Contacts of the helix formed by residues 262 - 276 (chain A) in PDB entry 2J0Q
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 GLU 262 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ARG* 3.4 25.2 + - - +
261A GLU* 1.3 72.7 - - + +
263A TRP* 1.3 80.2 + - + +
264A LYS 3.1 0.4 - - - -
265A PHE* 3.4 20.1 + - - +
266A ASP* 3.8 9.7 + - - +
292A TRP* 5.3 6.5 - - + -
296A LYS* 4.4 18.6 + - - +
352A TYR* 5.0 1.3 - - - -
171T ASP* 4.7 0.3 - - - +
172T ASP* 3.6 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 4.0 14.6 - - + -
259A GLU* 3.4 51.6 - - + -
260A ARG* 3.1 38.3 + - + +
262A GLU* 1.3 91.8 + - + +
264A LYS* 1.3 67.4 + - - +
265A PHE 3.1 0.4 - - - -
266A ASP* 3.3 15.8 + - + +
267A THR* 2.9 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 4.0 25.5 - - + +
261A GLU* 2.9 46.8 + - - +
262A GLU 3.1 0.2 - - - -
263A TRP* 1.3 80.0 - - - +
265A PHE* 1.3 60.1 + - - +
267A THR* 3.4 7.3 + - - -
268A LEU* 3.1 21.3 + - - +
352A TYR* 2.8 47.1 + - + +
353A ASP* 3.4 11.5 + - - +
380A PHE* 3.8 33.3 + - + -
382A LYS* 4.8 9.1 - - - +
385A ASP* 5.4 3.6 + - - -
173T ASP* 5.1 0.8 + - - -
182T ILE* 3.5 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU* 3.4 13.1 + - - +
263A TRP 3.1 0.8 - - - -
264A LYS* 1.3 76.1 - - - +
266A ASP* 1.3 71.4 + - - +
268A LEU* 3.1 18.2 + - + +
269A CYS* 3.4 23.2 + - - -
292A TRP* 5.1 0.9 - + + -
293A LEU* 3.8 18.8 - - + -
296A LYS* 3.6 67.5 - - + +
297A MET* 3.8 35.0 - - + -
300A ALA* 4.4 12.1 - - + -
352A TYR* 3.1 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU 4.0 10.8 - - - +
263A TRP* 3.3 17.0 + - - +
265A PHE* 1.3 84.3 - - - +
267A THR* 1.3 63.0 + - - +
269A CYS* 3.1 17.9 + - - +
270A ASP* 3.2 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 3.8 23.0 - - + +
258A VAL* 4.1 11.4 - - - +
263A TRP 2.9 14.4 + - - -
264A LYS* 3.5 9.6 - - - -
266A ASP* 1.3 79.1 - - - +
268A LEU* 1.3 60.8 + - - +
270A ASP* 3.4 12.6 + - + +
271A LEU* 3.1 29.4 + - + +
380A PHE* 3.5 27.6 - - + -
403A MET* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LYS 3.1 11.9 + - - +
265A PHE* 3.1 12.9 + - + +
267A THR* 1.3 76.7 - - - +
269A CYS* 1.3 57.3 + - - +
271A LEU* 3.5 3.9 + - - +
272A TYR* 2.9 26.3 + - - +
275A LEU* 4.3 3.9 - - + +
282A ILE* 3.8 20.2 - - + -
293A LEU* 4.0 28.9 - - + -
297A MET* 3.9 32.5 - - + -
332A ILE* 5.9 0.2 - - + -
350A ILE* 3.5 33.0 - - + -
352A TYR* 4.1 8.7 - - + -
380A PHE* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 3.6 34.1 - - - -
266A ASP* 3.1 10.4 + - - +
268A LEU* 1.3 75.2 - - - +
270A ASP* 1.3 68.8 + - - +
271A LEU 3.1 1.3 - - - -
272A TYR* 3.2 16.5 + - - +
273A ASP* 4.1 6.4 - - - +
297A MET* 4.9 4.3 - - - -
300A ALA* 5.6 0.4 - - - -
302A PHE* 3.3 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP* 3.2 14.0 + - - +
267A THR* 3.6 14.8 - - + +
269A CYS* 1.3 78.8 - - - +
271A LEU* 1.3 64.0 + - + +
273A ASP* 3.7 16.4 - - - +
274A THR* 5.1 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A THR* 3.1 23.3 + - + +
268A LEU* 3.7 4.9 - - - +
269A CYS 3.1 0.2 - - - -
270A ASP* 1.3 80.5 - - + +
272A TYR* 1.3 66.0 + - - +
273A ASP 3.1 2.9 - - - -
274A THR* 2.7 36.8 + - - +
275A LEU* 3.1 18.6 + - + -
348A LEU* 5.7 1.6 - - + -
350A ILE* 3.7 22.7 - - + -
378A ILE* 3.9 29.2 - - + -
380A PHE* 3.7 22.4 - - + -
403A MET* 3.9 17.7 - - + -
407A VAL* 4.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU 2.9 13.1 + - - +
269A CYS 3.2 15.2 + - - +
271A LEU* 1.3 75.2 - - - +
273A ASP* 1.3 70.7 + - - +
275A LEU* 3.2 28.3 + - + +
276A THR* 3.5 26.0 + - + +
297A MET* 4.0 11.9 - - + -
302A PHE* 3.4 40.6 - + + -
303A THR* 2.6 41.5 + - - -
304A VAL* 4.1 14.4 - - + -
330A VAL* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A CYS 4.1 4.6 - - - +
270A ASP* 3.7 15.2 - - - +
271A LEU 2.8 4.0 + - - -
272A TYR* 1.3 86.4 - - - +
274A THR* 1.3 62.8 + - + +
276A THR* 3.1 21.5 + - - -
277A ILE* 3.6 10.3 - - - +
302A PHE* 5.4 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASP 5.7 2.0 - - - +
271A LEU* 2.7 36.0 + - - +
273A ASP* 1.3 75.0 - - + +
275A LEU* 1.3 61.1 + - - +
276A THR 3.3 0.4 - - - -
277A ILE* 3.5 23.5 + - + +
278A THR 5.2 0.3 + - - -
348A LEU* 3.3 24.3 - - - +
405A MET 5.8 0.7 - - - +
407A VAL* 4.6 11.6 - - + +
408A ALA* 3.9 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.3 11.2 - - + +
271A LEU* 3.1 21.2 + - + +
272A TYR* 3.4 25.8 - - + +
273A ASP 3.2 0.6 - - - -
274A THR* 1.3 79.4 - - - +
276A THR* 1.3 57.6 + - - +
277A ILE 3.3 4.1 + - - -
278A THR* 4.0 1.7 + - - -
279A GLN* 3.8 14.7 + - - +
280A ALA* 3.6 27.8 - - + +
282A ILE* 3.9 26.9 - - + -
297A MET* 5.6 0.4 - - + -
330A VAL* 4.1 16.8 - - + +
348A LEU* 3.5 24.4 - - + +
350A ILE* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.6 32.6 + - + +
273A ASP* 3.1 14.5 + - - -
274A THR 3.3 0.6 - - - -
275A LEU* 1.3 75.4 - - - +
277A ILE* 1.3 61.3 + - - +
278A THR 3.2 3.5 + - - +
329A ARG* 3.6 38.5 + - + +
330A VAL* 3.4 28.5 - - + -
----------------------------------------------------------
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