Contacts of the helix formed by residues 377 - 389 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289G CYS* 4.1 18.8 - - + -
375G GLU 4.8 0.4 - - - +
376G MET* 1.4 93.4 - - + +
378G ALA* 1.3 63.8 + - - +
379G GLU 3.4 1.3 - - - -
380G ARG* 3.2 34.9 + - + +
381G HIS* 3.1 42.5 + - + +
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Residues in contact with ALA 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289G CYS* 4.3 8.1 - - - -
360G SER 4.8 2.1 - - - +
363G ALA* 4.4 6.5 - - + -
364G ILE* 4.0 27.8 - - + +
367G LEU* 3.8 26.7 - - + -
371G GLY* 4.2 4.9 - - - +
376G MET* 3.3 2.2 - - + -
377G PRO* 1.3 79.4 - - - +
379G GLU* 1.3 63.4 + - - +
381G HIS* 3.1 14.5 + - - +
382G TYR* 3.1 21.7 + - - +
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Residues in contact with GLU 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASP* 4.7 0.5 - - - +
364G ILE* 4.1 9.0 - - - -
371G GLY 3.4 19.0 + - - +
372G TYR 4.5 2.7 - - - +
373G VAL 3.8 27.4 - - - +
374G THR* 3.8 24.9 - - + +
376G MET 4.3 4.5 + - - +
378G ALA* 1.3 75.7 - - - +
380G ARG* 1.3 66.6 + - - +
382G TYR* 3.5 4.0 - - - +
383G ARG* 2.8 68.3 + - - +
231H LEU* 3.6 33.7 - - + +
234H ARG* 5.6 0.9 + - - -
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Residues in contact with ARG 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ALA* 3.6 36.2 + - - +
58G ALA* 4.4 11.3 - - - +
61G ASP* 3.5 33.0 - - - +
108G GLY 4.7 4.9 + - - -
109G CYS* 5.4 3.6 - - - +
110G ALA 5.5 2.2 - - - +
377G PRO* 3.2 33.5 + - + +
378G ALA 3.2 0.6 - - - -
379G GLU* 1.3 82.4 + - - +
381G HIS* 1.3 85.5 + - - +
383G ARG* 3.2 23.9 + - - +
384G ASP* 2.9 43.5 + - - +
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Residues in contact with HIS 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G ARG 5.1 2.7 - - - -
282G ILE* 3.6 13.0 - - + +
285G THR* 3.3 38.5 + - + +
286G ALA* 3.9 34.1 - - + -
289G CYS* 4.8 2.7 - - + -
360G SER* 3.9 4.5 - - - -
377G PRO* 3.1 43.8 + - + +
378G ALA* 3.1 10.1 + - - +
380G ARG* 1.3 98.7 + - - +
382G TYR* 1.3 53.6 + - - +
384G ASP* 3.3 5.0 + - - -
385G ALA* 2.7 37.6 + - - +
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Residues in contact with TYR 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G THR* 4.2 5.6 + - + -
360G SER* 3.4 23.8 - - - +
361G HIS* 3.5 44.0 - - + -
364G ILE* 3.7 18.6 - - + -
378G ALA 3.1 11.5 + - - +
379G GLU 3.5 9.6 - - - +
381G HIS* 1.3 76.3 - - - +
383G ARG* 1.3 62.6 + - + +
385G ALA* 3.7 1.9 + - - +
386G ARG* 3.4 21.1 + - - +
231H LEU* 4.2 13.5 - - + -
357H THR* 4.0 7.1 + - - +
382H TYR* 3.2 57.0 + + - -
383H ARG* 5.8 0.7 - - + -
386H ARG* 3.6 31.4 - - + +
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Residues in contact with ARG 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASP* 2.9 40.4 + - - -
231G LEU* 3.0 57.3 + - + +
232G GLY* 4.2 3.2 - - - -
234G ARG* 3.2 22.2 - - - +
374G THR* 5.7 0.2 - - - +
379G GLU* 2.8 46.7 + - - +
380G ARG* 3.2 18.4 + - - +
382G TYR* 1.3 81.3 - - + +
384G ASP* 1.3 57.0 + - - +
