Contacts of the strand formed by residues 680 - 686 (chain A) in PDB entry 2V5I
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 THR 680 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A VAL* 3.2 17.2 - - - +
676A LEU 4.4 0.3 + - - -
677A ASP* 2.6 46.6 + - + +
678A ILE 3.7 2.2 - - - +
679A ASN* 1.3 85.2 - - - +
681A MET* 1.3 62.2 + - - +
694A ILE* 3.5 6.0 - - - +
695A ARG 3.1 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A VAL* 4.7 0.9 - - - -
680A THR* 1.3 78.2 - - - +
682A SER* 1.3 66.2 + - - +
683A LEU* 3.9 29.1 - - + +
692A ALA* 3.8 29.8 - - + -
693A LEU 3.3 4.7 - - - -
694A ILE* 3.8 15.9 - - + -
706A LEU* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A LEU* 3.7 17.3 - - - -
674A GLY 2.9 26.5 + - - -
675A VAL* 4.0 7.0 - - - +
681A MET* 1.3 76.3 + - - +
683A LEU* 1.3 63.5 + - - +
684A TYR* 4.2 0.7 - - - -
692A ALA* 3.5 2.4 - - - -
693A LEU* 2.8 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A ILE* 4.7 18.2 - - + -
664A PRO 5.4 1.1 + - - +
665A ILE* 3.7 30.8 - - + +
666A SER* 3.1 20.6 + - - -
670A LEU* 4.1 4.0 - - - +
681A MET* 3.9 27.6 - - + -
682A SER* 1.3 75.7 - - - +
684A TYR* 1.3 63.5 + - - +
690A LEU* 4.3 17.3 - - + -
691A TRP 3.4 13.9 - - - +
692A ALA* 4.1 6.1 - - + -
706A LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A ILE* 4.6 1.3 - - - -
666A SER* 3.3 14.8 - - - +
668A THR 3.6 13.5 - - - +
669A VAL* 3.8 22.0 - - + +
670A LEU* 3.8 21.1 - - + -
682A SER 4.2 3.6 - - - -
683A LEU* 1.3 77.5 - - - +
685A LEU* 1.3 74.1 + - - +
686A ASP* 3.9 19.0 + - + -
690A LEU* 3.7 5.7 - - - +
691A TRP* 2.8 65.4 + - + +
692A ALA 4.0 1.1 - - - -
693A LEU* 3.9 19.7 - - + -
703A ARG* 3.0 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A ILE* 3.9 26.9 - - + -
666A SER 3.0 11.0 + - - +
667A GLY* 4.0 25.7 - - - +
668A THR* 3.7 16.6 - - - -
669A VAL* 3.7 1.9 + - - +
684A TYR* 1.3 81.3 - - - +
686A ASP* 1.3 63.9 + - - +
687A ALA 4.3 0.2 - - - -
688A GLY* 4.9 8.7 - - - +
689A ALA 3.2 21.3 - - - +
690A LEU* 4.4 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A VAL* 3.4 33.3 - - + +
684A TYR* 3.9 9.9 + - + -
685A LEU* 1.3 76.6 - - - +
687A ALA* 1.3 80.7 + - - +
689A ALA* 2.9 24.8 + - - +
691A TRP* 3.7 29.3 + - + -
----------------------------------------------------------
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