Contacts of the helix formed by residues 247 - 275 (chain V) in PDB entry 4BOG
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 247 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245V ALA* 2.7 7.6 + - - -
246V GLY* 1.3 68.5 + - - -
248V LYS* 1.3 52.3 - - - +
249V MET* 2.4 51.2 + - + +
250V SER* 4.3 0.5 + - - -
251V LEU* 4.4 4.6 + - - +
318W SER 5.4 0.3 - - - +
320W HIS* 2.4 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238V VAL* 2.7 56.7 + - - +
241V LEU* 3.2 34.9 - - + +
242V PRO* 3.6 22.0 - - + -
245V ALA* 2.3 29.4 + - - +
246V GLY 2.5 5.3 + - - +
247V GLU* 1.3 66.8 - - - +
249V MET* 1.3 61.3 + - - +
250V SER 2.7 1.4 + - - -
251V LEU* 2.9 16.0 + - - -
252V SER* 2.5 69.9 + - - +
305V HIS* 3.9 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241U GLU* 4.5 23.6 - - + +
242U LYS* 5.7 3.4 - - + -
245U LEU* 3.6 3.6 - - + +
246V GLY 2.8 10.2 + - - +
247V GLU* 2.4 43.9 - - + +
248V LYS* 1.3 75.8 - - - +
250V SER* 1.3 99.3 + - - +
252V SER* 2.2 23.1 + - - -
253V ILE* 4.9 0.2 - - - +
305V HIS* 5.7 2.0 - - - -
312V HIS* 3.2 46.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242U LYS* 5.4 0.7 - - - -
244U THR* 6.4 0.9 - - - -
245U LEU* 3.0 42.8 - - - +
247V GLU 4.3 0.2 + - - -
248V LYS 2.7 0.4 + - - -
249V MET* 1.3 106.9 - - - +
251V LEU* 1.3 63.1 + - - +
252V SER 2.7 15.5 + - - -
253V ILE 2.7 13.7 + - - -
254V SER 3.3 1.9 + - - -
258W SER* 4.4 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241V LEU* 3.2 43.1 - - + -
245V ALA* 5.6 1.6 - - + -
247V GLU 4.7 4.0 - - - +
248V LYS* 3.5 18.1 - - - +
249V MET* 4.3 0.2 - - - -
250V SER* 1.3 82.9 + - - +
252V SER* 1.3 65.8 + - - +
254V SER* 2.7 29.6 + - - -
255V ALA* 3.1 8.6 + - + -
257W MET* 5.8 5.8 - - + -
258W SER* 4.5 16.1 + - - +
261W ILE* 3.1 46.4 - - + -
310W LEU* 5.6 3.1 - - + -
314W PHE* 5.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238V VAL* 4.6 1.0 - - - +
248V LYS* 2.5 55.2 + - - +
249V MET* 2.2 32.9 + - - -
250V SER 2.7 1.0 + - - -
251V LEU* 1.3 75.2 - - - +
253V ILE* 1.3 60.6 + - - +
255V ALA* 2.9 27.5 + - - +
256V LEU* 3.2 8.5 + - - +
302V LEU* 4.9 2.0 - - - +
305V HIS* 4.3 18.1 - - - -
312V HIS* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228U LEU* 5.4 1.3 - - + -
235U LEU* 5.2 8.5 - - + -
242U LYS* 4.4 10.5 - - + +
245U LEU* 3.2 46.9 - - + +
246U SER* 5.4 2.2 - - - -
248U SER* 3.3 22.0 - - - +
249U VAL* 5.0 13.7 - - + +
250V SER 2.7 7.1 + - - -
252V SER* 1.3 77.5 + - - +
254V SER* 1.3 61.8 + - - +
256V LEU* 3.2 4.0 + - + +
257V LEU* 2.9 26.8 + - + +
302V LEU* 3.2 50.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245U LEU* 5.5 2.9 - - - -
248U SER* 5.1 4.9 - - - -
250V SER 3.3 5.1 + - - -
251V LEU* 2.7 23.3 + - - -
253V ILE* 1.3 79.5 - - - +
255V ALA* 1.3 53.9 + - - +
257V LEU* 3.5 6.8 + - - +
258V ALA 3.0 13.9 + - - -
258W SER* 5.9 2.0 - - - -
261W ILE* 3.5 18.7 - - - +
262W CYS* 5.7 3.8 - - - -
265W LEU* 2.3 39.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234V LEU* 6.0 4.2 - - + +
238V VAL* 3.2 31.0 - - + -
