Contacts of the strand formed by residues 402 - 406 (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 VAL 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 5.8 0.7 - - + -
91B LEU* 4.8 2.2 - - + -
92B PRO* 3.2 39.3 - - + +
93B PRO 2.8 13.7 + - - +
94B ALA* 3.3 10.2 - - + +
95B VAL 2.8 26.9 + - - -
401B VAL* 1.3 72.6 - - - +
403B TYR* 1.3 69.6 - - - +
404B VAL* 3.9 3.4 + - + +
433B SER* 3.5 19.5 - - - +
435B PHE* 3.7 49.6 - - + -
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Residues in contact with TYR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 3.4 31.0 - - + -
97B LEU* 4.2 13.7 - - + -
393B GLN* 3.1 37.2 + - + +
396B SER* 3.8 4.5 + - - -
398B LEU* 3.6 21.1 + - - +
401B VAL* 3.8 10.1 - - + -
402B VAL* 1.3 74.2 - - - +
404B VAL* 1.3 56.9 + - - +
405B LEU* 4.1 9.0 - - + +
427B LEU* 3.5 36.3 - - + +
432B ASN* 3.7 32.3 + - + -
433B SER 2.9 10.0 + - - -
434B LEU* 3.5 16.8 - - + -
435B PHE* 2.7 32.9 + - - +
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 3.9 23.3 - - + +
54B PHE* 3.8 33.3 - - + -
58B TYR* 4.3 21.5 - - + +
94B ALA* 4.5 4.3 - - + -
95B VAL 2.9 12.1 + - - +
96B ALA* 3.7 4.5 - - - -
97B LEU 3.2 24.8 + - - -
386B GLN* 4.6 0.5 + - - -
402B VAL* 4.1 15.9 - - + +
403B TYR* 1.3 78.0 - - - +
405B LEU* 1.3 64.5 + - - +
435B PHE* 3.3 24.9 - - + +
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Residues in contact with LEU 405 (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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54B PHE* 3.9 4.1 - - - -
97B LEU* 4.2 19.5 - - + -
386B GLN* 3.6 15.0 - - + +
390B LEU* 4.1 19.5 - - + -
403B TYR* 4.1 19.5 - - + +
404B VAL* 1.3 78.8 - - - +
406B ASP* 1.3 60.2 + - - +
407B GLU 4.0 0.7 - - - -
408B PRO* 3.8 37.0 - - + -
424B LEU* 4.2 5.6 - - + -
427B LEU* 5.5 0.7 - - + -
434B LEU* 4.1 17.5 - - + -
435B PHE 2.8 12.2 + - - +
436B VAL* 3.5 17.6 - - + -
437B VAL* 2.9 31.6 + - - +
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Residues in contact with ASP 406 (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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50B SER* 5.4 4.2 - - - -
54B PHE* 3.7 20.2 - - + -
98B GLN* 2.7 37.1 + - + +
386B GLN* 2.9 25.3 - - - +
405B LEU* 1.3 71.4 - - - +
407B GLU* 1.3 78.2 + - - +
437B VAL* 3.9 22.8 - - - +
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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