Contacts of the helix formed by residues 333 - 341 (chain A) in PDB entry 2GPV
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 ASP 333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP 3.9 4.0 - - - +
323A GLU* 3.6 30.7 - - + +
331A ILE 3.7 1.2 + - - -
332A MET* 1.3 73.1 - - - +
334A GLU* 1.3 60.2 + - - +
335A ASP* 3.2 29.3 + - - +
336A GLN* 2.6 43.9 + - - +
337A SER* 2.7 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP* 4.1 9.9 + - + +
333A ASP* 1.3 75.3 - - - +
335A ASP* 1.3 70.1 + - - +
337A SER* 2.9 10.7 + - - -
338A LYS* 2.9 50.3 + - - +
343A LEU* 4.4 15.4 - - + +
347A ASN* 5.6 2.1 - - - +
334B GLU* 4.0 19.6 - - - +
338B LYS* 4.9 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ASP* 3.2 17.0 + - - +
334A GLU* 1.3 84.9 - - - +
336A GLN* 1.3 64.5 + - + +
338A LYS* 3.1 16.2 + - - +
339A LEU* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 5.4 7.1 - - - +
264A ALA* 5.1 1.7 - - - +
330A TYR* 5.3 8.3 - - - -
331A ILE 3.0 27.1 + - - +
332A MET* 3.6 17.6 - - + +
333A ASP* 2.6 34.1 + - - +
335A ASP* 1.3 77.8 - - + +
337A SER* 1.3 60.3 + - - +
339A LEU* 3.4 12.3 + - + +
340A ALA* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A MET* 3.8 13.6 + - - +
333A ASP 2.7 19.4 + - - -
334A GLU* 2.9 9.7 + - - -
336A GLN* 1.3 74.6 - - - +
338A LYS* 1.3 63.5 + - - +
339A LEU 3.2 0.2 - - - -
340A ALA* 3.1 1.1 + - - -
341A GLY* 3.0 20.3 + - - -
342A LEU 3.2 21.6 + - - +
343A LEU* 3.9 12.4 + - - -
346A ASN* 3.5 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLU* 2.9 47.5 + - - +
335A ASP* 3.1 16.4 + - - +
337A SER* 1.3 77.1 - - - +
339A LEU* 1.3 60.4 + - - +
340A ALA 3.4 0.5 + - - -
341A GLY* 3.6 7.7 + - - +
343A LEU* 3.9 35.1 - - + +
334B GLU* 4.3 15.2 + - - -
343B LEU* 4.8 7.1 - - - +
347B ASN* 4.3 16.8 - - - +
381E HIS* 3.2 21.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 4.1 20.9 - - + +
260A SER* 4.0 34.1 - - - +
261A ASP* 3.3 19.7 + - - +
335A ASP 3.0 11.9 + - - +
336A GLN* 3.7 14.6 - - + +
337A SER 3.2 0.4 - - - -
338A LYS* 1.3 78.9 - - - +
340A ALA* 1.3 57.2 + - + +
381E HIS* 3.3 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASP* 3.9 14.7 - - - +
264A ALA* 3.4 33.2 - - + -
265A LEU* 4.2 14.9 - - + +
332A MET* 4.1 9.4 - - + -
336A GLN 3.2 11.7 + - - +
337A SER 3.1 5.3 + - - +
339A LEU* 1.3 77.7 - - - +
341A GLY* 1.3 63.0 + - - +
342A LEU* 3.3 17.2 + - + +
434A HIS* 5.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER 3.0 6.2 + - - -
338A LYS* 3.6 7.2 + - - -
339A LEU 3.5 3.0 + - - -
340A ALA* 1.3 77.6 - - - +
342A LEU* 1.3 57.4 + - - +
343A LEU* 3.4 6.8 + - - -
344A ASP 5.3 0.5 + - - -
434A HIS* 3.5 25.5 + - - -
----------------------------------------------------------
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