386G ARG* 3.4 13.3 + - - +
231H LEU* 3.7 21.1 - - + -
234H ARG* 5.4 2.5 - - - +
372H TYR* 2.8 25.9 + - - -
382H TYR* 5.8 0.9 - - + -
383H ARG* 4.3 2.7 - - + +
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Residues in contact with ASP 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASP* 4.8 3.3 - - - +
110G ALA* 3.4 31.8 + - + +
111G SER* 5.8 0.2 - - - -
232G GLY* 3.6 4.3 - - - -
233G ILE* 2.8 32.8 + - + +
282G ILE* 3.7 12.3 - - + +
380G ARG* 2.9 43.4 + - - +
381G HIS* 3.6 7.1 + - - +
383G ARG* 1.3 73.3 - - - +
385G ALA* 1.3 65.0 + - - +
386G ARG 3.1 2.3 + - - -
387G ILE* 3.2 23.9 - - - +
388G THR* 4.2 0.2 - - - +
372H TYR* 4.0 3.6 - - - -
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Residues in contact with ALA 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282G ILE* 3.9 14.3 - - + +
356G ALA* 3.4 38.4 - - + +
357G THR* 3.6 11.1 + - - +
360G SER* 3.5 7.9 - - - +
381G HIS 2.7 21.5 + - - +
382G TYR 3.9 2.5 - - - +
383G ARG 3.5 0.2 - - - -
384G ASP* 1.3 73.1 - - - +
386G ARG* 1.3 62.2 + - - +
388G THR* 2.8 26.2 + - - -
389G GLU 4.1 1.4 + - - -
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Residues in contact with ARG 386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G LEU* 3.9 22.4 - - + -
357G THR* 3.9 4.9 - - - +
382G TYR 3.4 10.9 + - - +
383G ARG 3.6 12.8 - - - +
384G ASP 3.1 2.0 - - - -
385G ALA* 1.3 78.4 - - - +
387G ILE* 1.3 61.6 + - - +
388G THR 3.4 0.3 + - - -
389G GLU* 3.5 19.5 + - - +
390G ILE* 3.6 12.0 - - - +
361H HIS* 2.9 55.0 + - - -
364H ILE* 3.7 18.2 - - + +
365H GLN* 2.8 38.4 + - - +
372H TYR* 4.0 5.6 - - + -
382H TYR* 3.6 24.9 - - + -
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Residues in contact with ILE 387 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G ILE* 4.0 20.6 - - + -
384G ASP 3.2 15.7 + - - +
386G ARG* 1.3 75.9 - - - +
388G THR* 1.3 65.6 + - + +
390G ILE* 2.8 33.8 + - + -
391G TYR* 3.1 55.7 + - + +
501G FAD 3.6 33.4 - - + -
372H TYR* 3.5 39.2 - - + +
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Residues in contact with THR 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275G ILE* 4.3 6.5 - - + -
278G GLN* 3.6 24.2 - - - +
279G ALA* 3.8 22.3 - - + +
282G ILE* 4.1 17.9 - - + -
349G LYS* 2.8 30.0 + - - -
353G SER* 3.2 31.2 + - - -
356G ALA* 4.2 1.7 - - - +
384G ASP 4.2 3.4 - - - +
385G ALA 2.8 20.0 + - - +
387G ILE* 1.3 79.0 - - + +
389G GLU* 1.3 56.4 + - - +
390G ILE 3.3 0.2 - - - -
391G TYR* 4.1 7.9 - - + -
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Residues in contact with GLU 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349G LYS* 3.9 3.6 - - - +
353G SER* 3.8 29.6 - - - +
354G GLU* 3.5 21.9 - - - +
357G THR* 2.8 29.3 + - - +
386G ARG* 3.5 19.7 + - - +
387G ILE 3.1 1.2 + - - -
388G THR* 1.3 77.7 + - - +
390G ILE* 1.3 57.5 + - - +
394G THR* 3.4 0.2 - - - -
395G SER* 3.1 34.9 + - - +
361H HIS* 2.7 39.1 + - - -
365H GLN* 3.1 12.6 + - - +
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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