Contacts of the strand formed by residues 1088 - 1091 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086G LEU 3.7 2.2 + - - +
1087G ASP* 1.3 75.1 - - - +
1089G VAL* 1.3 64.4 + - - +
1101G ALA 3.4 1.8 - - - +
1102G LEU* 3.8 15.5 - - + -
1148G PHE* 3.5 37.7 - - + -
1164G PRO* 3.8 3.3 - - - +
1165G LEU* 3.0 47.6 + - + +
1195G ALA* 3.6 25.8 - - + +
1196G LEU* 4.7 2.2 - - + -
1198G HIS* 4.2 6.3 - - + -
1199G ARG* 3.8 29.8 - - + -
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Residues in contact with VAL1089 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083G LEU* 4.0 17.9 - - + -
1087G ASP* 4.3 4.7 - - + +
1088G LEU* 1.3 81.9 - - - +
1090G TRP* 1.3 64.0 + - - +
1091G ALA* 4.3 1.3 - - + -
1100G PRO* 3.4 4.2 - - - +
1101G ALA* 2.8 56.5 + - + +
1103G ILE* 3.8 36.6 - - + -
1145G VAL* 4.4 2.7 - - + -
1162G LEU* 4.2 19.7 - - + -
1163G VAL 3.3 14.1 - - - +
1164G PRO* 4.4 2.0 - - + -
1165G LEU* 3.6 8.5 - - - +
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Residues in contact with TRP1090 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089G VAL* 1.3 72.2 - - - +
1091G ALA* 1.3 59.4 + - - +
1098G SER* 3.7 34.3 - - - -
1099G TYR 3.7 4.0 - - - -
1100G PRO* 3.7 24.2 - - + -
1161G LYS 3.6 1.6 - - - +
1162G LEU* 3.3 5.7 - - - -
1163G VAL* 2.7 45.1 + - + +
1164G PRO 3.9 2.9 - - - -
1165G LEU* 3.6 23.1 - - + +
1171G LEU* 3.8 21.1 - - + +
1172G ASP* 2.8 35.3 + - - -
1175G LYS* 3.6 23.6 - - + -
1176G MET* 3.7 24.2 - - + -
1188G VAL* 3.7 8.7 - - + -
1192G TYR* 3.6 27.1 - + - -
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Residues in contact with ALA1091 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089G VAL* 4.3 1.6 - - + -
1090G TRP* 1.3 73.3 - - - +
1092G LYS* 1.3 60.2 + - - +
1093G CYS 3.9 2.5 + - - -
1097G PRO 4.3 0.7 - - - +
1098G SER* 3.6 1.0 - - - -
1099G TYR* 2.9 39.5 + - - +
1101G ALA* 4.0 13.5 - - + -
1145G VAL* 4.3 3.6 - - + -
1147G PHE* 3.8 16.1 - - + -
1157G LEU* 3.7 12.1 - - + -
1161G LYS 3.6 4.0 - - - -
1162G LEU* 3.6 19.1 - - + -
36H M3L 5.4 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