Contacts of the strand formed by residues 1163 - 1168 (chain B) in PDB entry 1W21
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 ALA1163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LYS 5.5 2.7 - - - +
110A ASN* 5.8 2.5 - - - +
1140B LEU* 3.4 6.4 - - - -
1141B SER* 2.9 32.5 + - - -
1161B PHE 4.1 2.2 + - - +
1162B ARG* 1.3 77.8 - - - +
1164B LEU* 1.3 63.0 + - - +
1165B ILE* 3.5 6.4 + - + +
1180B VAL* 4.0 12.3 - - + -
1182B CYS 3.3 13.9 - - - +
1183B ILE* 3.8 18.2 - - + -
1184B GLY 3.7 6.1 - - - +
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Residues in contact with LEU1164 (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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1127B TYR* 3.4 24.0 - - + +
1138B PHE* 4.0 7.9 - - + -
1139B ALA 3.4 31.4 - - - +
1140B LEU* 3.9 9.3 - - + +
1163B ALA* 1.3 70.9 - - - +
1165B ILE* 1.3 57.4 + - - +
1180B VAL* 3.5 3.8 - - - -
1181B GLU* 2.7 59.2 + - + -
1182B CYS* 2.9 20.5 + - - +
1187B SER* 3.4 21.8 - - - +
1188B THR 4.3 3.4 - - - +
1189B SER* 4.4 0.9 - - - -
1198B SER* 4.2 9.2 - - - -
1200B CYS* 3.5 18.9 - - - -
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Residues in contact with ILE1165 (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 LEU* 3.9 20.0 - - + -
1123B THR* 4.2 8.5 - - + -
1138B PHE* 3.3 5.4 - - - +
1139B ALA 2.9 37.5 + - - +
1141B SER* 3.9 19.3 - - - -
1163B ALA* 4.3 8.1 - - + +
1164B LEU* 1.3 79.3 - - - +
1166B SER* 1.3 60.3 + - - +
1167B TRP* 3.7 19.8 - - + -
1173B PRO* 4.0 7.2 - - + -
1178B THR* 3.9 27.6 - - + +
1179B ARG 3.1 9.9 - - - +
1180B VAL* 4.2 18.4 - - + -
1181B GLU* 4.5 2.9 - - - -
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Residues in contact with SER1166 (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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1136B ARG* 2.8 28.9 + - - -
1137B MET 3.2 9.0 - - - -
1138B PHE* 3.5 26.0 - - - -
1165B ILE* 1.3 73.7 - - - +
1167B TRP* 1.3 66.8 + - - +
1178B THR* 3.5 1.0 - - - -
1179B ARG* 2.9 33.7 + - - +
1181B GLU* 2.6 28.5 + - - -
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Residues in contact with TRP1167 (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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1109B ASP* 4.0 1.6 - - - -
1123B THR* 4.9 1.3 - - + -
1136B ARG* 3.4 15.7 - - - +
1137B MET* 2.9 56.3 + - + -
1138B PHE 3.8 13.9 - - - -
1139B ALA* 3.8 19.3 - - + -
1165B ILE* 3.7 28.0 - - + -
1166B SER* 1.3 84.1 - - - +
1168B GLU* 1.3 80.7 + - - +
1169B MET 3.3 0.3 + - - -
1171B GLN* 2.7 37.0 + - + -
1172B ALA 4.2 3.6 - - - -
1173B PRO* 3.7 38.3 - - + -
1177B ASN* 3.4 22.7 - - - +
1178B THR* 3.8 12.1 - - + -
1451B ILE* 3.7 16.6 - - + -
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Residues in contact with GLU1168 (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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1135B CYS 4.9 1.1 - - - +
1136B ARG* 3.6 17.2 - - - +
1167B TRP* 1.3 87.4 - - - +
1169B MET* 1.3 76.3 + - - +
1171B GLN* 3.3 28.6 + - - +
1177B ASN 4.8 1.4 + - - -
3178D THR 4.0 5.4 - - - +
3179D ARG* 3.5 46.3 + - + +
3180D VAL 4.4 1.7 + - - -
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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
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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