Contacts of the helix formed by residues 374 - 379 (chain A) in PDB entry 2VGB
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 LEU 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A MET* 1.3 97.5 - - - +
375A GLU* 1.3 63.9 + - - +
376A SER 3.3 2.2 - - - -
377A MET* 2.9 31.8 + - + +
383A PRO* 4.4 7.9 - - + -
387A GLU* 3.5 25.6 - - + +
388A THR 4.4 0.4 - - - +
391A VAL* 3.6 20.2 - - + -
404A LEU* 4.0 6.5 - - + -
407A GLU* 3.0 26.6 + - + +
417A ALA* 3.6 25.4 - - - +
420A MET* 4.0 13.2 - - + -
421A GLN* 3.6 21.1 - - + +
424A ILE* 4.5 6.5 - - + -
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN* 3.3 52.2 + - + +
374A LEU* 1.3 74.6 - - - +
376A SER* 1.3 66.4 + - - +
378A ILE* 2.8 51.0 + - - +
379A THR* 5.4 0.2 - - - -
387A GLU* 3.0 8.4 + - - +
405A SER* 5.9 0.7 - - - -
406A GLY* 4.8 4.3 + - - -
407A GLU* 3.7 11.4 + - - +
380C LYS* 5.4 5.4 + - - -
384C THR* 4.6 14.7 - - + +
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 1.3 77.0 - - - +
377A MET* 1.3 57.0 + - - +
379A THR* 2.9 12.0 + - - -
380A LYS* 2.8 41.5 + - - +
382A ARG 3.4 14.2 + - - -
383A PRO* 3.6 0.2 - - - +
384A THR* 3.4 21.1 - - - +
387A GLU* 2.5 31.0 + - - -
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU* 2.9 30.6 + - + +
376A SER* 1.3 72.3 + - - +
378A ILE* 1.3 61.7 + - - +
379A THR 2.8 5.8 + - - -
380A LYS 3.1 19.1 - - - +
381A PRO* 3.4 27.8 - - + +
382A ARG* 3.9 1.1 - - - +
383A PRO* 3.8 38.4 - - + -
407A GLU* 4.8 3.5 - - + +
413A PHE* 3.5 20.8 + - + +
416A GLU* 3.9 27.1 - - + +
417A ALA* 3.9 28.0 - - + +
420A MET* 4.3 5.8 - - + -
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Residues in contact with ILE 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU 4.1 1.0 + - - -
375A GLU* 2.8 55.5 + - - +
377A MET* 1.3 70.2 - - - +
379A THR* 1.3 67.7 + - - +
406A GLY* 3.4 37.0 - - - -
407A GLU* 3.7 6.9 - - + +
410A LYS* 5.2 10.8 - - + -
411A GLY* 3.3 16.4 - - - +
412A ASN* 3.0 26.3 + - - +
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Residues in contact with THR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A SER* 2.9 6.1 + - - +
377A MET 2.8 0.4 - - - -
378A ILE* 1.3 88.7 + - - +
380A LYS* 1.3 75.7 + - + +
381A PRO* 4.9 0.2 - - - +
412A ASN* 5.1 9.5 + - - +
413A PHE* 3.9 12.1 - - - -
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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