Contacts of the helix formed by residues 309 - 314 (chain A) in PDB entry 3V4R
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 TYR 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 3.8 45.5 - - + -
289A ARG 4.6 0.5 + - - -
290A THR* 4.0 16.2 + - + +
293A ASP* 2.9 40.3 + - + +
294A LEU* 5.7 0.4 - - + -
297A MET* 3.6 24.0 - - + -
303A CYS* 4.2 2.5 - - - -
305A GLY 3.9 8.1 - - - -
306A ILE* 2.9 17.6 + - - +
308A ASN* 1.3 76.9 - - + +
310A SER* 1.4 52.3 + - - +
311A ARG 3.3 2.5 - - - -
312A HIS* 2.9 37.2 + + - +
313A LEU* 3.3 18.2 + - + -
367A ARG* 3.8 18.6 + - - -
368A LEU* 4.3 14.4 - - + -
370A SER* 5.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 4.7 9.2 - - - -
306A ILE 3.5 3.4 + - - -
307A GLU* 3.1 22.8 + - - -
308A ASN 3.3 0.4 - - - -
309A TYR* 1.4 74.6 - - - +
311A ARG* 1.4 64.0 + - - +
313A LEU* 3.2 12.9 + - - +
314A THR* 3.1 33.1 + - - +
373A ASP 5.0 0.9 + - - -
374A ASN* 3.4 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 4.1 7.5 + - - +
308A ASN 5.0 1.2 + - - -
309A TYR 3.1 3.8 + - - -
310A SER* 1.4 78.9 + - - +
312A HIS* 1.3 86.6 + - + +
314A THR* 3.4 8.8 + - - -
315A LEU* 3.4 15.2 + - - -
316A ARG* 3.4 32.3 + - + +
317A PRO 3.8 14.1 - - - +
318A PRO* 3.6 32.8 - - - +
320A SER* 5.4 2.5 - - - -
369A PRO 5.5 0.2 - - - -
370A SER* 3.4 33.3 + - - +
373A ASP* 2.8 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA* 3.3 20.7 - - - +
262A ASN* 3.6 42.0 + - + +
263A ILE* 3.6 31.6 - - + +
266A GLU* 3.2 27.4 + - + +
309A TYR* 2.9 16.1 + + - +
311A ARG* 1.3 97.1 + - + +
313A LEU* 1.3 62.7 + - - +
315A LEU* 3.3 15.5 + - - +
370A SER* 3.3 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 4.5 14.4 - - + -
251A THR* 5.3 15.0 - - - -
255A LYS* 4.4 7.1 - - - +
256A MET* 5.7 2.7 - - + +
259A ALA* 3.9 19.5 - - + -
260A ILE* 6.0 1.1 - - + -
263A ILE* 4.7 7.0 - - + -
297A MET* 4.8 11.9 - - - -
306A ILE* 3.7 41.1 - - + +
309A TYR* 3.5 19.7 - - + +
310A SER* 3.2 15.3 + - - +
312A HIS* 1.3 76.9 - - - +
314A THR* 1.3 59.1 + - + +
315A LEU* 3.3 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A SER* 3.1 17.7 + - - +
311A ARG* 3.4 11.1 + - - -
313A LEU* 1.3 78.8 - - + +
315A LEU* 1.4 64.0 - - - +
316A ARG* 3.0 34.4 + - - +
----------------------------------------------------------
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