Contacts of the helix formed by residues 377 - 389 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A CYS* 4.0 14.4 - - + -
375A GLU 4.6 1.1 - - - +
376A MET* 1.3 101.0 - - + +
378A ALA* 1.3 64.1 + - - +
379A GLU 3.4 1.3 - - - -
380A ARG* 3.2 31.3 + - + +
381A HIS* 3.1 41.0 + - + +
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A CYS* 4.5 6.3 - - - -
360A SER 4.7 2.1 - - - +
363A ALA* 4.4 7.9 - - + -
364A ILE* 3.9 28.6 - - + +
367A LEU* 3.9 26.0 - - + -
371A GLY* 4.4 4.5 - - - +
376A MET* 3.4 2.7 - - + -
377A PRO* 1.3 77.5 - - - +
379A GLU* 1.3 65.9 + - - +
381A HIS* 3.2 14.5 + - - +
382A TYR* 3.1 22.9 + - - +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 4.7 0.9 - - - +
364A ILE* 4.0 10.1 - - - -
371A GLY 3.6 15.2 + - - +
372A TYR 4.6 2.0 - - - +
373A VAL 3.7 27.1 - - - +
374A THR* 3.7 25.0 - - + +
376A MET 4.2 4.4 + - - +
378A ALA* 1.3 77.4 - - - +
380A ARG* 1.3 69.7 + - - +
382A TYR* 3.3 3.3 + - - +
383A ARG* 3.0 64.1 + - - +
231B LEU* 3.2 34.8 - - + +
234B ARG* 5.5 1.4 + - - -
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Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PHE* 6.3 1.0 - - - -
57A ALA* 3.4 35.1 + - - +
58A ALA* 4.2 12.8 - - - +
61A ASP* 3.6 31.2 - - - +
107A ARG 5.2 1.4 + - - -
108A GLY 4.0 10.1 + - - -
109A CYS* 5.1 3.0 - - - +
110A ALA 5.5 1.2 - - - +
377A PRO* 3.2 34.4 + - + +
378A ALA 3.2 0.6 - - - -
379A GLU* 1.3 85.7 + - - +
381A HIS* 1.3 80.1 + - - +
383A ARG* 3.3 26.2 + - - +
384A ASP* 2.9 51.9 + - - +
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Residues in contact with HIS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 6.4 0.2 - + - -
107A ARG 5.1 0.4 - - - -
282A ILE* 3.6 13.1 - - + +
285A THR* 3.1 41.5 + - + +
286A ALA* 3.8 32.5 - - + -
289A CYS* 4.8 2.6 - - + +
360A SER* 3.8 5.4 - - - -
377A PRO* 3.1 39.8 + - + +
378A ALA* 3.2 11.8 + - - +
380A ARG* 1.3 104.1 + - - +
382A TYR* 1.3 56.2 + - - +
384A ASP* 4.5 4.6 + - - -
385A ALA* 2.9 32.2 + - - +
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Residues in contact with TYR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A THR* 4.3 5.2 + - + -
360A SER* 3.3 23.3 - - - +
361A HIS* 3.6 36.3 - + + -
364A ILE* 3.6 25.6 - - + -
378A ALA 3.1 5.5 + - - +
379A GLU 3.5 7.4 - - - +
380A ARG 3.2 0.2 - - - -
381A HIS* 1.3 76.7 - - - +
383A ARG* 1.3 62.6 + - + +
385A ALA* 3.9 1.7 - - - +
386A ARG* 3.5 20.4 + - - +
231B LEU* 4.1 13.5 - - + -
357B THR* 3.8 7.4 + - - +
382B TYR* 3.2 58.3 + + - -
383B ARG* 5.8 1.1 - - + -
386B ARG* 3.6 36.5 - - + -
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Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 2.8 43.4 + - - -
231A LEU* 2.9 69.4 + - + +
232A GLY* 4.0 4.3 - - - -
234A ARG* 3.3 19.6 - - - +
