Contacts of the strand formed by residues 265 - 271 (chain A) in PDB entry 1QXP
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 SER 265 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER* 4.2 12.0 + - - -
116A LEU* 3.8 25.2 - - - +
238A LEU 3.2 16.3 + - - -
239A GLY* 3.9 5.3 - - - -
240A CYS* 4.6 0.7 - - - +
263A ALA* 5.1 1.2 - - - +
264A TYR* 1.3 77.7 + - - +
266A VAL* 1.3 67.6 + - - +
267A THR* 3.9 5.6 - - - +
284A MET* 3.2 3.9 - - - -
285A ARG 2.7 35.7 + - - -
287A PRO* 4.6 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 4.4 5.6 - - + -
232A LEU* 4.4 21.8 - - + +
236A SER 5.7 0.2 - - - +
238A LEU* 3.0 33.3 + - + +
240A CYS* 3.4 29.4 - - - -
265A SER* 1.3 74.6 - - - +
267A THR* 1.4 63.1 + - - +
268A ASP 4.0 7.4 - - - +
282A ILE* 3.5 36.1 - - + -
283A ARG 3.4 7.9 - - - +
284A MET* 3.8 17.9 - - + +
330A ASP* 5.1 0.7 - - - +
337A LYS* 5.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 6.0 2.9 - - + -
232A LEU* 3.7 16.0 - - - +
265A SER* 3.9 7.2 - - - +
266A VAL* 1.4 77.3 - - - +
268A ASP* 1.3 64.9 + - - +
283A ARG* 2.9 17.0 + - - +
285A ARG* 3.8 27.1 - - + +
319A MET* 2.6 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.6 7.1 - - - +
266A VAL* 3.7 4.2 - - - +
267A THR* 1.3 82.8 - - - +
269A ALA* 1.3 90.3 + - - +
270A LYS* 3.4 24.8 + - - +
282A ILE* 3.6 5.5 - - - +
283A ARG* 2.6 78.3 + - + +
318A LYS* 5.4 0.7 + - - -
325A TRP* 4.3 1.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 3.8 10.5 - - + +
228A ILE* 4.6 14.6 - - + -
229A LEU* 3.5 30.6 - - + +
232A LEU* 4.6 8.0 - - + +
268A ASP* 1.3 100.2 + - - +
270A LYS* 1.4 61.3 + - - +
281A LEU 4.2 3.8 - - - +
282A ILE* 4.7 2.0 - - - -
325A TRP* 4.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 3.1 12.6 + - - -
268A ASP* 3.4 23.3 + - - +
269A ALA* 1.4 71.3 + - - +
271A GLN* 1.4 64.9 + - - +
272A VAL* 3.9 9.6 - - + -
281A LEU* 2.7 42.5 + - + +
283A ARG* 5.2 0.6 - - - +
315A LEU* 4.0 29.1 + - + +
316A ARG* 6.1 0.2 - - - -
318A LYS* 4.7 13.1 - - - +
325A TRP* 2.9 33.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 3.9 15.0 - - + +
229A LEU* 3.9 24.0 - - - +
270A LYS* 1.4 78.5 - - - +
272A VAL* 1.3 62.0 + - - +
278A ARG 5.3 2.0 - - - +
279A VAL 4.0 6.7 - - - +
280A ASN* 3.4 22.6 + - - +
312A ARG* 3.6 14.1 + - - -
----------------------------------------------------------
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