Contacts of the helix formed by residues 377 - 388 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E CYS* 4.0 19.1 - - + -
375E GLU 4.8 0.7 - - - +
376E MET* 1.3 95.1 - - + +
378E ALA* 1.3 64.1 + - - +
379E GLU 3.4 2.0 - - - -
380E ARG* 3.2 36.4 + - + +
381E HIS* 3.0 38.1 + - - +
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Residues in contact with ALA 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E CYS* 4.3 8.7 - - - -
360E SER* 4.7 1.9 - - - +
363E ALA* 4.4 7.6 - - + -
364E ILE* 3.8 29.6 - - + +
367E LEU* 3.8 27.1 - - + -
371E GLY* 4.4 3.8 - - - -
376E MET* 3.3 2.8 - - - +
377E PRO* 1.3 80.5 - - - +
379E GLU* 1.3 62.7 + - - +
381E HIS* 3.2 13.7 + - - +
382E TYR* 3.1 22.7 + - - +
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Residues in contact with GLU 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ASP* 4.8 0.3 - - - +
364E ILE* 4.1 7.4 - - - -
371E GLY 3.4 18.0 + - - +
372E TYR 4.5 4.3 - - - +
373E VAL 3.7 27.1 - - - +
374E THR* 3.7 24.8 - - - +
376E MET 4.3 4.0 + - - +
378E ALA* 1.3 77.5 - - - +
380E ARG* 1.3 68.9 + - - +
382E TYR* 3.4 3.6 + - - +
383E ARG* 2.9 63.5 + - - +
231F LEU* 3.4 34.1 - - + +
234F ARG* 5.5 1.7 + - - -
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Residues in contact with ARG 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E PHE 5.6 0.4 + - - -
57E ALA* 3.6 37.6 + - - +
58E ALA* 4.2 10.6 - - - +
61E ASP* 3.6 31.2 - - - +
107E ARG 5.8 0.2 + - - -
108E GLY 4.6 4.6 + - - -
109E CYS* 5.2 4.2 - - - +
110E ALA 5.4 1.2 - - - +
377E PRO* 3.2 35.8 + - + +
379E GLU* 1.3 85.4 + - - +
381E HIS* 1.3 83.0 + - - +
383E ARG* 3.2 24.1 + - - +
384E ASP* 3.0 41.9 + - - +
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Residues in contact with HIS 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ARG 5.2 2.0 - - - -
282E ILE* 3.7 13.5 - - + +
285E THR* 3.3 36.8 + - + +
286E ALA* 3.8 35.0 - - + -
289E CYS* 4.8 3.3 - - + +
360E SER* 3.8 5.2 - - - -
377E PRO* 3.0 41.9 + - + +
378E ALA* 3.2 11.2 + - - +
380E ARG* 1.3 101.4 + - - +
382E TYR* 1.3 56.7 + - - +
384E ASP* 4.5 4.2 + - - -
385E ALA* 2.9 32.7 + - - +
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Residues in contact with TYR 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E THR* 4.2 6.8 + - + -
360E SER* 3.3 25.4 - - - +
361E HIS* 3.5 45.0 - + + -
364E ILE* 3.5 27.6 - - + -
378E ALA 3.1 5.8 + - - +
379E GLU 3.6 5.2 - - - +
380E ARG 3.3 0.2 - - - -
381E HIS* 1.3 74.9 - - - +
383E ARG* 1.3 63.4 + - + +
385E ALA* 4.0 2.1 - - - +
386E ARG* 3.4 20.8 + - - +
231F LEU* 4.2 13.5 - - + -
357F THR* 3.6 10.6 + - - +
382F TYR* 3.2 58.9 + + - -
383F ARG* 5.8 0.7 - - + -
386F ARG* 3.7 28.1 - - + -
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Residues in contact with ARG 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ASP* 2.9 41.6 + - - -
231E LEU* 2.9 59.3 + - + +
232E GLY* 4.1 2.4 - - - -
234E ARG* 3.3 20.9 - - - +
374E THR* 5.7 0.6 - - - +
379E GLU* 2.9 43.0 + - - +
380E ARG* 3.2 18.3 + - - +
382E TYR* 1.3 79.2 - - + +
384E ASP* 1.3 61.8 + - - +
386E ARG* 3.5 8.6 + - - +
231F LEU* 3.6 21.1 - - + +
234F ARG* 5.5 1.9 - - - +
372F TYR* 2.8 25.7 + - - -
382F TYR* 5.9 0.9 - - + -
383F ARG* 4.3 2.7 - - + +
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Residues in contact with ASP 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ASP* 4.6 4.3 - - - +
110E ALA* 3.2 34.7 + - + +
111E SER 5.1 0.5 + - - -
232E GLY* 3.6 4.5 - - - -
233E ILE* 3.0 25.8 + - + +
282E ILE* 4.0 11.5 - - + +
380E ARG* 3.0 43.4 + - - +
381E HIS* 3.8 7.4 + - - +
383E ARG* 1.3 73.8 - - - +
385E ALA* 1.3 66.0 + - - +
386E ARG 3.1 2.7 + - - -
387E ILE* 3.3 24.4 - - - +
388E THR 4.3 0.2 + - - -
372F TYR* 4.0 4.0 - - - -
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Residues in contact with ALA 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ILE* 4.0 13.9 - - + +
356E ALA* 3.4 40.8 - - + +
357E THR* 3.7 8.9 + - - +
360E SER* 3.6 6.5 - - - +
381E HIS 2.9 18.5 + - - +
382E TYR 4.0 1.6 - - - +
384E ASP* 1.3 75.6 - - - +
386E ARG* 1.3 62.8 + - - +
388E THR* 2.6 28.9 + - - -
389E GLU* 4.1 1.2 + - - +
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Residues in contact with ARG 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E LEU* 4.2 14.8 - - + -
357E THR* 3.9 5.2 - - - +
382E TYR 3.4 11.4 + - - +
383E ARG 3.6 12.6 - - - +
384E ASP 3.1 1.2 - - - -
385E ALA* 1.3 80.0 - - - +
387E ILE* 1.3 60.3 + - - +
388E THR 3.4 0.2 + - - -
389E GLU* 3.5 21.3 + - - +
390E ILE* 3.7 10.9 - - - +
361F HIS* 2.8 53.1 + - - -
364F ILE* 3.6 18.1 - - + +
365F GLN* 2.9 38.0 + - - +
372F TYR* 4.0 10.3 - - + -
382F TYR* 3.6 29.6 - - + -
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Residues in contact with ILE 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ILE* 3.9 21.8 - - + -
278E GLN* 4.7 0.7 - - - +
384E ASP 3.3 16.7 + - - +
386E ARG* 1.3 76.7 - - - +
388E THR* 1.3 66.6 + - + +
390E ILE* 2.9 29.3 + - + -
391E TYR* 3.2 49.6 + - + +
501E FAD 3.7 38.4 - - + -
372F TYR* 3.5 32.4 - - + +
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Residues in contact with THR 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E ILE* 4.2 7.4 - - + +
278E GLN* 3.5 27.8 - - - +
279E ALA* 3.9 26.1 - - + +
282E ILE* 4.4 9.2 - - + -
349E LYS* 2.8 26.6 + - - -
353E SER* 3.2 34.4 + - - -
356E ALA* 4.3 1.2 - - - +
385E ALA* 2.6 22.7 + - - +
387E ILE* 1.3 81.2 - - + +
389E GLU* 1.3 55.8 + - - +
390E ILE 3.3 0.2 - - - -
391E TYR* 4.1 7.4 - - - -
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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