Contacts of the strand formed by residues 1167 - 1170 (chain B) in PDB entry 2IUK
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 ARG1167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1123B PHE 3.7 0.5 - - - +
1124B TYR* 3.2 5.2 - - - -
1125B ILE* 2.9 45.1 + - + +
1155B SER* 3.0 22.0 + - - -
1156B TRP 3.0 28.3 + - - -
1157B VAL* 4.1 11.3 - - + +
1163B TYR* 3.7 39.8 + - + -
1165B LYS 4.9 1.6 - - - -
1166B ASN* 1.3 72.9 - - - +
1168B ILE* 1.3 63.2 + - - +
1169B PHE* 3.7 28.8 - - + -
1191B GLU* 6.0 0.6 - - - +
1208B ARG* 3.4 51.0 - - - +
1266B ASP* 4.5 0.6 + - - -
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Residues in contact with ILE1168 (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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1071B ILE* 4.3 2.2 - - + -
1122B ALA* 4.0 19.3 - - + -
1123B PHE 3.2 17.0 - - - +
1124B TYR* 3.8 17.5 - - + -
1166B ASN 3.3 2.8 + - - -
1167B ARG* 1.3 80.0 + - - +
1169B PHE* 1.3 69.7 + - - +
1170B PHE* 3.8 22.7 - - + -
1187B TYR* 3.4 43.3 - - + +
1191B GLU* 3.5 36.6 - - + +
1208B ARG* 5.8 1.0 + - - -
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Residues in contact with PHE1169 (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 ALA* 3.1 5.2 - - - -
1123B PHE* 2.9 70.1 + + + -
1125B ILE* 3.3 27.4 - - + -
1135B LEU* 4.1 8.3 - - + -
1151B PHE* 3.9 3.9 - - - -
1152B VAL 5.2 1.6 - - - +
1153B CYS* 3.9 30.3 - - + -
1155B SER* 3.6 26.0 - - - -
1157B VAL* 3.7 22.4 - - + -
1167B ARG* 3.7 26.5 - - + -
1168B ILE* 1.3 78.7 - - - +
1170B PHE* 1.3 66.2 + - - +
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Residues in contact with PHE1170 (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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1121B GLY 3.8 8.1 - - - -
1122B ALA* 4.2 11.0 - - + -
1151B PHE* 3.1 23.1 - - - +
1152B VAL 4.6 5.4 + - - +
1168B ILE* 3.8 22.0 - - + -
1169B PHE* 1.3 75.7 - - - +
1171B VAL* 1.3 66.8 + - - +
1184B LEU* 4.1 20.9 - - + -
1187B TYR* 3.7 37.9 - - + -
1188B ARG* 3.7 11.4 - - + -
1191B GLU* 5.2 5.6 - - + -
1545B SER* 4.9 3.6 - - - -
1546B VAL* 3.8 27.8 - - + +
1547B LEU* 3.6 40.8 - - + -
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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