Contacts of the helix formed by residues 685 - 691 (chain B) in PDB entry 2VF8
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 ASN 685 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616B PHE* 3.0 14.3 - - - -
677B LEU* 3.1 60.6 + - - +
679B VAL 3.8 7.5 + - - -
680B GLU* 4.3 13.6 + - - +
684B LYS* 1.3 84.2 - - - +
686B ILE* 1.3 77.5 + - - +
687B ALA* 3.5 2.8 - - - +
688B ASP* 3.2 37.4 + - + +
689B VAL* 3.7 9.7 + - - +
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Residues in contact with ILE 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B PHE* 4.4 20.2 - - + -
612B VAL* 4.5 2.0 - - + -
613B ARG 5.5 0.9 - - - +
616B PHE* 3.6 40.8 - - + -
632B PHE* 4.3 16.8 - - + +
672B TYR* 4.2 33.0 - - + +
676B THR* 4.3 22.9 - - + +
677B LEU* 4.1 11.2 - - + -
679B VAL 3.9 0.8 + - - -
685B ASN* 1.3 90.2 - - - +
687B ALA* 1.3 60.9 + - - +
688B ASP 3.3 1.1 - - - -
689B VAL* 3.1 20.7 - - + +
690B LEU* 3.4 11.8 + - - +
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Residues in contact with ALA 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670B THR* 3.3 36.3 - - - +
672B TYR* 4.9 2.5 - - + -
677B LEU* 3.6 18.2 - - + -
685B ASN* 3.5 1.9 - - - +
686B ILE* 1.3 81.2 - - - +
688B ASP* 1.3 67.9 + - - +
690B LEU* 3.3 8.3 + - - +
691B ALA* 2.9 29.5 + - - +
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Residues in contact with ASP 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B GLU* 5.7 0.3 - - - +
683B GLY 5.2 1.7 - - - +
684B LYS* 4.1 22.0 + - + +
685B ASN* 3.2 40.3 + - + +
686B ILE 3.3 0.8 - - - -
687B ALA* 1.3 82.0 - - - +
689B VAL* 1.3 57.3 + - - +
691B ALA* 3.1 20.4 + - - +
692B LEU* 3.2 21.4 + - - +
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Residues in contact with VAL 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B PHE* 5.4 1.1 - - + -
612B VAL* 4.3 11.4 - - + -
616B PHE* 3.8 16.6 - - + -
684B LYS* 4.9 6.6 - - + +
685B ASN 3.7 15.0 + - - +
686B ILE* 3.1 27.6 - - + +
688B ASP* 1.3 74.1 - - - +
690B LEU* 1.3 62.5 + - + +
691B ALA 2.9 5.3 + - - -
692B LEU* 3.0 29.8 + - + +
700B PHE* 5.1 3.8 - - + -
701B PHE* 3.6 37.0 - - + -
724B LEU* 3.7 16.5 - - + +
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Residues in contact with LEU 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B ASN* 4.3 7.6 - - - +
603B ALA* 4.4 7.4 - - + -
609B PHE* 4.0 26.7 - - + -
634B PHE* 3.9 20.9 - - + -
670B THR 5.3 1.6 - - - +
671B ARG* 4.5 14.1 - - - +
672B TYR* 3.9 27.8 - - + -
686B ILE 3.4 7.8 + - - +
687B ALA* 3.3 11.2 + - - +
689B VAL* 1.3 83.0 - - + +
691B ALA* 1.3 58.1 + - - +
692B LEU 3.4 0.4 + - - -
723B ARG* 4.5 1.7 - - - +
724B LEU* 3.8 11.5 + - + +
725B GLY* 2.9 51.9 + - - +
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Residues in contact with ALA 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687B ALA 2.9 13.1 + - - +
688B ASP* 3.2 14.6 - - - +
689B VAL 2.9 0.8 - - - -
690B LEU* 1.3 77.5 - - - +
692B LEU* 1.3 65.9 + - - +
693B THR* 3.7 0.9 + - - +
723B ARG* 3.4 25.1 - - - +
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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