Contacts of the helix formed by residues 377 - 388 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289D CYS* 4.0 18.8 - - + -
375D GLU 4.7 0.7 - - - +
376D MET* 1.3 96.9 - - + +
378D ALA* 1.3 63.2 + - - +
379D GLU 3.4 1.3 - - - -
380D ARG* 3.2 38.2 + - + +
381D HIS* 3.2 38.0 + - + +
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Residues in contact with ALA 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D CYS* 4.5 5.4 - - - -
360D SER 4.7 2.1 - - - +
363D ALA* 4.5 5.8 - - + -
364D ILE* 3.9 29.3 - - + +
367D LEU* 3.7 27.4 - - + -
371D GLY* 4.3 5.2 - - - +
376D MET* 3.3 2.3 - - + -
377D PRO* 1.3 79.0 - - - +
379D GLU* 1.3 63.8 + - - +
381D HIS* 3.1 15.7 + - - +
382D TYR* 3.1 21.0 + - - +
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Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LEU* 3.6 35.1 - - + +
234C ARG* 5.4 1.7 + - - -
61D ASP* 4.8 0.3 - - - +
364D ILE* 4.1 8.5 - - - -
371D GLY 3.5 16.4 + - - +
372D TYR 4.6 1.6 - - - +
373D VAL 3.6 27.6 - - - +
374D THR* 3.8 25.0 - - - +
376D MET 4.2 5.1 - - - +
378D ALA* 1.3 77.9 - - - +
380D ARG* 1.3 69.3 + - - +
382D TYR* 3.5 3.1 + - - +
383D ARG* 2.9 64.1 + - - +
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Residues in contact with ARG 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 5.7 1.6 + - - -
57D ALA* 3.5 37.3 + - - +
58D ALA* 4.4 12.3 - - - +
61D ASP* 3.7 36.6 - - - +
107D ARG 5.9 0.6 + - - -
108D GLY 4.6 5.3 + - - -
109D CYS* 5.3 4.2 - - - +
110D ALA 5.5 1.4 - - - +
377D PRO* 3.2 35.7 + - + +
379D GLU* 1.3 83.5 + - - +
381D HIS* 1.3 78.6 + - - +
383D ARG* 3.1 18.0 + - - +
384D ASP* 2.8 48.6 + - - +
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Residues in contact with HIS 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D PHE* 6.3 1.1 - + - -
107D ARG 5.4 1.3 - - - -
282D ILE* 3.8 12.8 - - + +
285D THR* 3.5 33.3 + - + +
286D ALA* 3.8 37.5 - - + -
289D CYS* 4.8 3.9 - - + +
360D SER* 3.8 6.3 - - - -
377D PRO* 3.2 42.7 + - + +
378D ALA* 3.1 11.3 + - - +
380D ARG* 1.3 99.6 + - - +
382D TYR* 1.3 53.7 + - - +
384D ASP* 4.4 4.9 + - - -
385D ALA* 2.8 37.9 + - - +
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Residues in contact with TYR 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LEU* 4.2 12.1 - - + -
357C THR* 3.9 7.6 + - - +
382C TYR* 3.2 56.7 + + - -
383C ARG* 5.9 0.9 - - + -
386C ARG* 3.7 30.0 - - + +
357D THR* 4.3 4.6 + - + -
360D SER* 3.3 21.7 - - - +
361D HIS* 3.5 45.3 - + + -
364D ILE* 3.6 25.8 - - + -
378D ALA 3.1 6.5 + - - +
379D GLU 3.6 6.7 - - - +
380D ARG 3.2 0.2 - - - -
381D HIS* 1.3 77.9 - - - +
383D ARG* 1.3 63.0 + - + +
385D ALA* 3.9 2.8 - - - +
386D ARG* 3.4 20.1 + - - +
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Residues in contact with ARG 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LEU* 3.7 21.5 - - + -
