Contacts of the helix formed by residues 499 - 506 (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 SER 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476B THR* 3.6 23.5 + - - -
497B THR* 3.3 9.0 + - - +
498B ARG* 1.3 74.3 - - - +
500B ALA* 1.3 65.7 + - - +
501B GLN* 3.7 6.8 + - - +
502B ALA* 3.0 23.5 + - - +
503B ALA 2.9 17.7 + - - -
516B LEU* 4.0 1.1 - - - -
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Residues in contact with ALA 500 (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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498B ARG 3.2 7.8 + - - +
499B SER* 1.3 70.8 - - - +
501B GLN* 1.3 62.5 + - - +
503B ALA* 3.2 5.7 - - - +
504B ARG* 3.2 41.9 + - - +
516B LEU* 3.8 29.4 - - + -
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Residues in contact with GLN 501 (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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279B GLY* 4.5 4.9 + - - -
280B VAL 4.1 17.0 + - - -
281B ASP* 4.0 10.4 + - - +
307B GLY* 4.0 21.0 - - - -
308B ILE* 4.5 4.2 + - - +
499B SER* 3.1 5.7 + - - +
500B ALA* 1.3 76.0 - - - +
502B ALA* 1.3 67.5 + - - +
504B ARG* 2.8 40.7 + - - +
505B GLN* 2.9 36.1 + - + +
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Residues in contact with ALA 502 (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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476B THR 3.7 18.2 - - - +
477B THR* 4.0 21.1 - - - +
478B GLY* 4.4 2.7 - - - +
497B THR* 4.4 6.7 - - + +
499B SER* 3.0 23.0 + - - +
501B GLN* 1.3 75.8 - - - +
503B ALA* 1.3 63.8 + - - +
505B GLN* 3.2 12.9 + - - +
506B VAL* 3.0 29.6 + - - +
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Residues in contact with ALA 503 (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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150B PRO* 4.5 10.3 - - + +
497B THR* 3.7 17.2 - - + +
499B SER 2.9 13.5 + - - +
500B ALA* 3.2 15.3 - - - +
501B GLN 3.1 0.2 - - - -
502B ALA* 1.3 76.0 - - - +
504B ARG* 1.3 60.6 + - - +
506B VAL* 3.9 4.5 + - - -
507B HIS* 4.2 2.4 + - - -
514B PRO* 3.2 41.2 - - + +
516B LEU* 4.6 16.2 - - + -
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Residues in contact with ARG 504 (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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135B ARG* 6.0 1.9 - - - +
148B TYR* 6.0 0.4 + - - -
150B PRO* 4.4 11.9 - - + -
151B VAL 3.5 27.1 - - - +
152B ALA* 3.7 14.2 - - - +
153B ILE* 5.9 1.1 - - - -
279B GLY 4.8 4.4 + - - -
281B ASP* 2.3 47.2 + - - +
282B ILE* 5.1 0.3 - - - +
500B ALA* 3.4 30.6 + - - +
501B GLN* 2.8 37.0 + - - +
503B ALA* 1.3 75.0 - - - +
505B GLN* 1.3 62.2 + - - +
506B VAL 3.1 2.9 + - - -
507B HIS* 3.3 28.7 + - - +
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Residues in contact with GLN 505 (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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281B ASP* 3.1 35.1 + - + +
282B ILE* 4.6 9.1 - - + +
307B GLY* 2.6 33.4 + - - +
308B ILE* 3.5 0.8 - - - +
309B LYS* 3.3 35.3 - - + +
477B THR 5.1 2.3 - - - +
501B GLN* 2.9 37.2 + - + +
502B ALA* 3.2 11.0 + - - +
504B ARG* 1.3 75.9 - - - +
506B VAL* 1.3 63.7 + - + +
508B LEU* 3.1 25.9 + - - +
509B CYS* 5.3 0.9 - - - -
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Residues in contact with VAL 506 (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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475B THR* 5.5 0.4 - - + -
477B THR 5.3 0.2 - - - +
478B GLY* 3.8 31.6 - - - +
481B ALA* 4.5 5.4 - - + -
482B GLN* 5.6 0.7 - - + +
495B ALA* 4.7 4.3 - - + -
502B ALA 3.0 19.4 + - - +
503B ALA* 4.1 5.2 - - - +
504B ARG 3.1 0.6 - - - -
505B GLN* 1.3 77.6 - - - +
507B HIS* 1.3 57.2 + - - +
508B LEU 3.0 0.4 - - - -
509B CYS* 3.0 35.0 + - - +
512B VAL* 2.7 44.4 - - + +
514B PRO* 4.3 14.6 - - + -
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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