Contacts of the helix formed by residues 792 - 798 (chain A) 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 LYS 792 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A SER* 5.8 1.3 + - - -
439A HIS* 3.8 35.7 + - - +
440A ASP* 4.2 22.8 - - - +
441A LEU 5.6 0.2 - - - +
761A THR* 4.3 28.9 + - + +
764A LEU 4.0 10.5 + - - -
766A PRO* 5.1 5.1 - - + +
769A VAL* 5.2 2.6 - - + +
790A GLU* 3.3 21.5 + - - +
791A HIS* 1.3 78.9 - - + +
793A MET* 1.3 62.8 + - - +
794A GLN* 4.7 16.6 - - + +
795A VAL* 3.9 15.8 + - + -
796A VAL* 3.4 8.0 + - - +
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Residues in contact with MET 793 (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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413A HIS* 5.7 0.9 - - - -
414A PRO* 4.4 15.3 - - + -
529A THR* 4.7 12.6 - - + -
791A HIS* 3.4 13.4 + - - +
792A LYS* 1.3 70.5 - - - +
794A GLN* 1.3 69.9 + - - +
795A VAL 3.1 2.2 - - - -
796A VAL* 2.6 23.6 + - + -
797A ALA* 2.6 15.0 + - - +
833A THR* 3.4 43.7 - - - +
836A TYR* 3.9 22.2 - - + +
837A LEU* 3.6 26.9 - - + +
840A ALA* 4.0 18.4 - - + -
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Residues in contact with GLN 794 (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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484A TYR* 4.9 7.3 - - - -
766A PRO* 4.1 13.4 + - - +
769A VAL* 2.8 41.7 - - + +
770A GLU* 4.1 18.4 + - - +
773A GLN* 3.9 13.8 + - - +
792A LYS* 4.7 14.2 - - + +
793A MET* 1.3 77.7 - - - +
795A VAL* 1.3 64.5 + - + +
797A ALA* 3.3 17.3 + - - +
798A ALA* 3.5 6.1 + - - +
840A ALA* 4.7 6.2 - - - +
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Residues in contact with VAL 795 (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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525A MET* 5.0 14.2 - - + +
527A SER* 4.0 6.1 + - - +
761A THR* 3.9 20.2 - - + -
769A VAL* 5.1 3.6 - - + -
772A LEU* 6.5 0.4 - - + -
773A GLN* 3.4 30.1 - - + +
776A LEU* 5.9 4.3 - - + -
788A ALA* 5.8 0.7 - - + -
790A GLU* 2.8 43.1 - - + +
792A LYS* 3.9 7.6 - - + +
793A MET 2.9 2.4 + - - -
794A GLN* 1.3 78.8 - - + +
796A VAL* 1.3 67.0 + - - +
798A ALA* 3.1 12.3 + - - +
799A SER* 3.4 7.1 + - - -
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Residues in contact with VAL 796 (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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527A SER* 3.3 22.2 - - - +
529A THR* 3.1 35.9 - - + -
790A GLU* 4.0 11.4 - - + +
792A LYS 3.4 15.2 + - - +
793A MET* 2.6 20.6 + - + +
795A VAL* 1.3 72.3 - - - +
797A ALA* 1.3 54.4 + - - +
799A SER* 2.6 28.9 + - - -
802A VAL* 4.0 21.1 - - + -
822A PRO* 3.9 4.2 - - + +
837A LEU* 4.2 20.6 - - + -
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Residues in contact with ALA 797 (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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494A HIS* 4.6 8.7 + - - +
793A MET 2.6 16.3 + - - +
794A GLN* 3.3 13.5 - - - +
796A VAL* 1.3 70.8 - - - +
798A ALA* 1.3 57.7 + - - +
799A SER 3.7 1.0 + - - +
822A PRO* 4.0 14.0 - - - +
837A LEU* 4.3 6.0 - - + +
840A ALA* 3.8 13.7 - - + +
841A LEU* 3.3 33.8 - - + +
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Residues in contact with ALA 798 (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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494A HIS* 3.5 35.6 - - + +
525A MET* 5.1 4.0 - - - +
773A GLN* 3.1 34.3 - - - +
794A GLN 3.5 3.5 + - - +
795A VAL 3.1 7.5 + - - +
796A VAL 3.0 1.4 - - - -
797A ALA* 1.3 78.0 - - - +
799A SER* 1.3 66.9 + - - +
800A ASP* 4.6 0.7 - - - +
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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