Contacts of the strand formed by residues 1088 - 1091 (chain A) in PDB entry 2X4X
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 LEU1088 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086A LEU 3.7 2.1 + - - +
1087A ASP* 1.3 75.2 - - - +
1089A VAL* 1.3 64.4 + - - +
1101A ALA 3.4 2.2 - - - +
1102A LEU* 3.9 14.1 - - + -
1148A PHE* 3.5 37.9 - - + -
1164A PRO* 3.8 3.1 - - - +
1165A LEU* 3.0 49.3 + - + +
1195A ALA* 3.5 27.4 - - + +
1196A LEU* 4.6 2.2 - - + -
1198A HIS* 4.1 6.5 - - + -
1199A ARG* 3.9 29.4 - - + +
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Residues in contact with VAL1089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083A LEU* 4.3 12.8 - - + -
1087A ASP* 4.3 4.7 - - + +
1088A LEU* 1.3 79.7 - - - +
1090A TRP* 1.3 64.7 + - - +
1091A ALA 3.7 0.2 + - - -
1100A PRO* 3.5 3.8 - - - +
1101A ALA* 2.9 53.7 + - + +
1103A ILE* 4.0 34.8 - - + -
1145A VAL* 4.3 3.1 - - + -
1162A LEU* 4.0 21.3 - - + -
1163A VAL 3.3 19.1 - - - +
1164A PRO* 4.3 3.4 - - + -
1165A LEU* 3.6 8.7 - - - +
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Residues in contact with TRP1090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A VAL* 1.3 71.2 - - - +
1091A ALA* 1.3 59.4 + - - +
1092A LYS 4.2 0.4 - - - -
1098A SER* 3.6 41.7 - - - +
1099A TYR 3.9 2.2 - - - -
1100A PRO* 3.7 11.9 - - + -
1161A LYS 3.6 1.2 - - - +
1162A LEU* 3.3 6.2 - - - -
1163A VAL* 2.7 48.7 + - + +
1164A PRO 3.9 3.6 - - - -
1165A LEU* 3.6 20.4 - - + +
1171A LEU* 5.4 0.9 - - + -
1172A ASP* 2.9 32.9 + - - -
1175A LYS* 3.4 42.2 - - + +
1176A MET* 3.5 25.8 - - + -
1188A VAL* 3.7 15.3 - - + -
1192A TYR* 3.6 24.7 - + - -
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Residues in contact with ALA1091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A VAL* 3.7 1.5 + - + -
1090A TRP* 1.3 72.9 - - - +
1092A LYS* 1.3 60.9 + - - +
1093A CYS 3.8 2.1 + - - -
1097A PRO 4.3 0.7 - - - +
1098A SER* 3.7 1.2 - - - -
1099A TYR* 2.9 32.4 + - - +
1101A ALA* 4.1 13.0 - - + -
1145A VAL* 4.3 2.9 - - + -
1147A PHE* 3.7 24.5 - - + -
1157A LEU* 3.5 21.3 - - + -
1161A LYS 3.6 4.0 - - - -
1162A LEU* 3.7 9.4 - - + -
36B M3L 5.5 0.3 - - - -
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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