Contacts of the helix formed by residues 374 - 379 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B MET* 1.3 95.4 - - - +
375B GLU* 1.4 52.0 + - - +
376B SER 3.3 2.5 - - - -
377B MET* 2.9 43.0 + - + +
383B PRO* 4.4 8.3 - - + -
387B GLU* 3.5 24.7 - - + +
388B THR 4.5 0.4 - - - +
391B VAL* 3.6 19.1 - - + -
404B LEU* 3.9 7.6 - - + -
407B GLU* 3.0 26.2 + - + +
417B ALA* 3.6 25.4 - - - +
420B MET* 4.1 12.3 - - + -
421B GLN* 3.6 20.9 - - + +
424B ILE* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B THR* 5.8 0.2 - - - +
372B GLN* 3.2 53.2 + - + +
374B LEU* 1.4 71.7 - - - +
376B SER* 1.3 61.4 + - - +
378B ILE* 2.8 56.3 + - - +
379B THR* 5.4 0.3 - - - -
387B GLU* 3.1 8.2 + - - +
405B SER* 5.8 1.0 - - - -
406B GLY 4.8 4.0 + - - -
407B GLU* 3.5 11.1 + - - +
380D LYS* 5.7 3.3 + - - -
384D THR* 4.8 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLU* 1.3 71.9 - - - +
377B MET* 1.3 57.6 + - - +
379B THR* 2.8 11.0 + - - -
380B LYS* 2.8 41.3 + - - +
382B ARG 3.5 10.2 + - - -
383B PRO* 3.6 0.5 - - - +
384B THR* 3.3 25.2 + - - +
387B GLU* 2.5 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 2.9 27.4 + - + +
376B SER* 1.3 73.9 + - - +
378B ILE* 1.3 52.5 + - - +
379B THR 2.7 15.3 + - - -
380B LYS 3.1 17.5 + - - +
381B PRO* 3.3 30.1 - - + +
382B ARG* 4.0 0.7 - - - -
383B PRO* 3.9 40.4 - - + -
407B GLU* 4.7 4.0 - - + -
413B PHE* 3.5 20.1 + - + +
416B GLU* 3.9 26.7 - - + +
417B ALA* 3.9 27.8 - - + +
420B MET* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU 4.0 1.0 + - - -
375B GLU* 2.8 54.7 + - - +
377B MET* 1.3 71.2 - - - +
379B THR* 1.3 66.9 + - - +
406B GLY* 3.4 37.5 - - - +
407B GLU* 3.5 7.9 - - + +
410B LYS* 5.2 10.1 - - + -
411B GLY* 3.3 17.2 - - - +
412B ASN* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLU 5.4 0.2 - - - -
376B SER* 2.8 5.9 + - - +
377B MET 2.7 1.6 + - - -
378B ILE* 1.3 91.9 + - - +
380B LYS* 1.3 72.6 + - + +
381B PRO* 4.9 0.2 - - - +
412B ASN* 5.0 9.6 + - - +
413B PHE* 3.9 13.3 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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