Contacts of the helix formed by residues 377 - 388 (chain B) in PDB entry 2VIG
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 PRO 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B CYS* 4.0 20.4 - - + -
375B GLU 4.8 0.4 - - - +
376B MET* 1.3 93.7 - - + +
378B ALA* 1.3 63.0 + - - +
379B GLU 3.4 0.9 - - - -
380B ARG* 3.3 33.3 + - + +
381B HIS* 3.1 40.6 + - + +
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Residues in contact with ALA 378 (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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289B CYS* 4.4 6.9 - - - -
360B SER* 4.7 1.9 - - - +
363B ALA* 4.4 6.7 - - + -
364B ILE* 3.9 28.8 - - + +
367B LEU* 3.8 27.1 - - + -
371B GLY* 4.3 4.3 - - - +
376B MET* 3.3 2.4 - - + -
377B PRO* 1.3 79.5 - - - +
379B GLU* 1.3 63.1 + - - +
381B HIS* 3.1 23.2 + - - +
382B TYR* 3.1 13.7 + - - +
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Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 3.3 35.7 - - + +
234A ARG* 5.5 1.4 + - - -
61B ASP* 4.7 0.3 - - - +
364B ILE* 4.0 8.1 - - - -
371B GLY 3.4 18.5 + - - +
372B TYR 4.6 2.5 - - - +
373B VAL 3.7 25.8 - - - +
374B THR* 3.6 26.5 - - - +
376B MET 4.3 4.2 + - - +
378B ALA* 1.3 78.5 - - - +
380B ARG* 1.3 66.5 + - - +
382B TYR* 3.5 2.6 + - - +
383B ARG* 2.9 65.9 + - - +
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Residues in contact with ARG 380 (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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54B PHE* 6.3 1.0 - - - -
57B ALA* 3.5 37.0 + - - +
58B ALA* 4.3 10.4 - - - +
61B ASP* 3.6 34.1 - - - +
107B ARG 6.0 0.2 + - - -
108B GLY 4.8 4.0 + - - -
109B CYS* 5.2 5.5 - - - +
110B ALA 5.3 1.4 - - - +
376B MET 5.5 0.2 - - - +
377B PRO* 3.3 35.4 + - + +
378B ALA 3.2 0.4 - - - -
379B GLU* 1.3 83.1 - - - +
381B HIS* 1.3 77.9 + - - +
383B ARG* 3.4 22.3 + - - +
384B ASP* 3.0 45.7 + - - +
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Residues in contact with HIS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 6.4 0.4 - + - -
107B ARG 5.4 1.6 - - - -
282B ILE* 3.6 12.1 - - + +
285B THR* 3.3 36.4 + - + +
286B ALA* 3.8 35.0 - - + -
289B CYS* 4.8 3.9 - - + +
360B SER* 3.8 5.8 - - - -
377B PRO* 3.1 43.3 + - + +
378B ALA* 3.1 11.7 + - + +
380B ARG* 1.3 102.1 + - - +
382B TYR* 1.3 56.9 + - - +
384B ASP* 4.5 4.4 + - - +
385B ALA* 2.9 34.1 + - - +
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Residues in contact with TYR 382 (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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231A LEU* 4.1 13.2 - - + -
357A THR* 3.9 7.4 + - - +
382A TYR* 3.2 56.3 + + - -
383A ARG* 5.9 0.7 - - + -
386A ARG* 3.7 26.0 - - + +
357B THR* 4.2 5.3 + - + -
360B SER* 3.3 23.0 - - - +
361B HIS* 3.4 47.4 - + + -
364B ILE* 3.5 28.0 - - + -
378B ALA 3.1 5.3 + - - +
379B GLU 3.6 5.6 - - - +
380B ARG 3.2 0.2 - - - -
381B HIS* 1.3 77.6 - - - +
383B ARG* 1.3 62.8 + - + +
