Contacts of the helix formed by residues 792 - 797 (chain B) 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 LYS 792 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B GLU* 5.6 0.4 + - - -
414B PRO* 5.8 0.7 - - - -
439B HIS* 5.4 4.0 - - - +
759B GLU* 3.6 8.4 + - - +
761B THR* 2.7 50.5 + - - +
762B THR 4.4 4.7 + - - -
764B LEU 3.4 23.4 + - - -
769B VAL* 4.3 8.1 - - + +
790B GLU* 3.7 0.7 + - - +
791B HIS* 1.3 81.0 - - + +
793B MET* 1.3 58.3 + - - +
794B GLN* 3.0 19.2 + - + +
795B VAL* 3.2 23.9 + - + +
796B VAL* 3.3 13.0 - - - +
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Residues in contact with MET 793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B HIS* 5.0 2.9 - - - -
414B PRO* 4.2 19.4 - - + +
529B THR* 5.3 5.8 - - + -
791B HIS 4.4 9.4 - - - +
792B LYS* 1.3 69.0 - - - +
794B GLN* 1.3 62.0 + - - +
795B VAL 3.3 0.4 - - - -
796B VAL* 3.8 22.6 - - + +
797B ALA* 3.4 22.9 + - - +
833B THR* 3.8 22.4 - - - +
836B TYR* 4.0 22.4 - - + +
837B LEU* 3.3 40.6 - - + +
840B ALA* 3.6 25.6 - - + +
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Residues in contact with GLN 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B LEU* 5.8 1.2 - - - +
484B TYR* 4.4 9.9 + - - -
491B THR* 5.4 7.9 + - - +
766B PRO* 2.8 49.4 + - - +
769B VAL* 3.1 25.9 - - + +
770B GLU* 4.5 5.7 - - - +
773B GLN* 5.6 0.9 - - - +
792B LYS* 3.0 14.3 + - + +
793B MET* 1.3 78.7 - - - +
795B VAL* 1.3 60.2 + - + +
797B ALA* 4.0 9.2 + - - +
798B ALA* 4.0 9.4 + - - +
840B ALA* 5.4 1.6 - - - -
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Residues in contact with VAL 795 (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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525B MET* 4.0 17.0 - - + -
527B SER* 4.2 1.8 - - - +
760B PRO* 6.1 0.7 - - + -
761B THR* 4.1 17.0 - - + -
769B VAL* 5.0 4.9 - - + -
773B GLN* 3.3 29.3 - - - +
776B LEU* 5.6 0.4 - - + -
790B GLU* 3.2 45.1 - - + +
792B LYS* 3.2 14.8 + - + +
794B GLN* 1.3 75.7 - - + +
796B VAL* 1.3 61.2 + - - +
797B ALA 3.1 2.2 - - - -
798B ALA* 2.9 23.2 + - - +
799B SER* 3.2 8.3 + - - -
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Residues in contact with VAL 796 (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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527B SER* 3.9 3.8 - - - +
529B THR* 3.9 18.4 - - + -
790B GLU* 3.8 16.6 - - + +
792B LYS 3.3 18.4 - - - +
793B MET* 3.8 23.8 - - + +
795B VAL* 1.3 77.3 - - - +
797B ALA* 1.3 60.9 + - - +
799B SER* 3.2 13.5 + - - -
802B VAL* 3.6 32.3 - - + -
822B PRO* 3.2 22.1 - - - +
837B LEU* 4.0 19.3 - - + -
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Residues in contact with ALA 797 (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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494B HIS* 4.1 14.1 + - - +
793B MET 3.4 17.6 + - - +
794B GLN 4.0 6.3 - - - +
795B VAL 3.1 0.6 - - - -
796B VAL* 1.3 78.4 - - - +
798B ALA* 1.3 56.6 + - - +
799B SER 3.3 4.1 + - - +
822B PRO* 4.2 8.4 - - - +
837B LEU* 4.2 10.5 - - + +
840B ALA* 4.3 13.0 - - + +
841B LEU* 4.0 29.4 - - + +
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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