Contacts of the helix formed by residues 377 - 386 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289C CYS* 4.2 14.6 - - + -
375C GLU 4.8 0.4 - - - +
376C MET* 1.4 101.1 - - + +
378C ALA* 1.3 62.8 + - - +
379C GLU 3.4 0.9 - - - -
380C ARG* 3.2 37.3 + - + +
381C HIS* 3.1 37.0 + - - +
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Residues in contact with ALA 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C CYS* 4.4 7.2 - - - -
360C SER 4.6 2.1 - - - +
363C ALA* 4.4 7.2 - - + -
364C ILE* 3.9 27.1 - - + +
367C LEU* 3.7 27.1 - - + -
371C GLY* 4.4 3.6 - - - +
376C MET* 3.3 2.8 - - + -
377C PRO* 1.3 79.6 - - - +
379C GLU* 1.3 63.3 + - - +
381C HIS* 3.1 15.3 + - - +
382C TYR* 3.1 21.1 + - - +
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Residues in contact with GLU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ASP* 4.8 0.5 - - - +
364C ILE* 4.0 8.5 - - - -
371C GLY 3.5 18.3 + - - +
372C TYR 4.6 2.2 - - - +
373C VAL 3.7 25.6 - - - +
374C THR* 3.7 25.3 - - - +
376C MET 4.2 5.3 + - - +
378C ALA* 1.3 77.2 - - - +
380C ARG* 1.3 67.6 + - - +
382C TYR* 3.4 3.5 + - - +
383C ARG* 2.9 64.9 + - - +
231D LEU* 3.1 34.8 - - + +
234D ARG* 5.5 1.2 + - - -
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Residues in contact with ARG 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 5.7 0.8 + - - -
57C ALA* 3.5 38.6 + - - +
58C ALA* 4.4 9.8 - - - +
61C ASP* 3.6 33.0 - - - +
107C ARG 5.9 0.4 + - - -
108C GLY 4.5 5.5 + - - -
109C CYS* 5.3 3.6 - - - +
110C ALA 5.4 1.2 - - - +
377C PRO* 3.2 34.3 + - + +
379C GLU* 1.3 80.8 + - - +
381C HIS* 1.3 85.7 + - - +
383C ARG* 3.1 23.2 + - - +
384C ASP* 2.9 42.0 + - - +
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Residues in contact with HIS 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG 5.3 1.8 - - - -
282C ILE* 3.8 11.8 + - + +
285C THR* 3.3 35.6 + - + +
286C ALA* 3.8 35.9 - - + -
289C CYS* 4.8 3.1 - - + +
360C SER* 3.8 6.1 - - - -
377C PRO* 3.1 36.5 + - + +
378C ALA* 3.1 12.2 + - - +
380C ARG* 1.3 105.1 + - - +
382C TYR* 1.3 56.1 + - - +
384C ASP* 4.7 3.6 + - - -
385C ALA* 2.9 33.4 + - - +
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Residues in contact with TYR 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C THR* 4.2 5.9 + - + -
360C SER* 3.4 21.5 - - - +
361C HIS* 3.5 36.8 - + + -
364C ILE* 3.4 28.9 - - + -
378C ALA 3.1 5.0 + - - +
379C GLU 3.6 5.2 - - - +
380C ARG 3.3 0.2 - - - -
381C HIS* 1.3 75.7 - - - +
383C ARG* 1.3 62.8 + - + +
385C ALA* 3.9 1.9 - - - +
386C ARG* 3.5 20.8 + - - +
231D LEU* 4.2 14.4 - - + -
357D THR* 3.7 9.7 + - - +
382D TYR* 3.2 59.3 + + - -
383D ARG* 5.8 0.4 - - + -
386D ARG* 3.5 34.9 - - + -
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Residues in contact with ARG 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ASP* 2.9 40.2 + - - -
231C LEU* 3.0 59.1 + - + +
232C GLY* 4.1 2.7 - - - -
234C ARG* 3.2 23.7 - - - +
374C THR* 5.7 0.4 - - - +
379C GLU* 2.9 43.6 + - - +
380C ARG* 3.1 19.2 + - - +
382C TYR* 1.3 78.3 - - + +
384C ASP* 1.3 58.2 + - - +
386C ARG* 3.5 8.3 + - - +
231D LEU* 3.6 20.9 - - + -
234D ARG* 5.5 1.9 - - - +
372D TYR* 2.7 31.9 + - - -
382D TYR* 5.9 1.6 - - + -
383D ARG* 4.3 2.7 - - + +
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Residues in contact with ASP 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASP* 4.5 3.8 - - - +
110C ALA* 3.3 34.4 + - + +
111C SER* 5.2 0.5 + - - -
232C GLY* 3.6 4.5 - - - -
233C ILE* 3.0 25.7 + - + +
282C ILE* 4.0 13.7 - - + +
380C ARG* 2.9 42.7 + - - +
381C HIS* 4.0 6.3 + - - +
383C ARG* 1.3 71.1 - - - +
385C ALA* 1.3 65.9 + - - +
386C ARG 3.1 2.0 + - - -
387C ILE* 3.1 26.0 - - - +
388C THR* 4.2 0.3 - - - +
372D TYR* 3.8 4.9 - - - -
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Residues in contact with ALA 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ILE* 3.8 18.3 - - + +
356C ALA* 3.4 35.7 - - + +
357C THR* 3.8 8.1 + - - +
360C SER* 3.6 6.7 - - - +
381C HIS 2.9 19.3 + - - +
382C TYR 3.9 2.9 - - - +
384C ASP* 1.3 76.4 - - - +
386C ARG* 1.3 62.5 + - - +
388C THR* 2.7 28.9 + - - -
389C GLU* 4.2 1.0 + - - +
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Residues in contact with ARG 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LEU* 4.2 14.8 - - + -
357C THR* 3.9 4.7 - - - -
382C TYR 3.5 11.4 + - - +
383C ARG 3.6 12.1 - - - +
384C ASP 3.1 1.0 - - - -
385C ALA* 1.3 78.6 - - - +
387C ILE* 1.3 60.0 + - - +
388C THR 3.5 0.3 + - - -
389C GLU* 3.5 25.1 + - - +
390C ILE* 3.7 11.2 - - - +
361D HIS* 2.9 47.3 + - - -
364D ILE* 3.5 20.4 - - + +
365D GLN* 2.8 41.0 + - - +
372D TYR* 4.0 8.5 - - + -
382D TYR* 3.7 27.1 - - + -
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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