385B ALA* 3.8 2.6 + - - +
386B ARG* 3.5 20.1 + - - +
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Residues in contact with ARG 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 3.7 21.5 - - + -
234A ARG* 5.6 1.9 - - - +
372A TYR* 2.8 31.5 + - - -
382A TYR* 5.8 1.3 - - + -
383A ARG* 4.4 2.9 - - + +
61B ASP* 2.9 41.2 + - - -
231B LEU* 3.0 56.1 + - + +
232B GLY* 4.1 2.6 - - - -
234B ARG* 3.1 24.6 - - - +
374B THR* 5.7 0.2 - - - +
379B GLU* 2.9 45.6 + - - +
380B ARG* 3.4 16.7 - - - +
381B HIS 3.3 0.2 - - - -
382B TYR* 1.3 79.5 - - + +
384B ASP* 1.3 56.8 + - - +
386B ARG* 3.6 7.6 + - - +
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Residues in contact with ASP 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A TYR* 3.9 4.0 - - - -
61B ASP* 4.6 3.6 - - - +
110B ALA* 3.5 33.6 + - + +
111B SER* 5.9 0.2 - - - -
232B GLY* 3.6 4.0 - - - -
233B ILE* 2.8 27.6 + - + +
282B ILE* 3.9 12.8 - - + +
380B ARG* 3.0 44.8 + - - +
381B HIS* 3.9 6.8 + - - +
383B ARG* 1.3 72.3 - - - +
385B ALA* 1.3 63.4 - - - +
386B ARG 3.1 2.2 + - - -
387B ILE* 3.2 25.1 - - - +
388B THR* 4.1 0.2 - - - +
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE* 3.9 14.5 - - + +
356B ALA* 3.5 37.9 - - + +
357B THR* 3.9 9.5 + - - +
360B SER* 3.7 7.2 - - - +
381B HIS 2.9 18.7 + - - +
382B TYR 3.8 2.5 - - - +
384B ASP* 1.3 75.7 - - - +
386B ARG* 1.3 62.7 + - - +
388B THR* 2.7 28.3 + - - -
389B GLU* 4.0 1.2 + - - +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS* 2.9 45.1 + - - -
364A ILE* 3.5 21.4 - - + +
365A GLN* 2.9 42.4 + - - +
372A TYR* 4.0 7.2 - - + -
382A TYR* 3.6 31.0 - - + +
231B LEU* 4.1 13.9 - - + -
357B THR* 3.9 5.2 - - - -
382B TYR 3.5 10.4 + - - +
383B ARG 3.7 12.3 - - - +
384B ASP 3.1 1.4 - - - -
385B ALA* 1.3 78.7 - - - +
387B ILE* 1.3 62.9 + - - +
388B THR 3.4 0.5 + - - -
389B GLU* 3.5 23.9 + - - +
390B ILE* 3.7 10.7 - - - +
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Residues in contact with ILE 387 (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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372A TYR* 3.4 34.0 - - + +
233B ILE* 3.9 19.5 - - + -
278B GLN* 5.0 0.2 - - - +
384B ASP 3.2 17.3 + - - +
386B ARG* 1.3 77.5 - - - +
388B THR* 1.3 63.5 + - + +
390B ILE* 2.8 30.7 + - + -
391B TYR* 3.1 55.2 + - + +
501B FAD 3.5 40.2 - - + -
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Residues in contact with THR 388 (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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275B ILE* 4.1 9.2 - - + -
278B GLN* 3.6 24.5 - - - +
279B ALA* 4.0 15.6 - - + +
282B ILE* 4.1 14.8 - - + -
349B LYS* 2.6 34.9 + - - -
353B SER* 3.3 29.3 + - - -
356B ALA* 4.3 1.7 - - - +
384B ASP 4.1 5.2 - - - +
385B ALA 2.7 20.8 + - - +
387B ILE* 1.3 84.2 - - + +
389B GLU* 1.3 50.2 + - - +
390B ILE 3.2 1.1 - - - -
391B TYR* 3.9 8.1 - - + -
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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