6 55.2 + - - +
1171B VAL* 2.8 24.5 + - - +
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Residues in contact with ASP1168 (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* 3.1 31.5 + - - -
1146B LYS* 4.4 11.7 - - - +
1167B ASP* 1.3 75.0 - - - +
1169B GLU* 1.3 60.0 + - - +
1171B VAL* 3.3 18.6 + - - +
1172B LYS* 3.3 26.8 + - - +
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Residues in contact with GLU1169 (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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1167B ASP* 2.9 15.2 + - - +
1168B ASP* 1.3 78.1 - - - +
1170B GLU* 1.3 58.6 + - + +
1172B LYS* 3.8 7.1 + - - +
1173B ARG* 3.3 21.8 + - - +
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Residues in contact with GLU1170 (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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1164B LYS* 3.3 27.2 + - - -
1165B VAL 3.7 8.7 - - - +
1166B ILE* 3.6 11.4 - - + -
1167B ASP* 2.6 37.3 + - - +
1169B GLU* 1.3 72.3 - - + +
1171B VAL* 1.3 60.7 + - - +
1172B LYS 3.2 1.8 - - - -
1173B ARG* 3.3 39.9 + - - +
1174B LEU* 2.9 33.4 + - - +
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Residues in contact with VAL1171 (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* 3.5 23.6 - - - +
1146B LYS* 4.4 11.2 - - + -
1150B PHE* 4.1 25.8 - - + -
1166B ILE* 3.6 8.5 - - + +
1167B ASP 2.8 18.2 + - - +
1168B ASP* 3.3 21.3 + - - +
1170B GLU* 1.3 76.8 - - - +
1172B LYS* 1.3 59.7 + - - +
1174B LEU* 3.9 4.0 - - - +
1175B ILE* 3.1 26.0 + - + +
1231B ASP* 3.7 31.9 - - - +
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Residues in contact with LYS1172 (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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1168B ASP* 3.3 19.3 + - - +
1169B GLU* 3.9 7.6 - - - +
1170B GLU 3.2 0.2 - - - -
1171B VAL* 1.3 73.0 - - - +
1173B ARG* 1.3 65.8 + - - +
1174B LEU 3.1 2.3 + - - -
1175B ILE* 3.1 24.0 + - + +
1176B ARG* 3.3 33.9 + - - +
1231B ASP* 3.7 27.0 + - + +
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Residues in contact with ARG1173 (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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1157B MET* 4.2 18.6 - - - +
1164B LYS* 4.4 7.2 - - - +
1166B ILE* 4.7 1.0 - - - +
1169B GLU 3.3 15.3 + - - +
1170B GLU* 3.3 44.1 + - - +
1172B LYS* 1.3 77.6 - - - +
1174B LEU* 1.3 88.6 + - - +
1176B ARG* 3.3 18.1 + - - +
1177B GLU* 2.6 72.0 + - + +
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Residues in contact with LEU1174 (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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1150B PHE* 4.4 12.6 - - + -
1153B ILE* 4.0 19.1 - - + -
1157B MET* 4.0 12.1 - - + -
1166B ILE* 3.3 35.7 - - + -
1170B GLU 2.9 20.1 + - - +
1171B VAL 3.9 4.7 - - - +
1173B ARG* 1.3 104.4 - - - +
1175B ILE* 1.3 55.4 + - - +
1176B ARG 2.7 12.8 + - - -
1177B GLU* 4.5 3.4 - - + -
1178B LEU* 2.4 56.1 + - + +
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Residues in contact with ILE1175 (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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1150B PHE* 4.1 4.7 - - + -
1171B VAL* 3.1 27.8 + - + +
1172B LYS* 3.1 16.0 + - + +
1174B LEU* 1.3 76.2 - - - +
1176B ARG* 1.3 56.7 + - + +
1202B LEU* 3.5 25.9 + - + +
1203B VAL* 2.8 57.4 + - + +
1206B LEU* 5.4 0.4 - - + -
1228B LEU 3.3 25.6 - - - +
1229B ALA* 3.3 27.6 - - - +
1231B ASP* 4.5 9.2 - - + -
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Residues in contact with ARG1176 (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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1172B LYS* 3.3 35.1 + - - +
1173B ARG* 3.5 23.4 - - - +
1174B LEU 2.7 5.3 + - - -
1175B ILE* 1.3 74.4 - - + +
1177B GLU* 1.3 62.0 + - + +
1178B LEU 3.5 0.2 - - - -
1201B LYS* 3.2 28.6 - - - +
1203B VAL* 4.1 24.9 - - + +
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Residues in contact with GLU1177 (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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1173B ARG* 2.6 60.2 + - + +
1174B LEU* 4.4 5.8 - - + -
1176B ARG* 1.3 73.0 - - + +
1178B LEU* 1.3 59.8 + - - +
1179B ASP 3.3 0.9 + - - -
1201B LYS* 2.9 24.9 + - - +
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Residues in contact with LEU1178 (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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1150B PHE* 4.9 3.4 - - + -
1153B ILE* 3.4 50.7 - - + -
1157B MET* 5.0 7.0 - - + -
1174B LEU* 2.4 52.3 + - + +
1175B ILE* 5.2 0.7 - - - -
1177B GLU* 1.3 71.3 - - - +
1179B ASP* 1.3 75.5 + - - +
1180B ILE 3.6 0.9 + - - -
1182B ASP* 3.9 24.9 - - + +
1183B VAL* 4.2 13.0 - - + -
1201B LYS* 3.4 13.1 - - - +
1202B LEU* 3.8 15.0 + - + +
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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