Contacts of the strand formed by residues 754 - 757 (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 VAL 754 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B LEU* 5.9 3.4 - - + -
522B LEU* 5.4 4.7 - - + -
544B LEU* 5.7 1.6 - - + -
548B LEU* 3.8 29.6 - - + -
583B ILE* 4.5 20.4 - - + +
585B ARG 3.1 16.4 + - - +
586B LEU* 3.5 8.3 - - + +
587B VAL 3.3 17.3 + - - -
753B THR* 1.3 75.0 + - - +
755B TYR* 1.3 64.1 + - - +
756B VAL* 5.9 0.9 - - + -
785B THR* 3.5 16.4 - - + +
787B ILE* 3.6 30.3 - - + -
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Residues in contact with TYR 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B ARG* 4.3 0.9 + - - -
587B VAL* 3.2 36.1 - - + +
589B VAL* 5.2 2.9 - - + -
741B LEU* 5.8 2.9 - - + -
744B GLU* 3.5 32.1 + - + +
748B SER* 3.7 20.3 + - - -
753B THR* 3.6 17.7 + - - +
754B VAL* 1.3 73.9 - - - +
756B VAL* 1.3 57.4 + - - +
757B LEU* 4.2 15.0 - - + -
779B LEU* 3.4 34.1 - - + +
784B ASN* 3.5 25.3 - - + -
785B THR 2.7 21.3 + - - +
786B VAL* 3.4 13.4 - - + -
787B ILE* 2.8 34.5 + - - +
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Residues in contact with VAL 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B VAL* 3.5 34.5 - - + +
541B SER* 5.7 3.6 - - - +
544B LEU* 3.9 20.6 - - + -
545B VAL* 4.2 11.7 - - + -
586B LEU* 3.5 29.6 - - + -
587B VAL 3.0 3.6 + - - -
588B ARG* 3.2 21.1 + - + +
589B VAL 2.8 28.6 + - - +
754B VAL* 5.9 1.1 - - + -
755B TYR* 1.3 71.7 - - - +
757B LEU* 1.3 61.9 + - - +
758B ASP 4.0 0.8 + - - +
787B ILE* 3.5 12.3 - - + +
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Residues in contact with LEU 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B VAL* 5.2 2.2 - - - +
541B SER* 5.1 0.2 - - - -
589B VAL* 3.7 31.9 - - + +
737B GLN* 4.9 1.1 - - - +
741B LEU* 5.3 6.5 - - + -
755B TYR* 4.2 20.4 - - + +
756B VAL* 1.3 82.4 - - - +
758B ASP* 1.3 61.0 + - - +
759B GLU 3.8 0.5 + - - -
760B PRO* 3.8 28.0 - - + -
776B LEU* 3.8 38.6 - - + -
786B VAL* 5.2 4.7 - - + -
787B ILE 2.9 9.7 + - - +
788B ALA* 3.1 35.1 - - + +
789B VAL* 3.1 8.5 + - - +
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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