251V LEU* 3.1 10.5 + - + +
252V SER* 2.9 17.2 + - - +
254V SER* 1.3 79.9 + - - +
256V LEU* 1.3 48.6 + - - +
258V ALA* 3.2 3.5 - - - +
259V LEU* 2.3 39.2 + - + +
261W ILE* 6.0 0.4 - - + -
265W LEU* 3.7 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238V VAL* 4.8 16.2 - - + -
239V PHE* 5.1 0.7 - - + -
252V SER 3.2 8.0 + - - +
253V ILE 3.2 6.5 + - - +
255V ALA* 1.3 77.7 - - - +
257V LEU* 1.3 61.1 + - + +
259V LEU* 3.7 20.0 - - + -
260V THR* 2.5 44.0 + - - +
298V SER* 2.8 58.8 - - - +
299V VAL* 4.2 2.7 - - + +
301V VAL* 4.8 1.3 - - + -
302V LEU* 3.3 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228U LEU* 5.1 2.0 - - + -
248U SER* 2.8 52.5 - - - +
249U VAL* 3.2 24.7 - - + -
252U SER* 2.5 32.5 - - - +
256U PHE* 3.7 6.7 - - + -
253V ILE* 2.9 19.8 + - + +
254V SER* 3.6 9.4 - - - +
256V LEU* 1.3 76.2 - - + +
258V ALA* 1.4 56.0 + - - +
260V THR* 4.7 2.7 - - - -
261V VAL* 2.8 37.0 + - - +
265W LEU* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234V LEU* 6.2 0.4 - - + -
254V SER 3.0 1.2 + - - -
255V ALA 3.2 1.3 - - - +
257V LEU* 1.4 80.5 - - - +
259V LEU* 1.3 61.6 + - - +
261V VAL* 4.7 1.3 - - - -
262V PHE* 2.5 50.8 + - + -
265W LEU* 2.6 57.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231V ILE* 3.2 34.3 - - + +
234V LEU* 4.9 11.4 - - + +
235V ALA* 4.3 19.5 - - + +
238V VAL* 5.4 2.5 - - + -
239V PHE* 5.1 0.4 - - + -
255V ALA 2.3 31.2 + - - +
256V LEU* 2.9 27.6 + - + +
258V ALA* 1.3 68.6 - - - +
260V THR* 1.3 62.8 + - - +
262V PHE* 3.6 8.5 - - - +
263V LEU* 3.1 44.3 + - + +
294V SER* 5.2 8.5 - - - +
295V VAL* 6.4 0.7 - - - -
298V SER* 4.9 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224U LEU* 5.7 11.2 - - + -
256U PHE* 3.3 25.8 - - + -
256V LEU* 2.5 34.5 + - - +
257V LEU* 3.9 1.1 - - - -
259V LEU* 1.3 72.3 - - - +
261V VAL* 1.3 65.8 + - - +
263V LEU* 3.3 5.3 + - + +
264V LEU* 2.9 41.8 + - + +
295V VAL* 6.0 8.2 - - + +
298V SER* 5.2 4.7 + - - -
299V VAL* 5.6 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255U VAL* 5.1 5.2 - - + -
256U PHE* 3.0 32.2 - - + -
259U VAL* 6.6 0.2 - - + -
257V LEU 2.8 19.3 + - - +
258V ALA* 3.7 1.8 - - - +
260V THR* 1.3 72.2 - - - +
262V PHE* 1.3 83.3 + - + +
264V LEU* 2.9 6.9 + - + +
265V LEU* 2.8 52.3 + - + +
269W VAL* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231V ILE* 4.7 20.4 - - + -
234V LEU* 4.9 11.9 - - + -
258V ALA* 2.5 43.7 - - + +
259V LEU* 3.6 7.6 - - - +
261V VAL* 1.3 91.4 - - + +
263V LEU* 1.3 58.9 + - - +
265V LEU* 3.3 13.1 + - - +
266V LEU* 3.0 31.2 + - + +
265W LEU 3.2 24.5 - - - -
268W ALA* 3.4 22.0 - - + -
269W VAL* 3.4 19.7 - - + -
272W LEU* 3.6 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228V CYS* 6.4 2.7 - - - -
231V ILE* 4.0 15.0 - - + -
259V LEU* 3.1 43.1 + - + +
260V THR* 3.3 5.4 + - + +
262V PHE* 1.3 77.4 - - + +
264V LEU* 1.3 64.5 + - + +
266V LEU* 3.3 25.8 - - + +
267V ALA* 2.9 22.7 + - - +
291V VAL* 3.3 38.4 - - + +
294V SER* 5.0 11.4 - - - -
295V VAL* 5.4 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221U PRO* 6.1 4.3 - - + -
