Contacts of the helix formed by residues 369 - 372 (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 GLY 369 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E LEU 3.4 0.4 + - - -
368E GLY* 1.3 70.9 - - - -
370E MET* 1.3 63.3 + - - +
372E TYR* 3.0 19.3 + - - +
373E VAL 3.9 1.9 + - - -
185F TRP* 3.4 20.8 - - - -
390F ILE* 4.0 3.1 - - - +
501F FAD 2.8 49.5 + - - -
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Residues in contact with MET 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E TYR* 3.8 23.8 - - + +
297E ARG* 6.1 0.9 - - - +
367E LEU* 3.4 16.1 + - + +
368E GLY 3.2 0.6 - - - -
369E GLY* 1.3 75.3 - - - +
371E GLY* 1.3 60.2 + - - +
372E TYR 3.1 1.5 + - - -
373E VAL* 3.4 24.8 + - - +
375E GLU* 4.1 18.6 - - + -
376E MET* 3.4 48.5 - - + +
185F TRP* 3.6 26.3 - - + -
501F FAD 4.6 0.2 + - - -
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Residues in contact with GLY 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364E ILE* 3.7 26.8 - - - +
367E LEU* 3.4 24.8 - - - +
368E GLY 3.0 12.2 + - - -
370E MET* 1.3 78.2 - - - +
372E TYR* 1.3 56.1 + - - +
373E VAL 3.5 1.1 - - - -
376E MET* 5.8 0.2 - - - -
378E ALA* 4.4 2.7 - - - -
379E GLU* 3.4 27.3 + - - +
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Residues in contact with TYR 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364E ILE* 5.2 0.4 - - + -
368E GLY 3.9 0.8 + - - -
369E GLY 3.0 12.5 + - - +
371E GLY* 1.3 79.2 - - - +
373E VAL* 1.3 60.0 + - + +
379E GLU* 4.5 1.7 - - - +
230F LYS* 3.5 19.2 - - + -
231F LEU* 2.8 54.8 + - + +
232F GLY* 3.2 40.9 - - - -
233F ILE* 3.8 1.9 + - + -
383F ARG 2.9 21.7 + - - -
384F ASP 4.0 0.3 + - - -
386F ARG* 3.9 5.4 - - + -
387F ILE* 3.4 53.1 - - + +
390F ILE* 4.2 22.9 - - + -
501F FAD 4.4 9.2 - - + -
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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
------------------------------------------------------------
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