Contacts of the helix formed by residues 322 - 330 (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 ARG 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ARG 3.7 14.1 - - - +
290B LYS* 3.1 31.4 - - - +
318B GLU* 2.8 44.8 + - + +
319B GLY 3.5 0.2 + - - -
320B VAL 3.3 0.2 - - - -
321B LYS* 1.3 79.3 - - + +
323B PHE* 1.3 64.4 + - - +
324B ASP* 3.3 2.7 - - - -
325B GLU* 2.9 60.4 + - - +
326B ILE* 3.1 16.0 + - + +
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Residues in contact with PHE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 4.3 9.4 - - + -
319B GLY 3.2 9.4 + - - +
320B VAL* 3.3 17.7 - - - +
321B LYS 3.3 2.4 - - - -
322B ARG* 1.3 77.9 - - - +
324B ASP* 1.3 69.6 + - - +
326B ILE* 3.0 6.4 + - - +
327B LEU* 2.8 48.2 + - + -
333B ILE* 3.7 21.8 - - + -
355B MET* 4.6 3.8 - - + -
356B MET* 3.4 46.2 - - + -
359B ARG* 3.6 44.0 - - + +
360B CYS* 4.0 15.9 - - - -
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Residues in contact with ASP 324 (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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321B LYS 5.1 0.4 + - - -
322B ARG 3.3 1.6 + - - -
323B PHE* 1.3 83.7 - - - +
325B GLU* 1.3 62.6 + - - +
327B LEU* 3.3 5.2 + - - +
328B GLU* 3.2 24.1 + - - +
359B ARG* 3.1 42.2 + - - +
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Residues in contact with GLU 325 (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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290B LYS* 3.5 0.9 - - - +
291B ALA* 2.9 40.0 + - + +
292B SER 4.9 0.2 + - - -
322B ARG* 2.9 65.8 + - - +
324B ASP* 1.3 80.0 - - - +
326B ILE* 1.3 69.1 + - + +
328B GLU* 3.5 17.8 + - - +
329B VAL* 3.7 14.0 + - - +
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Residues in contact with ILE 326 (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* 3.6 30.3 - - + +
289B ARG 3.7 27.4 - - - +
290B LYS* 3.9 22.4 - - - +
291B ALA* 4.8 4.5 - - - +
294B VAL* 4.9 1.8 - - + -
312B SER* 3.7 9.4 - - - -
314B ILE* 4.1 10.5 - - + -
319B GLY 3.7 14.4 - - - +
322B ARG 3.4 21.5 - - - +
323B PHE* 3.0 6.6 + - - +
325B GLU* 1.3 78.0 - - - +
327B LEU* 1.3 59.6 + - - +
329B VAL* 3.2 4.8 + - - +
330B SER* 2.6 39.2 + - - +
333B ILE* 4.2 4.5 - - + -
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Residues in contact with LEU 327 (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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323B PHE* 2.8 50.2 + - + +
324B ASP* 3.8 5.8 - - - +
326B ILE* 1.3 74.9 - - - +
328B GLU* 1.3 52.8 + - - +
329B VAL 2.9 1.9 + - - -
330B SER* 3.1 9.8 + - - +
332B GLY* 4.9 3.1 - - - +
333B ILE* 4.2 17.2 - - + +
359B ARG* 4.4 9.2 - - + +
360B CYS* 4.3 6.1 - - - -
363B ALA* 3.5 26.2 - - + -
365B LYS* 2.8 61.2 + - + -
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Residues in contact with GLU 328 (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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324B ASP 3.2 13.2 + - - +
325B GLU* 3.7 10.7 - - - +
326B ILE 3.4 0.2 - - - -
327B LEU* 1.3 79.9 - - - +
329B VAL* 1.3 60.9 - - + +
365B LYS* 3.4 14.8 + - - +
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Residues in contact with VAL 329 (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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291B ALA* 4.0 19.7 - - + +
294B VAL* 3.1 39.7 - - + +
295B ALA* 5.0 1.3 - - + +
298B ARG* 2.9 35.0 + - - +
325B GLU 3.9 11.9 - - - +
326B ILE 3.2 2.6 + - - +
327B LEU 3.0 0.6 - - - -
328B GLU* 1.3 82.3 - - + +
330B SER* 1.3 60.9 + - - +
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Residues in contact with SER 330 (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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294B VAL* 4.0 10.0 - - - +
298B ARG* 4.8 1.3 - - - +
310B ILE* 4.1 4.7 - - - -
312B SER* 2.5 30.2 + - - -
326B ILE* 2.6 25.3 + - - +
327B LEU* 3.1 7.4 + - - +
329B VAL* 1.3 81.9 - - - +
331B ASP* 1.3 64.0 + - - +
332B GLY 3.3 15.5 - - - -
365B LYS* 2.7 31.4 + - - +
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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