Contacts of the helix formed by residues 374 - 379 (chain W) in PDB entry 1G3I
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 VAL 374 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342W GLU* 3.6 33.9 - - + +
345W LEU* 3.6 22.2 - - + -
346W THR* 4.7 14.8 - - + -
353W THR* 5.2 2.7 - - + -
369W PHE* 4.3 14.8 - - + +
370W THR 3.2 17.9 - - - +
371W THR* 3.1 13.8 + - + +
373W ALA* 1.3 77.6 - - - +
375W LYS* 1.3 60.9 + - - +
377W ILE* 3.4 7.6 + - + +
378W ALA* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 375 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342W GLU* 3.6 37.8 + - - +
371W THR 3.7 9.6 + - - +
372W ASP* 4.6 11.7 - - - +
374W VAL* 1.3 76.1 - - - +
376W LYS* 1.3 57.9 + - + +
377W ILE 2.8 4.3 + - - -
378W ALA* 4.6 3.6 - - - -
379W GLU* 2.6 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372W ASP 4.3 10.3 - - - +
373W ALA* 3.9 8.7 + - - +
374W VAL 3.4 0.4 - - - -
375W LYS* 1.3 78.7 - - + +
377W ILE* 1.3 59.7 + - - +
379W GLU* 4.7 13.2 - - - +
380W ALA* 3.7 16.6 - - + +
423W ALA* 4.2 37.6 + - + +
426W VAL* 3.2 25.3 - - + +
427W ALA* 4.2 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 377 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345W LEU* 3.4 22.9 - - + -
369W PHE* 5.8 4.7 - - + -
373W ALA 3.0 26.2 - - - +
374W VAL* 3.7 7.4 - - + +
375W LYS 2.9 0.2 - - - -
376W LYS* 1.3 80.6 - - - +
378W ALA* 1.3 60.6 + - - +
379W GLU 3.5 0.7 - - - -
380W ALA* 3.9 7.4 - - - -
381W ALA* 3.5 18.9 + - - +
396W LEU* 4.0 4.5 - - + +
399W VAL* 4.2 14.6 - - + +
400W MET* 3.9 22.9 - - + -
403W LEU* 3.5 27.4 - - + -
421W ILE* 4.7 7.0 - - + -
426W VAL* 3.5 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338W ALA 3.9 8.9 - - - +
341W PHE* 3.3 27.2 - - + +
342W GLU* 3.2 35.9 - - + +
345W LEU* 4.5 1.8 - - + -
374W VAL 3.0 15.9 + - - +
375W LYS* 4.0 1.8 - - - +
377W ILE* 1.3 78.4 - - - +
379W GLU* 1.3 60.3 + - - +
380W ALA 3.2 1.6 - - - -
381W ALA* 3.6 2.9 + - - +
382W PHE* 3.4 19.4 + - - +
396W LEU* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 379 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338W ALA* 4.9 17.4 - - + +
375W LYS* 2.6 22.4 + - + +
376W LYS* 4.7 12.2 - - - +
378W ALA* 1.3 76.2 - - - +
380W ALA* 1.3 56.5 + - - +
381W ALA 3.2 3.6 - - - -
382W PHE* 3.9 7.9 - - + +
383W ARG* 3.1 26.3 + - + +
----------------------------------------------------------
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