Contacts of the strand formed by residues 1089 - 1094 (chain B) in PDB entry 2O8C
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 LEU1089 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088B PHE* 1.3 76.4 - - - +
1090B GLU* 1.3 63.8 + - - +
1091B LEU* 4.1 33.7 - - + -
1113B ILE* 4.6 7.9 - - + +
1114B LEU* 3.7 0.7 - - - -
1115B ILE* 2.8 69.8 + - + +
1117B CYS* 3.4 4.2 - - - -
1147B ALA* 4.9 12.1 - - + +
1151B ALA* 5.6 4.9 - - + -
1165B CYS* 5.5 1.8 - - - -
1166B ARG 3.8 3.4 - - - +
1167B LEU* 3.8 29.8 - - + -
1170B ILE* 5.5 3.4 - - + -
1209B LEU* 4.6 15.3 - - + -
1242B ARG* 4.5 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1090 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088B PHE* 4.2 9.2 - - + -
1089B LEU* 1.3 75.1 - - - +
1091B LEU* 1.3 62.6 + - - +
1092B LYS* 3.7 22.9 + - + -
1114B LEU* 3.7 18.1 - - + +
1117B CYS* 4.2 11.0 - - - -
1164B VAL* 3.5 17.7 - - + +
1165B CYS* 3.3 8.7 + - - -
1166B ARG* 2.8 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1091 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089B LEU* 4.2 26.0 - - + -
1090B GLU* 1.3 74.6 - - - +
1092B LYS* 1.3 62.9 + - - +
1093B GLY 4.2 0.2 - - - -
1094B SER* 3.9 13.5 - - - -
1112B ASP* 3.3 4.7 - - - -
1113B ILE* 3.0 57.7 + - + +
1114B LEU* 3.5 7.9 - - - +
1147B ALA* 4.8 4.7 - - - +
1150B LEU* 3.8 42.0 - - + -
1160B VAL* 4.9 1.8 - - + -
1162B ALA* 4.5 5.8 - - + -
1164B VAL 3.5 3.4 - - - +
1165B CYS* 3.8 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1092 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B GLU* 3.7 22.5 + - + -
1091B LEU* 1.3 77.7 - - - +
1093B GLY* 1.3 64.3 + - - +
1094B SER 3.3 0.8 + - - -
1112B ASP* 3.4 12.3 - - - +
1114B LEU* 4.4 17.3 - - + -
1162B ALA* 3.8 1.2 - - - +
1163B GLU* 3.2 30.9 + - - +
1164B VAL* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1093 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B PRO* 5.0 4.5 - - - +
1092B LYS* 1.3 72.0 - - - +
1094B SER* 1.3 65.1 + - - +
1095B ARG* 3.7 4.3 + - - +
1110B PRO* 3.7 20.5 - - - +
1111B ASN 3.1 4.9 + - - -
1112B ASP* 2.7 16.6 + - - -
1161B PRO 3.7 8.5 - - - +
1162B ALA* 3.8 5.4 - - - -
1163B GLU* 4.4 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1094 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091B LEU* 3.9 21.3 - - - +
1092B LYS 3.3 1.2 - - - -
1093B GLY* 1.3 76.5 - - - +
1095B ARG* 1.3 59.5 + - - +
1110B PRO* 3.5 3.6 - - - +
1111B ASN 2.7 42.8 + - - -
1113B ILE* 3.6 24.3 - - - +
1146B GLN* 3.4 8.1 + - - +
1150B LEU* 3.6 24.2 - - - -
1162B ALA* 3.9 9.6 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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