Contacts of the strand formed by residues 1140 - 1145 (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 VAL1140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006B VAL* 3.7 21.3 - - + -
1007B ASP 3.5 10.3 - - - +
1008B PHE* 3.5 28.7 - - + -
1009B ASP* 3.5 11.5 - - - +
1128B ILE* 4.9 0.2 - - + -
1129B LYS* 2.7 58.0 + - + +
1132B ILE* 4.0 22.9 - - + -
1138B ILE* 3.8 15.0 + - + +
1139B THR* 1.3 80.4 - - - +
1141B THR* 1.3 56.5 + - - +
1142B VAL* 4.5 2.9 - - + -
1162B GLY 3.8 0.5 + - - -
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Residues in contact with THR1141 (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 3.7 1.0 - - - +
1006B VAL* 3.6 1.9 - - - -
1007B ASP* 2.9 38.1 + - + +
1009B ASP* 3.6 4.4 + - - -
1140B VAL* 1.3 71.6 - - - +
1142B VAL* 1.3 64.3 + - - +
1143B GLY 3.8 0.2 + - - -
1155B ALA* 3.1 46.2 - - + +
1158B ALA* 2.9 7.0 + - + +
1159B LYS* 2.2 34.2 + - - +
1162B GLY 2.9 18.7 + - - +
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Residues in contact with VAL1142 (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* 3.6 21.5 - - + -
1005B PHE 3.5 4.3 - - - +
1006B VAL* 4.5 13.9 - - + -
1125B GLY* 3.9 16.2 - - - +
1128B ILE* 4.8 3.4 - - + -
1129B LYS* 3.9 24.5 - - + -
1140B VAL* 4.5 4.5 - - + -
1141B THR* 1.3 78.4 - - - +
1143B GLY* 1.3 59.9 + - - +
1144B ILE* 3.3 33.0 - - + -
1162B GLY 3.0 6.7 + - - +
1163B ILE* 3.5 11.1 - - + -
1164B LYS* 2.9 29.8 + - - +
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Residues in contact with GLY1143 (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 3.6 1.7 - - - +
1005B PHE* 2.7 39.6 + - - +
1142B VAL* 1.3 71.4 - - - +
1144B ILE* 1.3 59.5 + - - +
1151B ALA* 2.9 27.5 - - - +
1154B ALA* 3.3 3.8 - - - -
1155B ALA* 3.3 20.3 - - - +
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Residues in contact with ILE1144 (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* 3.6 27.6 - - + -
1003B VAL 3.4 5.6 - - - +
1004B LEU* 4.0 7.6 - - + -
1118B TYR* 4.8 5.6 - - + -
1121B ALA* 3.5 39.5 - - + +
1122B TYR* 3.8 11.0 - - - +
1142B VAL* 3.3 32.8 - - + -
1143B GLY* 1.3 73.8 - - - +
1145B SER* 1.3 63.4 + - - +
1151B ALA* 4.3 0.7 - - - -
1154B ALA* 3.5 2.6 - - - +
1163B ILE* 4.4 5.8 - - + -
1164B LYS 2.9 13.2 + - - +
1165B VAL* 3.4 19.3 - - + +
1166B ILE 3.0 26.3 + - - -
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Residues in contact with SER1145 (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* 3.7 1.0 - - - -
1003B VAL* 2.7 36.8 + - - +
1118B TYR* 3.4 16.1 + - - -
1144B ILE* 1.3 76.1 - - - +
1146B LYS* 1.3 61.5 + - - +
1147B ASN 3.3 2.8 + - - -
1150B PHE* 3.6 31.1 - - - +
1151B ALA* 4.0 2.4 - - - +
1166B ILE* 2.5 29.7 + - - +
1171B VAL* 3.5 13.3 - - - +
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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