Contacts of the helix formed by residues 693 - 701 (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 THR 693 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B GLU* 4.2 26.0 + - - +
691B ALA 3.7 1.0 + - - +
692B LEU* 1.3 74.0 - - - +
694B VAL* 1.3 61.3 + - - +
695B ASP* 3.9 3.6 + - - +
696B GLU* 3.2 35.5 + - - +
697B ALA* 2.8 30.8 + - - +
720B GLY 4.1 8.1 - - - -
721B TYR* 3.6 22.2 - - - +
722B LEU 3.7 4.7 - - - -
723B ARG* 4.1 13.2 - - + +
724B LEU* 4.2 1.3 - - - -
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Residues in contact with VAL 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B MET* 3.6 26.2 - - + -
693B THR* 1.3 74.2 - - - +
695B ASP* 1.3 61.8 + - - +
697B ALA* 4.0 1.0 - - - +
698B HIS* 3.1 26.9 + - - +
711B LEU* 4.1 18.9 - - + +
714B LEU* 4.0 17.0 - - + -
715B ARG* 3.8 21.4 + - + -
719B LEU 3.1 28.7 - - - +
720B GLY* 3.2 20.1 + - - +
722B LEU 3.1 7.9 + - - +
724B LEU* 4.4 4.5 - - + -
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Residues in contact with ASP 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LYS* 4.8 13.9 + - - +
693B THR* 3.3 3.3 + - - +
694B VAL* 1.3 76.0 - - - +
696B GLU* 1.3 62.2 + - - +
698B HIS* 3.5 3.5 + - - +
699B ASP* 3.4 23.6 + - - +
715B ARG* 3.2 37.8 + - - +
720B GLY* 3.1 33.2 + - - +
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Residues in contact with GLU 696 (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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459B GLU* 4.1 14.9 - - - +
684B LYS* 5.0 2.4 + - - -
692B LEU* 3.4 36.3 - - + +
693B THR* 3.2 31.1 + - - +
695B ASP* 1.3 73.7 - - - +
697B ALA* 1.3 61.9 + - - +
699B ASP* 3.1 10.9 + - + +
700B PHE* 2.8 28.4 + - - +
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Residues in contact with ALA 697 (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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692B LEU* 3.7 14.6 - - + -
693B THR 2.8 19.1 + - - +
694B VAL 4.0 0.7 - - - +
696B GLU* 1.3 77.1 - - - +
698B HIS* 1.3 57.0 + - - +
700B PHE* 3.1 0.4 + - - -
701B PHE* 2.9 41.0 + - + +
711B LEU* 3.6 21.0 - - + +
724B LEU* 3.8 28.7 - - + -
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Residues in contact with HIS 698 (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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694B VAL 3.1 19.3 + - - +
695B ASP 3.5 7.6 + - - +
697B ALA* 1.3 76.3 - - - +
699B ASP* 1.3 68.6 + - - +
702B ALA* 3.2 15.1 + - - +
708B PHE* 3.2 48.8 - + - -
711B LEU* 3.7 9.5 - - + +
712B ASP* 2.8 26.1 + - - -
715B ARG* 3.0 46.7 + - - +
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Residues in contact with ASP 699 (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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695B ASP 3.4 11.6 + - - +
696B GLU* 3.1 13.1 + - - +
698B HIS* 1.3 87.1 + - - +
700B PHE* 1.3 61.9 + - - +
701B PHE 3.3 0.3 + - - -
702B ALA* 3.4 15.4 + - - +
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Residues in contact with PHE 700 (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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616B PHE* 6.3 0.7 - + - -
681B TYR* 3.5 31.9 - + - -
682B ARG* 2.7 78.4 + - + +
684B LYS* 3.5 34.3 - - + -
689B VAL* 5.1 4.0 - - + -
692B LEU* 3.9 17.5 - - + -
696B GLU 2.8 18.7 + - - +
697B ALA 3.1 4.0 + - - +
699B ASP* 1.3 73.6 - - - +
701B PHE* 1.3 76.8 + + + +
702B ALA 3.5 0.9 + - - -
703B ASP* 4.2 0.2 - - - +
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Residues in contact with PHE 701 (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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612B VAL* 4.6 16.6 - - + -
615B LEU* 3.5 25.4 - - + -
616B PHE* 5.7 1.1 - + - -
681B TYR* 4.2 6.3 - + - -
689B VAL* 3.6 30.3 - - + -
692B LEU* 4.7 4.5 - - + -
697B ALA* 2.9 31.0 + - + +
698B HIS 3.7 2.9 - - - -
700B PHE* 1.3 102.1 - + + +
702B ALA* 1.3 67.4 + - - +
703B ASP* 3.2 8.7 - - - -
704B GLU* 3.0 42.5 + - + +
707B ILE* 3.8 30.7 - - + -
708B PHE* 3.6 7.4 - - - +
711B LEU* 4.7 0.9 - - + -
724B LEU* 4.9 2.9 - - + -
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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
------------------------------------------------------------
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