Contacts of the strand formed by residues 1088 - 1091 (chain K) in PDB entry 2X4Y
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086K LEU 3.7 2.4 + - - +
1087K ASP* 1.4 74.9 - - - +
1089K VAL* 1.3 64.8 + - - +
1101K ALA 3.5 2.2 - - - +
1102K LEU* 3.8 15.3 - - + -
1148K PHE* 3.7 36.3 - - + -
1164K PRO* 3.7 3.6 - - - +
1165K LEU* 2.9 51.2 + - + +
1195K ALA* 3.5 24.7 - - + +
1196K LEU* 4.6 2.5 - - + -
1198K HIS* 4.4 6.3 - - + -
1199K ARG* 3.8 27.6 - - + -
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Residues in contact with VAL1089 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083K LEU* 4.1 16.4 - - + -
1087K ASP* 4.3 5.6 - - + +
1088K LEU* 1.3 80.7 - - - +
1090K TRP* 1.3 62.5 + - - +
1091K ALA* 4.2 11.2 - - + -
1100K PRO* 3.4 4.2 - - - +
1101K ALA* 2.8 52.2 + - + +
1103K ILE* 3.7 38.1 - - + -
1145K VAL* 4.4 1.6 - - + -
1162K LEU* 4.3 11.2 - - + -
1163K VAL 3.3 12.8 - - - +
1164K PRO* 4.5 4.0 - - + -
1165K LEU* 3.7 8.1 - - - +
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Residues in contact with TRP1090 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089K VAL* 1.3 73.0 - - - +
1091K ALA* 1.3 60.0 + - - +
1092K LYS 4.2 0.2 + - - -
1098K SER* 3.9 9.6 - - - -
1099K TYR 3.7 18.2 - - - -
1100K PRO* 3.7 16.2 - - + -
1161K LYS 3.6 0.9 - - - +
1162K LEU* 3.2 6.1 - - - -
1163K VAL* 2.7 36.6 + - + +
1165K LEU* 3.7 22.8 - - + +
1171K LEU* 3.6 22.8 - - + +
1172K ASP* 2.9 36.6 + - - -
1175K LYS* 3.5 38.1 - - + -
1176K MET* 3.6 24.5 - - + -
1188K VAL* 3.7 22.7 - - + -
1192K TYR* 3.5 26.5 - + - -
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Residues in contact with ALA1091 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089K VAL* 3.8 1.5 - - + -
1090K TRP* 1.3 74.9 - - - +
1092K LYS* 1.3 60.6 + - - +
1093K CYS* 3.9 1.8 + - - -
1097K PRO 4.4 0.5 - - - +
1098K SER* 3.6 1.5 - - - -
1099K TYR* 2.9 31.2 + - - +
1101K ALA* 4.0 13.5 - - + -
1145K VAL* 4.2 2.9 - - + -
1147K PHE* 3.8 24.7 - - + -
1157K LEU* 3.6 11.4 - - + -
1161K LYS 3.6 3.8 - - - -
1162K LEU* 3.6 19.1 - - + -
36L M3L 5.5 0.2 - - - -
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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