Contacts of the strand formed by residues 692 - 695 (chain A) in PDB entry 2OR4
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 TYR 692 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A CYS 5.3 1.3 + - - -
467A THR* 5.2 1.1 - - - -
468A PRO* 3.2 31.5 - - + +
471A TYR* 4.5 1.4 + - - -
514A LYS* 3.6 33.8 - - + +
515A LEU 4.0 11.0 - - - +
525A PHE* 3.7 37.0 - + + -
526A GLN* 3.1 10.1 - - - +
600A TYR* 3.2 27.8 - + - -
603A VAL* 4.0 0.2 - - - +
607A TYR* 2.7 45.0 + + - -
689A HIS* 3.1 29.1 + + - +
691A ILE* 1.3 84.0 - - + +
693A ALA* 1.3 60.7 + - - +
703A GLU 3.2 7.6 - - - +
704A SER* 4.6 0.4 - - - -
706A PRO* 3.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLY* 4.3 1.3 - - - -
526A GLN* 3.6 10.1 - - - +
681A LEU* 3.6 17.5 - - + -
684A ARG* 4.0 5.6 - - - +
687A TYR* 4.7 2.5 - - + -
692A TYR* 1.3 76.9 - - - +
694A PRO* 1.3 79.5 - - + +
702A GLY* 3.5 1.9 - - - -
703A GLU* 2.8 31.9 + - - +
706A PRO* 3.5 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLY* 3.7 10.3 - - - +
517A SER* 3.5 20.4 - - - -
526A GLN* 3.8 12.3 - - + -
684A ARG* 3.0 21.7 + - - +
687A TYR* 3.4 44.6 - - + +
693A ALA* 1.3 92.2 - - + +
695A SER* 1.3 65.9 + - - +
696A SER 3.4 0.5 + - - -
699A LYS* 3.7 23.6 - - - +
701A ALA 3.4 7.9 - - - +
703A GLU* 5.1 0.3 - - - +
706A PRO* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASN* 4.5 0.9 + - - -
684A ARG* 4.6 0.5 + - - -
693A ALA 3.4 1.6 + - - -
694A PRO* 1.3 73.8 - - - +
696A SER* 1.3 59.0 + - - +
697A HIS* 3.0 27.4 + - - +
698A ASN* 3.1 32.8 + - - +
699A LYS* 3.6 4.0 + - - -
701A ALA* 2.8 25.0 + - - -
702A GLY 5.1 0.4 - - - -
703A GLU* 4.2 25.0 + - - +
709A TYR* 5.8 1.2 - - - -
----------------------------------------------------------
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