234C ARG* 5.4 2.1 - - - +
372C TYR* 2.9 21.0 + - - -
382C TYR* 5.8 1.1 - - + -
383C ARG* 4.3 3.1 - - + +
61D ASP* 2.9 39.4 + - - -
231D LEU* 3.0 59.2 + - + +
232D GLY* 4.1 2.7 - - - -
234D ARG* 3.2 23.4 - - - +
374D THR* 5.6 1.0 - - - +
379D GLU* 2.9 46.6 + - - +
380D ARG* 3.1 18.1 + - - +
382D TYR* 1.3 78.7 - - + +
384D ASP* 1.3 61.6 + - - +
386D ARG* 3.4 13.9 + - - +
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Residues in contact with ASP 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C TYR* 3.9 4.5 - - - -
61D ASP* 4.6 3.6 - - - +
110D ALA* 3.2 35.8 + - + +
111D SER* 5.6 0.4 + - - -
232D GLY* 3.6 4.7 - - - -
233D ILE* 3.0 25.3 + - + +
234D ARG 5.0 0.2 + - - -
282D ILE* 4.0 8.7 - - + +
380D ARG* 2.8 42.1 + - - +
381D HIS* 3.8 7.6 + - - +
383D ARG* 1.3 71.4 - - - +
385D ALA* 1.3 64.6 + - - +
386D ARG 3.1 2.2 + - - -
387D ILE* 3.1 25.6 - - - +
388D THR* 4.0 3.3 - - - +
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Residues in contact with ALA 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ILE* 3.9 14.5 - - + +
353D SER 4.5 0.2 - - - +
356D ALA* 3.4 42.2 - - + +
357D THR* 3.6 10.4 + - - +
360D SER* 3.6 6.3 - - - +
381D HIS 2.8 22.4 + - - +
382D TYR 3.9 2.5 - - - +
384D ASP* 1.3 72.2 - - - +
386D ARG* 1.3 60.6 + - - +
388D THR* 2.8 25.1 + - - -
389D GLU 4.1 1.0 + - - -
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Residues in contact with ARG 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C HIS* 2.7 54.1 + - - -
364C ILE* 3.4 17.9 - - + +
365C GLN* 3.0 39.8 + - - +
372C TYR* 3.9 9.6 - - + -
382C TYR* 3.5 34.9 - - + +
231D LEU* 4.2 11.9 - - + -
357D THR* 4.0 4.9 + - - -
382D TYR 3.4 10.3 + - - +
383D ARG 3.4 12.9 + - - +
384D ASP 3.1 1.4 - - - -
385D ALA* 1.3 79.4 - - - +
387D ILE* 1.3 61.0 + - - +
388D THR 3.4 0.3 + - - -
389D GLU* 3.5 18.5 + - - +
390D ILE* 3.7 11.7 - - - +
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Residues in contact with ILE 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C TYR* 3.5 36.4 - - + +
233D ILE* 3.9 21.8 - - + -
278D GLN* 4.8 0.2 - - - +
384D ASP 3.1 18.9 + - - +
386D ARG* 1.3 79.2 - - - +
388D THR* 1.3 63.2 + - + +
390D ILE* 2.9 30.0 + - + -
391D TYR* 3.1 55.7 + - + +
501D FAD 3.7 34.8 - - + -
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Residues in contact with THR 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D ILE* 4.3 7.2 - - + -
278D GLN* 3.7 23.1 - - - +
279D ALA* 4.0 15.6 - - + +
282D ILE* 4.3 14.1 - - + -
349D LYS* 2.8 28.6 + - - -
353D SER* 3.2 32.2 + - - -
356D ALA* 4.2 1.9 - - - +
384D ASP 4.0 5.6 - - - +
385D ALA* 2.8 20.2 + - - +
387D ILE* 1.3 85.1 - - + +
389D GLU* 1.3 56.1 + - - +
391D TYR* 4.1 8.3 - - - -
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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