Contacts of the strand formed by residues 259 - 263 (chain A) in PDB entry 1W31
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 GLY 259 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 3.5 14.3 - - - -
204A VAL 3.2 5.3 + - - +
205A LEU* 3.5 8.1 - - - -
206A SER 3.1 19.8 + - - -
257A ALA* 3.3 4.8 - - - +
258A ASP* 1.3 80.6 - - - +
260A ILE* 1.3 69.1 + - - +
282A LEU* 4.4 3.6 - - - -
283A PRO 3.4 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 3.6 1.7 - - - +
206A SER* 3.3 8.7 - - - +
208A ALA* 4.0 15.0 - - + -
249A LEU* 3.5 28.9 - - + +
252A ASP* 5.4 1.1 - - + -
253A MET 5.5 0.7 - - - +
257A ALA* 4.5 9.4 - - + -
259A GLY* 1.3 80.9 - - - +
261A ILE* 1.3 65.8 + - - +
262A VAL* 3.5 27.1 - - + -
275A ALA* 4.2 4.7 - - + -
279A CYS* 4.2 21.8 - - + -
282A LEU* 4.4 10.5 - - + -
283A PRO 3.1 8.3 + - - +
284A ILE* 3.6 18.1 - - + -
285A CYS* 2.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ALA* 4.3 2.5 - - + -
205A LEU* 3.4 47.6 - - + +
206A SER 2.8 11.7 + - - +
207A TYR* 3.8 48.7 - - + -
208A ALA 3.5 3.3 + - - -
209A ALA 3.4 23.9 + - - +
260A ILE* 1.3 77.9 - - - +
262A VAL* 1.3 67.6 + - - +
263A LYS* 4.1 0.4 + - + -
285A CYS* 3.2 18.2 - - + +
287A TYR* 3.9 24.7 - - + +
327A ILE* 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 3.6 12.8 - - + +
211A PHE* 5.3 0.9 - - + -
260A ILE* 3.5 23.6 - - + -
261A ILE* 1.3 72.4 - - - +
263A LYS* 1.3 63.9 + - - +
264A PRO 3.2 14.7 - - - +
265A SER* 4.3 1.0 + - - -
268A TYR* 4.2 6.7 - - + +
271A ILE* 4.0 25.4 - - + -
272A MET* 3.8 40.4 - - + -
275A ALA* 4.5 4.5 - - + -
284A ILE* 4.3 5.2 - - + -
285A CYS 2.8 13.4 + - - +
286A ALA* 3.8 2.1 - - - -
287A TYR 3.0 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 3.7 22.3 - - + -
209A ALA 2.9 12.7 + - - +
210A LYS* 3.3 17.7 - - + +
211A PHE* 3.0 24.5 + - - -
216A TYR* 3.5 16.6 + - + +
261A ILE* 4.0 4.6 - - + -
262A VAL* 1.3 77.3 - - - +
264A PRO* 1.3 66.1 + - - +
287A TYR* 3.5 16.6 - - + -
289A VAL* 3.3 22.7 - - + -
363A SHO 1.3 86.7 + - - +
----------------------------------------------------------
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