Contacts of the strand formed by residues 763 - 765 (chain S) in PDB entry 3ZPV
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 ALA 763 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757S VAL* 3.6 26.7 - - + -
758S ASN 5.7 0.2 - - - +
761S ASP* 3.5 6.4 + - + +
762S GLU* 1.3 75.3 - - - +
764S VAL* 1.3 67.2 + - - +
773S PHE* 5.2 0.9 - - + -
774S PHE 3.2 15.3 - - - +
775S HIS* 4.5 0.9 - - - -
776S ARG 4.1 1.6 - - - +
786S PHE* 3.4 17.6 - - - -
790S ASN* 5.1 1.9 - - - +
791W LYS 4.8 1.3 + - - +
793W VAL* 3.1 35.7 - - + +
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Residues in contact with VAL 764 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763S ALA* 1.3 79.7 - - - +
765S PHE* 1.3 61.6 + - - +
773S PHE* 3.4 7.3 - - - -
774S PHE* 2.9 41.2 + - + +
776S ARG* 5.2 2.9 - - + -
779S VAL* 4.5 4.5 - - + -
781S LEU* 3.9 25.1 - - + -
786S PHE* 4.0 15.9 - - + -
789S LEU* 5.1 4.5 - - + -
790S ASN* 5.0 5.6 - - - +
797S TRP* 3.4 48.9 - - + -
793W VAL* 4.0 7.0 - - - -
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Residues in contact with PHE 765 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7431 GLY 4.0 14.6 - - - -
7441 ALA* 4.1 4.9 - - + -
764S VAL* 1.3 78.0 - - - +
766S CYS* 1.3 73.0 + - - +
767S GLU* 3.3 36.9 + - + +
771S ASN* 3.5 40.4 - - - -
772S PHE 3.6 9.4 - - - -
773S PHE* 3.5 44.9 - + + -
796S GLU* 5.7 0.3 - - - +
797S TRP* 3.8 16.7 + - - +
793W VAL* 4.1 8.6 - - + +
322X HIS* 5.9 1.8 - + - -
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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
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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) + - + + + + + -
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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