Contacts of the strand formed by residues 763 - 765 (chain 1) 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 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7571 VAL* 3.6 26.5 - - + -
7611 ASP* 3.6 7.1 + - + +
7621 GLU* 1.3 74.9 - - - +
7641 VAL* 1.3 67.9 + - - +
7731 PHE* 5.3 0.9 - - + -
7741 PHE 3.2 14.6 - - - +
7751 HIS* 4.5 1.1 - - - -
7761 ARG 4.1 1.3 - - - +
7861 PHE* 3.4 17.7 - - - -
7901 ASN* 5.1 2.4 - - - +
791O LYS 4.8 1.6 + - - +
793O VAL* 3.0 35.0 - - + +
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Residues in contact with VAL 764 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7631 ALA* 1.3 79.3 - - - +
7651 PHE* 1.3 61.8 + - - +
7731 PHE* 3.4 6.9 - - - -
7741 PHE* 2.9 37.3 + - + +
7761 ARG* 5.2 2.7 - - + -
7791 VAL* 4.5 4.5 - - + -
7811 LEU* 3.9 25.1 - - + -
7861 PHE* 4.0 15.7 - - + -
7891 LEU* 5.1 4.7 - - + -
7901 ASN* 5.0 6.1 - - - +
7971 TRP* 3.4 49.4 - - + -
793O VAL* 3.9 7.0 - - - -
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Residues in contact with PHE 765 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7641 VAL* 1.3 78.8 - - - +
7661 CYS* 1.3 70.7 + - - +
7671 GLU* 2.9 42.6 + - + +
7711 ASN* 3.5 44.0 - - - -
7721 PHE 3.6 8.5 - - - -
7731 PHE* 3.5 45.1 - + + -
7961 GLU* 5.7 0.5 - - - +
7971 TRP* 3.8 16.5 + - - +
793O VAL* 4.0 9.9 - - + +
322P HIS* 5.6 3.6 - + - -
743S GLY 4.1 11.2 - - - -
744S ALA* 4.2 4.0 - - + -
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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