Contacts of the strand formed by residues 785 - 789 (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 785 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B PRO 3.5 24.0 - - - +
522B LEU* 3.5 14.3 - - + +
523B GLY* 2.6 24.5 + - - +
524B VAL 3.7 8.1 - - - +
583B ILE* 5.6 2.4 - - - +
753B THR 2.7 9.4 + - - -
754B VAL* 3.9 14.9 - - + +
755B TYR* 2.7 36.6 + - - -
783B GLY 4.4 0.9 + - - -
784B ASN* 1.3 75.2 - - - +
786B VAL* 1.3 60.8 + - - +
787B ILE* 3.9 20.6 - - + -
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Residues in contact with VAL 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B VAL 3.3 9.0 + - - +
525B MET* 3.8 35.2 - - + -
526B THR 3.0 21.5 + - - +
755B TYR* 3.4 24.5 - - + +
757B LEU* 5.2 6.5 - - + -
776B LEU* 4.4 24.0 - - + +
779B LEU* 4.7 7.0 - - + -
780B VAL* 3.9 22.9 - - + +
784B ASN 4.2 0.4 + - - -
785B THR* 1.3 81.4 - - - +
787B ILE* 1.3 65.5 + - - +
788B ALA* 5.3 0.7 - - + -
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Residues in contact with ILE 787 (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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503B LEU* 6.0 2.5 - - + -
520B PHE* 3.9 51.6 - - + -
522B LEU* 5.6 1.3 - - + -
526B THR* 3.5 13.9 - - - +
528B VAL* 4.0 9.0 - - + -
540B VAL* 4.0 19.5 - - + -
544B LEU* 4.7 10.5 - - + -
754B VAL* 3.6 30.7 - - + -
755B TYR 2.8 11.1 + - - +
756B VAL* 3.5 7.4 - - + -
757B LEU* 2.9 25.2 + - - +
785B THR* 3.9 11.9 - - + -
786B VAL* 1.3 77.5 - - - +
788B ALA* 1.3 66.5 + - - +
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Residues in contact with ALA 788 (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* 4.7 9.9 - - + -
526B THR 3.2 8.7 + - - +
527B SER* 3.3 5.5 + - - -
528B VAL* 2.7 28.1 + - - -
540B VAL* 5.2 1.3 - - - -
757B LEU* 3.1 28.7 - - + +
760B PRO* 4.3 4.9 - - + -
776B LEU* 5.9 0.2 - - + -
786B VAL* 5.3 2.5 - - + -
787B ILE* 1.3 81.2 - - - +
789B VAL* 1.3 62.7 + - - +
790B GLU* 3.8 16.3 + - - +
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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
----------------------------------------------------------
528B VAL* 3.6 12.3 - - + +
536B LYS* 3.7 47.1 - - + +
537B SER* 5.1 3.6 - - - +
540B VAL* 4.7 14.5 - - + +
541B SER* 5.3 0.7 - - - +
757B LEU 3.1 10.2 + - - +
758B ASP* 3.4 27.6 - - - +
759B GLU* 3.8 7.0 - - + +
760B PRO* 3.4 23.7 - - - +
788B ALA* 1.3 74.6 - - - +
790B GLU* 1.3 62.8 + - - +
791B HIS* 3.9 14.1 - - + +
1844B ADP 5.4 1.1 - - - +
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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