Contacts of the strand formed by residues 309 - 314 (chain B) in PDB entry 2VGB
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 LYS 309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B ASP 3.2 9.3 + - - +
282B ILE* 3.3 5.9 - - + +
283B VAL 2.9 25.6 + - - -
307B GLY 3.9 6.7 - - - +
308B ILE* 1.3 74.4 - - - +
310B ILE* 1.3 60.3 + - - +
311B ILE* 4.1 0.7 - - + -
331B ASP* 3.3 27.6 + - + +
477B THR 5.0 11.5 + - - -
482B GLN* 5.0 9.1 + - - -
505B GLN* 3.3 41.9 - - + +
508B LEU* 3.9 25.1 - - + -
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 3.8 8.1 - - + +
285B ALA* 4.8 6.5 - - + -
294B VAL* 4.2 22.4 - - + +
297B VAL* 3.2 37.5 - - + -
298B ARG* 4.2 31.4 - - - +
301B LEU* 3.9 17.7 - - + -
308B ILE 4.0 9.4 - - - +
309B LYS* 1.3 76.3 - - - +
311B ILE* 1.3 69.6 + - - +
312B SER* 4.0 5.7 + - - +
330B SER* 4.1 1.3 - - - -
331B ASP* 2.7 41.6 + - - +
332B GLY 3.5 1.0 + - - -
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE* 3.6 25.4 - - + -
283B VAL 2.8 8.5 + - - -
284B PHE* 3.4 28.1 - - + -
285B ALA 2.8 26.4 + - - -
310B ILE* 1.3 78.1 - - - +
312B SER* 1.3 61.2 + - - +
313B LYS 3.4 0.2 + - - -
331B ASP* 4.4 4.0 - - + -
332B GLY* 3.6 22.9 - - - +
333B ILE 3.5 30.7 - - - +
334B MET* 3.7 10.3 - - + +
366B PRO* 4.8 3.6 - - + -
368B VAL* 4.5 4.9 - - + -
508B LEU* 3.7 31.2 - - + -
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ALA* 4.0 1.7 - - - +
288B VAL* 3.7 34.7 - - - +
294B VAL* 4.3 7.3 - - - +
310B ILE* 4.0 3.0 - - - +
311B ILE* 1.3 71.6 - - - +
313B LYS* 1.3 62.1 + - - +
314B ILE* 3.7 1.5 + - - -
326B ILE* 3.7 10.6 - - - +
330B SER* 2.5 30.3 + - - -
332B GLY 3.1 6.7 + - - -
333B ILE* 3.4 12.7 - - - +
334B MET 2.8 22.7 + - - -
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Residues in contact with LYS 313 (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 ARG* 4.0 0.2 - - - +
156B ASP* 2.6 28.4 + - - +
284B PHE* 3.8 7.2 - - + -
285B ALA 2.9 31.0 + - - +
286B SER* 2.6 30.0 + - - +
287B PHE 4.1 1.0 + - - -
288B VAL* 3.3 28.1 + - - +
311B ILE 4.2 0.4 - - - +
312B SER* 1.3 72.4 - - - +
314B ILE* 1.3 60.8 + - - +
315B GLU* 3.7 17.1 + - + -
334B MET* 3.3 41.5 - - + -
336B ALA* 4.2 7.0 - - + -
581B PGA 3.3 27.8 + - - -
586B K 3.5 0.2 - - - -
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Residues in contact with ILE 314 (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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288B VAL 4.0 17.0 - - - +
312B SER* 4.7 1.1 - - - +
313B LYS* 1.3 72.9 - - - +
315B GLU* 1.3 61.0 + - - +
316B ASN 4.5 0.2 - - - +
319B GLY 3.9 15.5 - - - +
320B VAL* 3.7 33.0 - - + +
323B PHE* 4.3 4.3 - - + -
326B ILE* 4.1 24.9 - - + -
333B ILE* 4.0 22.4 - - + -
334B MET 2.9 11.2 + - - +
336B ALA* 3.2 22.9 + - - +
340B LEU* 4.1 7.5 - - + +
356B MET* 3.6 35.9 - - + -
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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