Contacts of the strand formed by residues 284 - 290 (chain B) in PDB entry 2VR1
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 PHE 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B PRO* 3.7 22.4 - - + +
210B VAL* 3.7 28.5 - - + -
212B ILE* 4.4 3.4 - - + -
227B GLU* 6.0 0.7 - - + -
248B ILE* 4.0 18.4 - - + -
252B LEU* 3.7 28.3 - - + -
255B TYR* 5.1 6.0 - + + -
256B ILE* 3.8 51.1 - - + -
277B PHE* 3.7 27.4 - + + -
278B LEU 3.6 1.8 - - - -
279B PHE* 3.7 29.4 - + + -
283B GLU* 1.3 74.7 - - - +
285B TYR* 1.3 71.6 + - - +
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Residues in contact with TYR 285 (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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129B PRO* 3.8 4.0 - - + -
130B CYS 3.6 16.8 - - - -
131B VAL* 4.2 11.7 - - + -
132B PRO* 4.0 23.3 - - + -
202B LYS* 4.6 14.7 + - + +
204B LEU* 3.6 49.1 - - + +
277B PHE* 3.2 4.9 - - - -
278B LEU* 2.8 51.9 + - + +
280B GLU* 4.2 13.7 + - + +
283B GLU* 3.5 44.3 + - + +
284B PHE* 1.3 81.2 - - - +
286B PHE* 1.3 63.7 + - - +
287B ILE* 4.2 0.3 - - - +
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Residues in contact with PHE 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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113B MET* 4.0 9.9 - - + -
119B ALA* 4.6 10.3 - - + -
120B ILE* 3.8 27.2 - - + +
123B MET* 3.7 38.8 - - + -
128B VAL* 4.1 16.4 - - + -
129B PRO 2.9 21.1 + - - +
130B CYS* 3.8 10.8 - - - +
131B VAL* 4.3 15.2 + - - +
275B PHE* 4.1 13.2 - + - -
276B GLU 4.0 6.1 - - - -
277B PHE* 3.6 12.5 - + + -
285B TYR* 1.3 72.6 - - - +
287B ILE* 1.3 74.2 + - - +
288B GLU* 3.3 32.8 - - - -
289B MET* 3.5 4.7 - - + -
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Residues in contact with ILE 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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116B LYS* 5.6 6.1 - - - +
120B ILE* 4.7 5.5 - - - +
209B HIS* 4.1 19.1 - - + +
276B GLU* 2.9 19.9 + - + +
277B PHE 3.7 16.4 - - - +
278B LEU* 3.5 45.1 - - + +
286B PHE* 1.3 85.8 - - - +
288B GLU* 1.3 75.1 + - + +
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Residues in contact with GLU 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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87B GLU* 5.7 0.7 - - - +
113B MET 5.3 6.7 - - - +
119B ALA* 6.1 1.1 - - + -
276B GLU* 2.9 53.0 + - - +
286B PHE* 3.3 14.5 - - - -
287B ILE* 1.3 93.3 - - + +
289B MET* 1.3 63.1 + - - +
290B ASN* 4.2 14.4 - - - +
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Residues in contact with MET 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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87B GLU* 3.7 6.4 - - - +
113B MET* 3.7 50.4 + - + +
214B VAL* 4.6 1.1 - - + -
264B CYS* 4.8 0.4 - - - -
267B ILE* 4.2 6.7 - - + -
269B TYR* 3.3 49.8 - - + +
273B GLY* 4.4 8.3 - - - -
274B THR 3.2 14.8 - - - +
275B PHE* 3.6 46.9 - - + +
286B PHE* 3.5 4.0 - - + -
288B GLU* 1.3 78.2 - - - +
290B ASN* 1.3 65.9 + - - +
291B THR* 3.6 9.5 + - - +
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Residues in contact with ASN 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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87B GLU* 3.5 7.2 - - - +
273B GLY* 3.3 1.9 - - - -
274B THR* 2.8 31.5 + - - +
276B GLU* 3.0 30.1 + - - +
288B GLU* 4.2 17.1 - - - +
289B MET* 1.3 72.7 - - - +
291B THR* 1.3 58.7 + - - +
292B ARG* 3.0 41.3 + - + +
294B GLN* 2.6 41.2 - - + +
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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