Contacts of the helix formed by residues 832 - 842 (chain A) in PDB entry 2VJ0
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 832 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831A MET* 1.3 78.5 - - - +
833A SER* 1.3 66.9 + - - +
834A GLN* 3.2 27.1 - - + +
835A ASP* 3.1 15.6 + - - +
836A PHE* 3.0 20.3 + - - +
880A VAL* 5.1 0.2 - - - -
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Residues in contact with SER 833 (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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831A MET 4.0 0.4 + - - -
832A ALA* 1.3 73.3 - - - +
834A GLN* 1.3 77.0 + - - +
836A PHE* 3.2 2.4 + - - +
837A PHE* 3.0 48.0 + - - -
879A GLU 4.0 17.0 + - - -
880A VAL* 4.1 21.6 + - - +
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Residues in contact with GLN 834 (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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832A ALA* 3.4 27.7 - - + +
833A SER* 1.3 84.5 + - - +
835A ASP* 1.3 63.9 + - - +
837A PHE* 3.5 5.4 + - - +
838A GLN* 3.1 34.4 + - - +
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Residues in contact with ASP 835 (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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831A MET* 4.3 5.5 - - + +
832A ALA* 3.1 22.5 + - - +
834A GLN* 1.3 78.0 - - - +
836A PHE* 1.3 67.2 + - - +
838A GLN* 3.3 20.5 + - - +
839A ARG* 3.0 60.5 + - - +
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Residues in contact with PHE 836 (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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831A MET* 3.6 14.1 - - + -
832A ALA 3.0 13.5 + - - +
833A SER* 3.5 7.6 - - - +
835A ASP* 1.3 76.1 - - - +
837A PHE* 1.3 66.7 + + - +
839A ARG* 3.1 4.3 + - - +
840A TRP* 2.8 58.7 + + + +
877A LEU* 3.7 19.5 - - + -
880A VAL* 3.6 20.9 - - + -
888A VAL* 3.3 24.9 - - + -
889A GLY 3.7 16.2 - - - -
903A LEU* 3.8 21.1 - - + -
904A LEU 4.4 1.6 - - - -
1Q PHE* 3.7 27.8 - + - -
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Residues in contact with PHE 837 (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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833A SER* 3.0 43.5 + - - +
834A GLN* 4.1 4.7 - - - +
836A PHE* 1.3 84.1 - + - +
838A GLN* 1.3 61.5 - - - +
840A TRP* 3.6 9.5 - + + +
841A LYS* 3.0 43.4 + - - +
880A VAL* 3.3 34.5 - - + -
881A ASP* 4.8 0.2 - - - -
882A PRO* 5.1 3.6 - - + -
1Q PHE* 3.8 46.9 - + - -
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Residues in contact with GLN 838 (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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834A GLN* 3.1 19.4 + - - +
835A ASP* 3.5 26.8 - - - +
837A PHE* 1.3 77.4 - - - +
839A ARG* 1.3 66.4 + - + +
841A LYS* 3.4 6.7 + - - +
842A GLN* 3.1 38.2 + - - +
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Residues in contact with ARG 839 (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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829A THR* 5.2 3.8 - - - +
831A MET* 3.6 41.8 - - - +
835A ASP* 3.0 46.3 + - - +
836A PHE* 3.6 4.0 - - - +
838A GLN* 1.3 77.9 + - + +
840A TRP* 1.3 67.5 + - - +
842A GLN* 3.2 29.8 + - - +
843A LEU* 3.4 18.6 + - + +
903A LEU* 3.7 14.8 - - + -
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Residues in contact with TRP 840 (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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836A PHE* 2.8 45.3 + + + +
837A PHE* 3.6 12.8 - + - +
839A ARG* 1.3 76.5 - - - +
841A LYS* 1.3 64.7 + - + +
843A LEU* 3.0 17.2 + - - +
849A GLU* 4.3 1.8 - - - -
903A LEU* 3.4 42.5 - - + +
904A LEU 4.3 3.4 - - - -
905A ARG* 4.3 6.1 - - + -
918A THR* 3.7 34.1 - - + -
920A ARG* 2.9 72.2 + - + +
1Q PHE* 3.5 41.8 - + + +
2Q GLU 5.3 2.2 - - - +
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Residues in contact with LYS 841 (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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837A PHE* 3.0 31.9 + - + +
838A GLN* 3.7 6.1 - - - +
840A TRP* 1.3 84.8 - - + +
842A GLN* 1.3 59.8 + - + +
843A LEU 3.1 1.5 + - - -
844A SER* 3.4 20.6 + - - -
920A ARG* 4.5 4.5 - - - +
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Residues in contact with GLN 842 (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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838A GLN* 3.1 30.5 + - - +
839A ARG* 3.2 24.5 + - - +
841A LYS* 1.3 75.0 - - - +
843A LEU* 1.3 66.2 + - + +
844A SER* 3.5 3.5 + - - -
848A GLN* 4.2 3.5 + - - +
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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