Contacts of the helix formed by residues 760 - 769 (chain A) in PDB entry 3H0G
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 SER 760 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753A VAL* 4.0 12.8 - - - +
759A GLY* 1.3 75.3 - - - -
761A PHE* 1.3 58.7 + - - +
762A ILE* 3.4 22.0 - - - +
763A ASN* 2.6 45.0 + - - +
764A ILE* 3.4 7.5 + - - +
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Residues in contact with PHE 761 (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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733A ASP* 4.9 9.9 - - + -
736A GLY* 3.6 10.3 - - - -
737A ARG* 3.4 53.8 - - + -
740A GLU* 4.0 23.6 - - + -
753A VAL* 4.5 5.4 - - + +
760A SER* 1.3 73.8 - - - +
762A ILE* 1.3 63.1 + - + +
764A ILE* 2.7 30.3 - - + +
765A SER* 3.0 19.7 + - - -
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Residues in contact with ILE 762 (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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732A ARG* 4.4 21.8 - - - +
760A SER* 3.4 20.2 - - - +
761A PHE* 1.3 79.4 - - + +
763A ASN* 1.3 62.9 + - - +
764A ILE 3.4 0.2 - - - -
765A SER* 3.4 10.9 + - - +
766A GLN* 3.4 43.1 + - + +
1089A TYR* 6.1 3.6 - - + +
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Residues in contact with ASN 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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753A VAL* 6.1 0.9 - - + -
759A GLY* 3.1 15.7 - - - -
760A SER* 2.6 46.0 + - - +
762A ILE* 1.3 78.5 - - - +
764A ILE* 1.3 59.0 + - + +
766A GLN* 4.1 5.2 + - - +
767A MET* 2.8 40.3 + - + +
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Residues in contact with ILE 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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674A ASP 5.8 1.6 - - - +
740A GLU* 2.6 42.4 - - + +
743A LEU* 5.5 3.4 - - + -
747A ASN* 5.9 0.4 - - - +
749A VAL* 3.6 33.2 - - + +
750A LYS* 5.1 13.0 - - + -
753A VAL* 5.1 11.9 - - + -
760A SER 3.6 4.5 - - - +
761A PHE* 2.7 37.5 - - + +
763A ASN* 1.3 78.5 - - + +
765A SER* 1.3 59.6 + - - +
766A GLN 3.1 1.8 - - - -
767A MET* 3.0 16.0 + - + +
768A SER* 2.7 26.7 + - - +
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Residues in contact with SER 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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732A ARG* 5.5 11.3 + - - -
733A ASP* 6.5 0.2 - - - -
736A GLY* 3.6 29.6 - - - -
740A GLU* 4.2 7.8 + - - -
761A PHE* 3.0 22.3 + - - -
762A ILE* 3.4 13.9 + - - +
764A ILE* 1.3 77.5 - - - +
766A GLN* 1.3 59.7 + - - +
768A SER* 4.5 0.7 - - - -
769A ALA* 2.9 35.2 + - - +
770A CYS* 3.3 5.6 + - - -
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Residues in contact with GLN 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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732A ARG* 5.4 9.0 - - - +
762A ILE* 3.4 45.6 + - + +
763A ASN* 4.2 7.0 + - - +
764A ILE 3.1 0.6 - - - -
765A SER* 1.3 80.3 + - - +
767A MET* 1.3 60.9 + - + +
770A CYS 3.0 19.5 - - - +
771A VAL* 4.1 25.8 + - - +
774A GLN* 4.9 7.7 + - - +
809A SER* 3.2 2.4 - - - -
810A TYR* 2.9 48.5 + - + -
1089A TYR* 5.3 6.3 + - - -
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Residues in contact with MET 767 (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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674A ASP 5.8 0.4 - - - +
675A THR* 3.8 22.4 + - - +
749A VAL* 4.3 27.8 - - + -
763A ASN* 2.8 32.5 - - + +
764A ILE* 3.0 7.7 + - + +
766A GLN* 1.3 80.2 - - + +
768A SER* 1.3 55.4 + - - +
809A SER* 2.4 24.3 + - - -
810A TYR* 3.9 18.7 + - + -
811A LEU* 3.7 14.0 - - - +
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Residues in contact with SER 768 (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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675A THR* 2.9 29.6 - - - -
677A ALA* 4.4 19.0 - - - +
682A MET* 3.2 26.2 - - - +
739A ALA* 4.6 6.9 - - - +
740A GLU* 4.3 7.6 + - - -
743A LEU* 5.3 5.5 - - - +
764A ILE* 2.7 19.7 + - - +
765A SER* 4.5 1.0 - - - -
767A MET* 1.3 79.0 - - - +
769A ALA* 1.3 59.6 + - - +
809A SER* 3.5 5.5 + - - -
811A LEU* 4.1 3.6 - - - +
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Residues in contact with ALA 769 (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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682A MET* 4.8 5.9 - - - +
685A VAL* 4.3 19.7 - - + -
735A ALA 4.2 22.9 - - - +
736A GLY* 4.5 1.3 - - - -
739A ALA* 4.5 5.8 - - + -
765A SER* 2.9 19.8 + - - +
768A SER* 1.3 80.7 + - - +
770A CYS* 1.3 74.1 + - - +
807A GLU 4.0 4.1 - - - +
808A ASN* 3.6 2.1 - - - -
809A SER* 3.2 18.8 + - - -
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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
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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