Contacts of the helix formed by residues 309 - 319 (chain A) in PDB entry 2V90
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 GLY 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLU* 3.8 8.5 - - - -
273A PRO* 4.0 9.2 - - - +
275A GLN* 3.3 2.5 - - - -
307A GLY 4.1 0.4 + - - -
308A LEU* 1.3 73.8 - - - +
310A HIS* 1.3 59.4 + - - -
311A GLU* 3.7 1.3 - - - -
312A GLU* 3.7 10.2 + - - +
313A THR* 2.9 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.1 46.3 + - + +
264A ARG* 4.3 0.2 - - - -
265A GLU* 3.1 29.6 + - + +
275A GLN* 2.7 25.6 + - - +
309A GLY* 1.3 68.7 - - - -
311A GLU* 1.3 71.5 + - - +
312A GLU 3.2 1.3 - - - -
313A THR* 3.0 2.6 + - - -
314A VAL* 2.9 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLY* 5.6 0.7 - - - -
310A HIS* 1.3 82.5 - - + +
312A GLU* 1.3 63.8 + - + +
314A VAL* 3.4 7.5 + - - +
315A SER* 2.9 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.8 28.3 - - + -
309A GLY* 3.7 15.2 + - - +
310A HIS 3.2 0.6 - - - -
311A GLU* 1.3 85.7 - - + +
313A THR* 1.3 59.6 + - - +
315A SER* 3.4 13.7 + - - -
316A ARG* 2.8 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.9 12.6 - - + -
275A GLN* 3.7 19.0 - - + +
297A LEU* 3.6 31.0 - - + -
300A VAL* 4.6 0.7 - - + -
305A VAL* 3.9 17.3 - - + +
308A LEU* 3.8 14.2 - - - +
309A GLY 2.9 17.7 + - - -
310A HIS 3.0 4.5 + - - -
312A GLU* 1.3 73.4 - - - +
314A VAL* 1.3 68.4 + - - +
316A ARG* 3.2 10.5 + - - +
317A ILE* 3.0 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.1 15.3 - - + -
310A HIS* 2.9 43.2 + - + +
311A GLU* 3.7 6.3 - - - +
313A THR* 1.3 76.0 - - - +
315A SER* 1.3 63.5 + - - +
317A ILE* 3.0 11.8 + - + +
318A GLN* 2.9 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLU 2.9 20.1 + - - -
312A GLU* 3.4 16.4 + - - -
313A THR 3.3 0.2 - - - -
314A VAL* 1.3 72.4 - - - +
316A ARG* 1.3 62.8 + - - +
318A GLN* 3.3 13.7 + - - +
319A GLY* 2.8 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 3.5 23.2 + - + +
301A ALA* 5.5 0.2 - - - +
303A GLU* 3.7 38.4 + - - +
304A SER 4.0 9.1 + - - -
305A VAL* 3.9 20.0 - - - +
308A LEU* 3.6 19.6 - - - +
312A GLU* 2.8 37.3 + - - +
313A THR* 3.2 8.0 + - - +
314A VAL 3.1 0.2 - - - -
315A SER* 1.3 84.2 + - - +
317A ILE* 1.3 60.8 + - - +
319A GLY* 3.4 8.3 + - - -
320A GLN* 3.7 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 4.1 27.8 - - + -
261A PHE* 4.3 20.2 - - + -
263A LEU* 4.1 18.2 - - + -
297A LEU* 4.0 21.1 - - + -
300A VAL* 3.8 22.7 - - + -
313A THR 3.0 16.7 + - - +
314A VAL* 3.0 10.3 + - + +
316A ARG* 1.3 75.9 - - - +
318A GLN* 1.3 66.1 + - + +
320A GLN* 3.3 18.0 + - - +
321A GLY 4.2 4.5 + - - +
324A VAL* 4.3 11.3 - - + +
326A LEU* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LYS* 5.5 8.4 + - - +
259A PHE* 6.2 0.9 - - - -
314A VAL* 2.9 40.2 + - + +
315A SER* 3.6 11.1 - - - +
317A ILE* 1.3 75.1 - - + +
319A GLY* 1.3 61.0 + - - +
320A GLN 3.1 6.3 + - - -
321A GLY* 3.3 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER 2.8 19.8 + - - -
316A ARG* 3.4 4.0 + - - -
317A ILE 3.2 0.8 - - - -
318A GLN* 1.3 74.1 - - - +
320A GLN* 1.3 68.8 + - - +
321A GLY 3.4 0.4 + - - -
----------------------------------------------------------
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