Contacts of the strand formed by residues 787 - 791 (chain B) in PDB entry 1VDV
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 787 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A TYR* 5.3 0.2 + - - -
758B GLY 4.2 3.4 - - - +
760B MET* 3.6 14.1 - - + -
762B LEU* 3.8 23.1 - - + -
773B GLN* 2.8 60.5 + - + +
776B VAL* 4.2 7.0 - - + -
777B ALA* 3.8 26.7 - - + +
780B LEU* 3.9 27.4 - - + -
782B VAL* 4.0 12.6 - - + -
783B PRO 4.3 0.7 - - - +
784B VAL 3.1 4.6 + - - +
785B ASN 3.4 2.1 - - - -
786B ARG* 1.3 87.1 - - - +
788B LEU* 1.3 61.5 + - - +
789B VAL* 4.3 3.1 - - + -
1068B THR* 3.7 0.5 + - - -
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Residues in contact with LEU 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A ARG* 4.3 11.0 - - - +
1065A GLU* 5.7 0.9 - - - +
760B MET 3.0 12.8 + - - +
761B GLU* 3.4 35.2 - - + +
762B LEU* 2.8 29.1 + - - +
786B ARG 4.1 0.6 + - - +
787B ILE* 1.3 74.0 - - - +
789B VAL* 1.3 67.7 + - - +
790B ARG* 4.1 15.0 - - + -
1067B SER* 4.4 0.2 - - - -
1068B THR* 3.6 14.1 - - - +
1069B ASN* 3.6 43.5 - - + +
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Residues in contact with VAL 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B LEU* 3.5 9.0 - - + -
764B VAL* 4.2 15.0 - - + -
766B THR* 4.7 0.2 - - + -
769B ALA* 3.9 29.4 - - + +
772B THR* 3.8 18.6 - - + -
773B GLN* 3.8 35.9 - - + +
776B VAL* 6.0 0.2 - - + -
787B ILE* 4.3 7.2 - - + -
788B LEU* 1.3 77.0 - - - +
790B ARG* 1.3 63.8 + - - +
791B VAL* 4.3 9.4 - - + -
1066B THR 4.0 0.3 - - - +
1067B SER* 3.3 4.9 - - - -
1068B THR* 3.0 35.7 + - + +
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Residues in contact with ARG 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A LYS* 4.3 7.1 - - - +
761A GLU* 3.0 39.3 + - - -
788A LEU* 4.4 8.7 - - - +
790A ARG* 3.4 4.0 - - - +
761B GLU* 2.8 43.5 + - - -
762B LEU 2.8 14.7 + - - +
763B PHE* 3.4 36.2 - - + +
764B VAL 3.1 24.3 + - - -
788B LEU* 4.1 16.6 - - + -
789B VAL* 1.3 78.1 - - - +
791B VAL* 1.3 64.3 + - - +
792B LYS 4.2 1.0 + - - -
1065B GLU* 3.0 36.6 + - - +
1066B THR 3.5 4.3 - - - +
1067B SER* 4.2 10.1 - - - -
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Residues in contact with VAL 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B VAL 3.5 22.7 - - - +
766B THR* 3.6 39.5 - - + +
769B ALA* 4.4 11.4 - - + -
789B VAL* 4.3 8.7 - - + -
790B ARG* 1.3 78.0 - - - +
792B LYS* 1.3 64.2 + - - +
793B ARG* 4.2 13.7 - - - +
794B MET* 4.4 5.6 - - + -
1036B THR* 4.0 22.1 - - + -
1065B GLU* 4.4 2.0 - - - -
1066B THR* 2.8 37.3 + - - +
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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
------------------------------------------------------------
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