374A THR* 5.6 0.8 - - - +
379A GLU* 3.0 44.6 + - - +
380A ARG* 3.4 14.8 - - - +
382A TYR* 1.3 77.1 - - + +
384A ASP* 1.3 57.6 + - - +
386A ARG* 3.6 4.2 + - - +
231B LEU* 3.7 18.8 - - + -
234B ARG* 5.5 2.3 - - - +
372B TYR* 2.7 34.3 + - - -
382B TYR* 5.9 0.7 - - + -
383B ARG* 4.4 3.6 - - + +
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Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 4.7 3.5 - - - +
110A ALA* 3.3 34.4 + - + +
232A GLY* 3.6 3.8 - - - -
233A ILE* 2.8 31.8 + - + +
282A ILE* 4.0 13.2 - - + +
380A ARG* 2.9 48.5 + - - +
381A HIS* 4.0 7.7 + - - +
383A ARG* 1.3 70.5 - - - +
385A ALA* 1.3 64.2 + - - +
387A ILE* 3.0 25.1 - - - +
388A THR* 4.1 0.2 - - - +
372B TYR* 3.9 3.8 - - - -
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ILE* 3.9 12.5 - - + +
356A ALA* 3.5 39.0 - - + +
357A THR* 3.7 9.2 + - - +
360A SER* 3.8 7.0 - - - +
381A HIS 2.9 19.0 + - - +
382A TYR 3.9 2.0 - - - +
383A ARG 3.4 0.2 - - - -
384A ASP* 1.3 75.8 - - - +
386A ARG* 1.3 63.1 + - - +
388A THR* 2.5 30.1 + - - -
389A GLU 4.0 0.5 + - - -
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 4.1 14.6 - - + -
357A THR* 3.8 5.6 + - - -
382A TYR 3.5 11.4 + - - +
383A ARG 3.6 12.3 - - - +
384A ASP 3.2 0.4 - - - -
385A ALA* 1.3 79.7 - - - +
387A ILE* 1.3 62.3 + - - +
388A THR 3.3 0.5 + - - -
389A GLU* 3.4 24.2 + - - +
390A ILE* 3.7 10.3 - - - +
361B HIS* 2.9 43.9 + - - -
364B ILE* 3.6 19.6 - - + +
365B GLN* 2.7 42.4 + - - +
372B TYR* 3.9 9.6 - - + -
382B TYR* 3.7 28.3 - - + -
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Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ILE* 4.0 20.2 - - + -
384A ASP 3.0 24.1 + - - +
386A ARG* 1.3 78.5 - - - +
388A THR* 1.3 63.3 + - + +
390A ILE* 2.8 30.4 + - + -
391A TYR* 3.1 57.0 + - + +
501A FAD 3.6 35.4 - - + -
372B TYR* 3.4 33.6 - - + +
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Residues in contact with THR 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ILE* 4.4 4.9 - - + -
278A GLN* 3.7 23.6 - - - +
279A ALA* 4.0 20.7 - - + +
282A ILE* 4.1 15.9 - - + -
349A LYS* 2.6 36.1 + - - -
353A SER* 3.2 30.1 + - - -
356A ALA* 4.4 0.5 - - - +
385A ALA* 2.5 23.7 + - - +
387A ILE* 1.3 85.9 - - + +
389A GLU* 1.3 50.9 + - - +
390A ILE 3.2 0.9 - - - -
391A TYR* 4.1 9.1 - - + +
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LYS* 3.9 3.8 - - - +
353A SER* 3.7 26.0 - - - +
354A GLU* 3.6 22.9 - - - +
357A THR* 2.8 28.7 + - - +
386A ARG* 3.4 20.8 + - - +
387A ILE 3.2 0.2 + - - -
388A THR* 1.3 77.3 - - - +
390A ILE* 1.3 58.2 + - - +
395A SER* 3.2 26.4 + - - +
361B HIS* 2.7 39.0 + - - -
365B GLN* 3.0 25.5 + - - +
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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