Contacts of the helix formed by residues 679 - 691 (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 ALA 679 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A ALA 3.4 2.9 + - - -
678A ASP* 1.3 80.6 + - - +
680A ASP* 1.3 63.2 + - - +
682A MET* 3.3 13.3 + - - +
683A LYS* 3.4 16.1 + - - +
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Residues in contact with ASP 680 (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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678A ASP* 3.4 11.8 + - - +
679A ALA* 1.3 77.5 - - - +
681A THR* 1.3 61.3 + - + +
683A LYS* 3.0 49.3 + - - +
684A GLU* 3.8 3.1 + - - +
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Residues in contact with THR 681 (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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677A ALA* 4.8 2.4 - - - +
678A ASP* 2.9 45.3 + - + +
680A ASP* 1.3 76.2 - - + +
682A MET* 1.3 57.1 + - - +
683A LYS 3.4 0.4 - - - -
684A GLU* 4.0 17.9 + - - +
685A VAL* 3.2 19.2 + - - +
738A SER* 5.5 5.1 - - - +
739A ALA* 5.6 1.9 - - - -
742A SER* 3.1 32.7 + - - +
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Residues in contact with MET 682 (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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677A ALA* 3.9 25.1 - - + +
678A ASP 2.9 17.8 + - - +
679A ALA* 3.5 8.1 - - - +
680A ASP 3.0 0.2 + - - -
681A THR* 1.3 77.6 - - - +
683A LYS* 1.3 66.6 + - - +
684A GLU 3.2 1.6 - - - -
685A VAL* 3.2 34.5 + - + +
686A THR* 3.4 11.3 + - - +
768A SER 3.2 26.7 - - - +
769A ALA* 4.8 6.7 - - - +
809A SER* 5.7 0.4 - - - +
811A LEU* 5.8 5.2 - - + -
812A ARG* 4.4 30.7 - - + +
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Residues in contact with LYS 683 (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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679A ALA 3.4 10.4 + - - +
680A ASP* 3.0 30.8 + - - +
682A MET* 1.3 80.2 - - - +
684A GLU* 1.3 54.7 + - - +
685A VAL 3.1 0.2 - - - -
686A THR* 3.1 27.7 - - + +
687A ARG* 3.2 27.4 + - - +
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Residues in contact with GLU 684 (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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680A ASP 3.8 4.1 + - - +
681A THR* 4.2 17.7 - - - +
682A MET 3.2 0.8 - - - -
683A LYS* 1.3 77.4 - - - +
685A VAL* 1.3 62.7 + - - +
687A ARG* 3.5 25.5 - - + +
688A THR* 3.6 19.3 + - - +
738A SER* 4.9 17.2 + - - -
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Residues in contact with VAL 685 (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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677A ALA* 5.7 1.6 - - + -
681A THR 3.2 20.9 - - - +
682A MET* 3.2 30.5 - - + +
683A LYS 3.1 0.2 - - - -
684A GLU* 1.3 75.3 - - - +
686A THR* 1.3 61.0 + - - +
687A ARG 3.0 4.0 - - - -
688A THR* 3.1 30.1 + - - +
689A VAL* 3.1 15.4 - - + +
735A ALA* 3.8 31.9 - - + +
738A SER* 5.1 5.4 - - - +
739A ALA* 5.1 10.1 - - + -
769A ALA* 4.3 19.3 - - + -
770A CYS* 5.7 0.4 - - - -
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Residues in contact with THR 686 (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* 3.4 9.6 + - - +
683A LYS* 3.1 25.8 - - - +
685A VAL* 1.3 82.1 - - - +
687A ARG* 1.3 60.6 + - + +
688A THR 3.5 0.2 - - - -
689A VAL* 4.0 8.0 - - - +
690A LYS* 3.3 53.2 + - + +
807A GLU* 5.4 1.6 + - - -
812A ARG* 4.9 12.8 + - - -
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Residues in contact with ARG 687 (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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683A LYS* 3.2 22.9 + - - +
684A GLU* 3.5 41.9 - - - +
685A VAL 3.0 0.8 - - - -
686A THR* 1.3 79.8 - - - +
688A THR* 1.3 58.6 + - - +
689A VAL 3.1 1.1 - - - -
690A LYS* 3.9 1.9 - - - +
691A GLU* 2.8 43.5 + - + +
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Residues in contact with THR 688 (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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684A GLU* 3.6 12.7 + - - +
685A VAL* 3.1 15.3 - - - +
687A ARG* 1.3 77.0 - - - +
689A VAL* 1.3 59.5 + - - +
691A GLU* 3.9 19.1 + - - -
692A ALA* 3.9 14.7 + - - +
731A ALA* 4.4 8.9 - - - +
734A ASN* 4.1 21.2 + - + +
735A ALA* 4.0 29.4 - - + +
738A SER* 5.2 1.1 - - - +
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Residues in contact with VAL 689 (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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685A VAL* 3.1 23.1 - - + +
686A THR* 4.0 8.3 - - - +
687A ARG 3.1 0.4 - - - -
688A THR* 1.3 79.1 - - + +
690A LYS* 1.3 57.4 + - + +
691A GLU 3.0 4.0 - - - -
692A ALA* 3.0 23.2 + - - +
693A ARG* 3.5 8.0 + - - +
731A ALA* 5.5 3.6 - - - +
732A ARG* 6.3 0.4 - - - -
735A ALA* 4.2 17.9 - - + -
770A CYS* 5.0 10.1 - - + -
805A PHE* 5.2 9.4 - - + -
807A GLU* 3.2 45.5 - - + +
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Residues in contact with LYS 690 (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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686A THR* 3.3 37.0 + - + +
687A ARG* 3.9 2.5 - - - +
689A VAL* 1.3 80.7 - - + +
691A GLU* 1.3 56.1 + - - +
692A ALA 3.1 1.3 - - - -
693A ARG* 3.4 32.5 + - + +
694A ARG* 4.1 3.5 + - - +
807A GLU* 3.9 25.1 - - - +
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Residues in contact with GLU 691 (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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687A ARG* 2.8 34.3 + - + +
688A THR* 4.0 16.7 - - - -
689A VAL 3.0 1.4 - - - -
690A LYS* 1.3 76.6 - - - +
692A ALA* 1.3 57.8 + - - +
693A ARG 3.5 0.4 - - - -
694A ARG* 4.4 17.0 - - - +
695A GLN* 3.6 26.0 + - - +
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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