Contacts of the strand formed by residues 254 - 257 (chain D) in PDB entry 2BS3
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 VAL 254 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D TYR* 4.0 17.3 - - + +
223D TYR* 3.9 21.8 - - + +
251D MET 3.7 16.8 - - - +
252D GLU 3.1 8.9 + - - +
253D ALA* 1.3 76.7 - - - +
255D GLN* 1.3 63.5 + - - +
256D PHE* 3.7 20.5 - - + -
368D GLN* 3.4 39.0 - - + +
370D TYR 3.8 3.6 - - - +
371D SER* 5.1 0.9 - - - +
372D MET* 3.9 2.9 - - - +
482D ARG* 4.1 8.6 + - - +
533D VAL* 4.2 5.4 - - + -
546D ALA* 3.3 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D VAL* 1.3 74.6 - - - +
256D PHE* 1.3 65.8 + - - +
302D ASP* 5.9 0.4 - - - +
368D GLN* 3.7 2.3 - - - -
369D HIS* 2.8 30.4 + - + -
370D TYR* 2.9 25.9 + - + +
372D MET* 3.6 16.3 - - + +
403D ASN* 2.9 29.2 - - - +
404D ARG* 2.8 66.2 + - - +
546D ALA* 4.3 3.1 - - + -
1657D CIT 3.6 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D TYR* 3.9 22.4 - + - -
254D VAL* 3.7 26.5 - - + -
255D GLN* 1.3 92.0 - - - +
257D HIS* 1.3 62.6 + - - +
258D PRO* 4.2 3.6 - - - +
301D ARG* 5.6 2.1 - - - +
305D SER* 4.4 7.5 + - - +
366D PRO 4.4 3.4 - - - -
367D MET* 3.1 15.9 - - - +
368D GLN* 3.3 28.0 - - + -
369D HIS* 4.1 2.7 - - - -
475D ASP* 5.0 6.1 - - - -
478D VAL 4.0 0.4 - - - -
479D GLY* 3.6 36.3 - - - -
480D ILE* 3.9 29.8 - - + -
482D ARG* 4.4 4.7 - - - -
546D ALA* 5.4 4.8 - - + +
1657D CIT 4.7 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D PHE* 1.3 75.0 - - - +
258D PRO* 1.3 62.6 - - + +
259D THR* 2.9 45.0 + - - -
260D PRO* 3.1 18.0 - - + +
267D LEU* 3.4 28.5 - - + +
268D LEU 4.0 5.1 + - - -
270D GLU 4.6 0.2 - - - -
301D ARG* 3.0 26.7 + - - -
305D SER* 4.0 1.8 - - - -
366D PRO* 3.0 2.8 - - - +
367D MET 2.7 29.8 + - - +
369D HIS* 3.7 21.9 - - + +
1657D CIT 2.4 42.6 + - + +
----------------------------------------------------------
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