Contacts of the helix formed by residues 761 - 766 (chain A) in PDB entry 3J0A
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 HIS 761 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700A SER* 3.8 17.7 + - - +
702A LYS* 3.4 46.5 + - + +
703A ASP* 3.2 32.8 + - - +
759A SER* 2.9 1.6 + - - -
760A ARG* 1.3 112.3 + - + +
762A PHE* 1.3 61.9 + - - +
763A LEU 3.0 5.6 - - - -
764A ARG* 3.0 26.4 + - + +
765A ASP* 3.6 7.5 + - - +
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Residues in contact with PHE 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A CYS* 3.6 44.2 - - - -
699A PHE* 3.7 24.9 - - - -
700A SER* 4.0 9.5 - - - -
756A CYS* 3.9 23.3 - - + -
757A LEU 3.6 8.3 - - - +
758A VAL* 3.6 22.4 - - + -
759A SER* 3.3 22.6 + - - +
761A HIS* 1.3 77.9 - - - +
763A LEU* 1.3 57.0 + - - +
766A GLY* 3.0 25.2 + - - +
767A TRP* 2.9 53.8 + + + -
770A GLU* 5.0 2.9 - - + -
806A ILE* 6.1 0.4 - - + -
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Residues in contact with LEU 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758A VAL* 5.9 0.4 - - + -
759A SER 3.4 11.6 + - - +
760A ARG 5.0 3.8 - - - +
761A HIS 3.0 0.6 - - - -
762A PHE* 1.3 78.4 - - - +
764A ARG* 1.3 66.1 + - + +
765A ASP 3.4 0.6 + - - -
767A TRP* 4.0 21.1 - - + +
768A CYS* 3.9 11.8 - - - -
795A LEU* 3.9 10.1 - - + -
799A GLN* 3.5 46.9 - - + +
800A LEU* 3.5 19.3 - - + -
801A MET* 4.6 8.0 - - + +
803A HIS* 4.4 13.4 + - + -
806A ILE* 3.8 32.8 - - + -
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Residues in contact with ARG 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760A ARG 3.8 17.7 + - - +
761A HIS* 3.0 17.2 + - + +
763A LEU* 1.3 79.2 - - - +
765A ASP* 1.3 67.6 + - - +
768A CYS* 3.2 14.6 - - - -
799A GLN* 3.2 39.2 + - - +
801A MET* 5.1 17.1 - - - +
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Residues in contact with ASP 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A SER* 4.2 15.8 + - - -
701A SER* 5.2 3.3 + - - -
702A LYS* 5.8 4.2 - - - +
761A HIS* 3.6 5.7 + - - +
763A LEU 3.4 0.2 - - - -
764A ARG* 1.3 85.0 - - - +
766A GLY* 1.3 64.8 + - - +
767A TRP 3.6 1.6 - - - -
768A CYS* 3.9 12.1 - - - -
769A LEU* 3.3 22.4 - - - +
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Residues in contact with GLY 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A CYS* 4.9 2.3 - - - -
699A PHE 5.4 3.1 - - - -
700A SER* 5.9 1.3 - - - -
761A HIS 4.4 0.2 + - - -
762A PHE* 3.0 36.7 + - - +
765A ASP* 1.3 83.5 + - - +
767A TRP* 1.3 60.3 + - - +
768A CYS 3.4 0.4 - - - -
769A LEU* 4.3 4.8 + - - +
770A GLU* 3.4 22.0 + - - +
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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
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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