Contacts of the helix formed by residues 686 - 691 (chain C) in PDB entry 2VF7
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 ILE 686 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C PHE* 3.8 16.8 - - + -
612C VAL* 3.7 17.9 - - + -
613C ARG* 4.8 2.7 - - - -
616C PHE* 3.4 43.1 - - + -
632C PHE* 4.3 25.6 - - + +
672C TYR* 3.5 49.4 - - + +
676C THR* 4.6 7.2 + - + +
677C LEU* 4.2 8.1 - - + -
679C VAL 4.3 0.6 + - - -
685C ASN* 1.3 72.7 - - - +
687C ALA* 1.3 58.2 + - - +
689C VAL* 3.5 4.7 + - - +
690C LEU* 3.1 27.7 + - + +
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Residues in contact with ALA 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670C THR* 3.9 32.1 - - + +
672C TYR* 4.6 1.3 - - + -
677C LEU* 3.8 18.4 - - + -
685C ASN* 3.1 9.5 + - - +
686C ILE* 1.3 78.1 - - - +
688C ASP* 1.3 63.9 + - - +
689C VAL 3.2 1.3 - - - -
690C LEU* 3.2 11.1 + - - +
691C ALA* 3.1 23.7 + - - +
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Residues in contact with ASP 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C GLU* 5.8 0.9 - - - -
683C GLY 4.8 2.1 - - - +
684C LYS* 3.7 19.3 - - + -
685C ASN* 2.9 50.4 + - - +
687C ALA* 1.3 73.9 - - - +
689C VAL* 1.3 62.7 + - - +
691C ALA* 3.4 15.2 + - - +
692C LEU* 3.7 17.7 + - - +
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Residues in contact with VAL 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C VAL* 4.0 17.9 - - + -
616C PHE* 4.1 17.3 - - + -
681C TYR* 5.5 1.3 - - + +
684C LYS* 4.1 17.0 - - + -
685C ASN 3.0 14.5 + - - +
686C ILE* 3.5 11.0 - - - +
688C ASP* 1.3 76.8 - - - +
690C LEU* 1.3 64.8 + - + +
691C ALA 3.1 0.2 - - - -
692C LEU* 3.1 28.3 + - + +
700C PHE* 4.4 17.0 - - + -
701C PHE* 4.0 26.7 - - + -
724C LEU* 4.0 14.2 - - + +
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Residues in contact with LEU 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C ASN* 4.6 5.2 - - - +
603C ALA* 4.1 12.1 - - + -
609C PHE* 3.7 37.0 - - + -
634C PHE* 4.4 10.5 - - + -
670C THR 5.2 1.6 - - - +
671C ARG* 4.8 9.9 - - - +
672C TYR* 4.0 24.7 - - + +
686C ILE 3.1 21.6 + - - +
687C ALA* 3.2 8.2 + - - +
689C VAL* 1.3 76.4 - - + +
691C ALA* 1.3 56.7 + - - +
692C LEU 3.3 2.1 + - - -
723C ARG* 4.1 3.5 - - - +
724C LEU* 3.9 6.8 + - + -
725C GLY* 2.8 49.8 + - - +
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Residues in contact with ALA 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687C ALA 3.1 13.9 + - - +
688C ASP* 3.8 9.9 - - - +
689C VAL 3.1 1.0 - - - -
690C LEU* 1.3 77.2 - - - +
692C LEU* 1.3 63.3 + - - +
693C THR 3.7 0.5 + - - -
696C GLU* 4.4 3.6 - - - +
723C ARG* 3.3 29.9 + - - +
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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