Contacts of the helix formed by residues 377 - 388 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289F CYS* 4.1 12.6 - - + -
375F GLU 4.7 1.1 - - - +
376F MET* 1.3 101.2 - - + +
378F ALA* 1.3 63.5 + - - +
379F GLU 3.4 1.6 - - - -
380F ARG* 3.2 37.9 + - + +
381F HIS* 3.1 37.2 + - - +
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Residues in contact with ALA 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F CYS* 4.4 5.6 - - - -
360F SER 4.7 1.7 - - - +
363F ALA* 4.3 8.3 - - + -
364F ILE* 3.8 29.6 - - + +
367F LEU* 3.9 26.0 - - + -
371F GLY* 4.3 4.7 - - - +
376F MET* 3.4 3.0 - - - +
377F PRO* 1.3 80.5 - - - +
379F GLU* 1.3 62.5 + - - +
381F HIS* 3.2 14.2 + - - +
382F TYR* 3.1 22.9 + - - +
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Residues in contact with GLU 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E LEU* 3.6 32.1 - - + +
234E ARG* 5.7 1.0 + - - -
61F ASP* 4.7 1.0 - - - +
364F ILE* 4.0 7.9 - - - -
371F GLY 3.4 17.0 + - - +
372F TYR 4.5 2.0 - - - +
373F VAL 3.6 28.3 - - - +
374F THR* 3.6 28.0 - - - +
376F MET 4.1 4.6 + - - +
378F ALA* 1.3 78.5 - - - +
380F ARG* 1.3 76.1 + - - +
382F TYR* 3.5 3.3 + - - +
383F ARG* 3.0 63.1 + - - +
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Residues in contact with ARG 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE* 5.7 2.2 + - - -
57F ALA* 3.4 37.3 + - - +
58F ALA* 4.3 10.8 - - - +
61F ASP* 3.6 35.4 - - - +
107F ARG 5.9 0.2 + - - -
108F GLY 4.5 5.7 + - - -
109F CYS* 5.2 3.8 - - - +
110F ALA 5.4 2.0 - - - +
377F PRO* 3.2 35.5 + - + +
379F GLU* 1.3 85.0 + - - +
381F HIS* 1.3 78.5 + - - +
383F ARG* 3.0 19.5 + - - +
384F ASP* 2.9 51.0 + - - +
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Residues in contact with HIS 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F PHE* 6.3 0.4 - + - -
107F ARG 5.1 2.2 - - - -
282F ILE* 3.5 14.7 - - + +
285F THR* 3.3 35.3 + - + +
286F ALA* 3.9 35.2 - - + -
289F CYS* 4.8 2.9 - - + +
360F SER* 3.8 4.0 - - - -
377F PRO* 3.1 35.3 + - + +
378F ALA* 3.5 10.3 - - - +
380F ARG* 1.3 106.4 + - - +
382F TYR* 1.3 55.7 + - - +
384F ASP* 4.5 4.3 + - - +
385F ALA* 2.8 32.9 + - - +
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Residues in contact with TYR 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E LEU* 4.1 13.2 - - + -
357E THR* 3.9 6.6 + - - +
382E TYR* 3.2 58.6 + + - -
383E ARG* 5.9 0.7 - - + -
386E ARG* 3.6 29.3 - - + +
357F THR* 4.2 4.8 + - + -
360F SER* 3.3 22.1 - - - +
361F HIS* 3.5 45.6 - + + -
364F ILE* 3.6 24.2 - - + -
378F ALA 3.1 5.8 + - - +
379F GLU 3.5 8.5 - - - +
380F ARG 3.2 0.2 - - - -
381F HIS* 1.3 76.8 - - - +
383F ARG* 1.3 64.6 + - + +
385F ALA* 3.7 2.3 + - - +
386F ARG* 3.4 20.4 + - - +
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Residues in contact with ARG 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E LEU* 3.5 23.1 - - + +
234E ARG* 5.5 2.5 - - - +
372E TYR* 2.9 21.4 + - - -
382E TYR* 5.8 0.9 - - + -
383E ARG* 4.3 2.2 - - + +
61F ASP* 2.9 42.6 + - - -
231F LEU* 2.9 55.1 + - + +
232F GLY* 4.0 3.0 - - - -
234F ARG* 3.2 22.1 - - - +
374F THR* 5.8 0.4 - - - +
379F GLU* 3.0 42.6 + - - +
380F ARG* 3.0 16.5 + - - +
382F TYR* 1.3 82.0 - - + +
384F ASP* 1.3 62.6 + - - +
386F ARG* 3.5 12.8 + - - +
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Residues in contact with ASP 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E TYR* 4.0 4.3 - - - -
61F ASP* 4.6 4.3 - - - +
110F ALA* 3.4 34.2 + - + +
232F GLY* 3.4 5.0 - - - -
233F ILE* 2.9 27.3 + - + +
282F ILE* 3.9 10.9 - - + +
380F ARG* 2.9 42.8 + - - +
381F HIS* 4.0 6.4 + - - +
383F ARG* 1.3 74.4 - - - +
385F ALA* 1.3 65.2 + - - +
386F ARG 3.1 1.3 + - - -
387F ILE* 3.2 24.9 + - - +
388F THR 4.2 0.2 + - - -
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Residues in contact with ALA 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F ILE* 3.9 14.9 - - + +
356F ALA* 3.4 39.3 - - + +
357F THR* 3.6 9.9 + - - +
360F SER* 3.6 6.5 - - - +
381F HIS 2.8 23.9 + - - +
382F TYR 3.9 2.5 - - - +
383F ARG 3.4 0.2 - - - -
384F ASP* 1.3 72.4 - - - +
386F ARG* 1.3 62.8 + - - +
388F THR* 2.7 26.6 + - - -
389F GLU 4.2 0.9 + - - -
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Residues in contact with ARG 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361E HIS* 2.7 52.1 + - - -
364E ILE* 3.5 18.4 - - + +
365E GLN* 3.0 38.4 + - - +
372E TYR* 3.9 10.8 - - + -
382E TYR* 3.7 27.8 - - + -
231F LEU* 4.0 15.3 - - + -
357F THR* 3.9 3.8 + - - -
382F TYR 3.4 10.6 + - - +
383F ARG 3.5 13.5 - - - +
384F ASP 3.1 1.0 - - - -
385F ALA* 1.3 78.8 - - - +
387F ILE* 1.3 61.9 + - - +
388F THR 3.3 0.3 + - - -
389F GLU* 3.4 21.7 + - - +
390F ILE* 3.7 13.5 - - - +
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Residues in contact with ILE 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372E TYR* 3.4 30.6 - - + +
233F ILE* 3.8 24.2 - - + -
278F GLN* 4.8 0.2 - - - +
384F ASP 3.2 17.1 + - - +
386F ARG* 1.3 75.6 - - - +
388F THR* 1.3 64.5 + - + +
390F ILE* 2.8 32.6 + - + -
391F TYR* 3.0 58.9 + - + +
501F FAD 3.8 32.1 - - + -
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Residues in contact with THR 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F ILE* 4.2 7.2 - - + -
278F GLN* 3.5 28.5 - - - +
279F ALA* 4.0 20.8 - - + +
282F ILE* 4.2 11.9 - - + -
349F LYS* 2.8 32.2 + - - +
353F SER* 3.2 32.3 + - - -
356F ALA* 4.3 1.9 - - - +
385F ALA* 2.7 20.1 + - - +
387F ILE* 1.3 83.5 - - + +
389F GLU* 1.3 50.8 + - - +
390F ILE 3.3 0.4 - - - -
391F TYR* 3.9 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