Contacts of the strand formed by residues 285 - 290 (chain B) in PDB entry 6VSB
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 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B VAL* 4.4 9.2 - - + -
37B TYR 4.0 20.6 - - - +
38B TYR* 3.1 35.8 + - + -
220B PHE* 4.0 19.4 - - + -
221B SER* 5.0 1.9 - - - -
222B ALA* 4.1 15.5 + - + +
277B LEU* 4.1 21.1 - - + -
278B LYS 3.2 8.7 - - - +
279B TYR* 3.6 23.1 - - + +
284B THR* 1.3 82.9 + - - +
286B THR* 1.3 59.7 + - - +
287B ASP 3.3 24.2 - - - +
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Residues in contact with THR 286 (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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220B PHE* 3.1 19.2 - - - -
278B LYS* 3.0 17.7 + - + +
280B ASN* 3.2 33.3 + - - +
284B THR* 4.1 4.7 + - - +
285B ILE* 1.3 72.8 - - - +
287B ASP* 1.3 75.4 + - - +
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Residues in contact with ASP 287 (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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220B PHE* 3.4 15.3 - - - +
277B LEU* 4.1 0.2 - - - -
278B LYS* 3.2 41.2 + - + +
285B ILE* 3.3 11.1 - - - +
286B THR* 1.3 92.8 - - - +
288B ALA* 1.3 66.7 + - - +
306B PHE* 3.4 30.4 - - + -
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Residues in contact with ALA 288 (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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33B THR* 5.3 0.2 + - - -
36B VAL* 4.2 4.5 - - + -
58B PHE* 4.0 23.3 - - + -
220B PHE* 3.9 20.4 - - + -
275B PHE* 4.4 4.9 - - + -
276B LEU 3.3 11.2 - - - +
277B LEU* 4.2 17.3 - - + -
287B ASP* 1.3 79.7 - - - +
289B VAL* 1.3 67.3 + - - +
290B ASP 4.3 0.2 - - - -
306B PHE* 3.6 4.6 - - - -
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Residues in contact with VAL 289 (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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58B PHE* 4.7 0.4 - - - -
275B PHE* 3.2 13.4 - - - +
276B LEU* 3.1 38.8 + - + -
288B ALA* 1.3 73.3 - - - +
290B ASP* 1.3 61.9 + - - +
291B CYS* 3.4 1.4 + - - -
297B SER* 3.8 26.9 - - - +
300B LYS* 3.8 32.3 - - + +
301B CYS* 3.7 19.3 - - - -
306B PHE* 3.5 32.5 - - + -
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Residues in contact with ASP 290 (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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57B PRO* 3.7 4.9 - - - +
58B PHE* 2.9 51.8 + - + +
273B ARG* 3.2 20.4 + - - +
275B PHE* 3.3 22.7 - - + -
289B VAL* 1.3 71.8 - - - +
291B CYS* 1.3 61.9 + - - +
292B ALA 2.8 15.5 + - - -
293B LEU* 3.2 23.5 + - + +
297B SER* 3.1 22.3 + - - +
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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
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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