224U LEU* 5.7 8.3 - - + -
256U PHE* 3.2 50.3 - - + -
260U ILE* 6.4 1.8 - - + -
260V THR* 2.9 29.4 + - + +
261V VAL* 2.9 5.4 + - + +
263V LEU* 1.3 76.5 - - + +
265V LEU* 1.3 62.9 + - - +
267V ALA* 2.8 30.9 + - + +
268V ASP* 2.9 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261V VAL* 2.8 35.4 + - + +
262V PHE* 3.5 17.7 - - + +
264V LEU* 1.3 76.5 - - - +
266V LEU* 1.3 55.8 + - - +
268V ASP* 2.7 45.6 + - + +
269V LYS* 3.0 7.0 + - - +
269W VAL* 4.7 7.9 - - + -
272W LEU* 3.5 33.9 - - + -
273W LEU* 4.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223V TYR* 5.9 2.5 - - + -
224V THR* 6.1 0.9 - - + -
227V PRO* 4.1 33.4 - - + -
231V ILE* 5.3 4.7 - - + -
262V PHE* 3.0 19.1 + - + +
263V LEU* 3.3 33.7 - - + +
265V LEU* 1.3 76.0 - - - +
267V ALA* 1.3 57.2 + - - +
269V LYS* 3.1 33.8 - - + +
270V VAL* 2.8 35.1 + - + +
276W GLN* 4.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217U ASN* 5.8 4.0 - - - +
263V LEU 2.9 11.4 + - - +
264V LEU* 2.8 28.9 + - + +
266V LEU* 1.3 76.0 - - - +
268V ASP* 1.3 50.2 + - - +
270V VAL* 4.1 5.3 - - - +
271V PRO* 2.5 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 268 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259U VAL* 4.8 11.6 - - - +
263U LEU* 3.0 36.4 - - - +
264V LEU* 2.9 9.5 + - - +
265V LEU* 2.7 35.4 + - + +
267V ALA* 1.3 76.4 - - - +
269V LYS* 1.3 56.9 + - - +
271V PRO* 2.9 20.0 - - - +
272V GLU* 3.9 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223V TYR* 5.2 11.0 + - - +
224V THR* 3.8 26.5 + - - +
265V LEU 3.0 4.8 + - - +
266V LEU* 3.1 41.1 - - + +
268V ASP* 1.3 76.0 - - - +
270V VAL* 1.3 95.2 + - + +
272V GLU* 3.5 3.7 + - - +
273V THR* 2.7 51.4 + - + +
276W GLN* 4.8 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266V LEU* 2.8 26.9 - - + +
267V ALA* 4.1 4.5 - - - +
269V LYS* 1.3 96.5 - - - +
271V PRO* 1.3 68.9 - - + +
273V THR* 2.8 18.1 + - - +
274V SER* 3.1 14.9 + - - -
284V LEU* 3.7 42.2 - - + -
287V ILE* 6.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 271 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213U TYR* 6.4 2.0 - - + -
267V ALA 2.5 31.6 - - - +
268V ASP* 2.9 16.6 - - - +
270V VAL* 1.3 88.3 - - + +
272V GLU* 1.3 56.7 + - + +
274V SER* 3.3 7.5 + - - +
275V LEU* 2.6 44.9 + - + +
284V LEU* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268V ASP 3.9 14.4 - - - +
269V LYS* 4.2 4.2 - - - +
270V VAL 3.3 0.2 - - - -
271V PRO* 1.3 84.8 - - + +
273V THR* 1.3 60.9 + - + +
275V LEU* 2.9 38.0 - - + +
276V SER* 4.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 273 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220V TYR* 6.3 3.8 - - + -
269V LYS* 2.7 40.8 + - + +
270V VAL* 2.8 17.8 + - - +
272V GLU* 1.3 77.9 - - + +
274V SER* 1.3 62.8 + - - +
275V LEU 3.0 1.9 + - - -
276V SER* 3.6 9.4 + - - -
277V VAL* 3.8 15.4 - - - +
283W LEU* 6.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270V VAL* 3.1 16.6 + - - -
271V PRO* 3.3 12.6 + - - +
273V THR* 1.3 73.4 + - - +
275V LEU* 1.3 54.5 + - - +
276V SER 2.5 19.4 + - - -
277V VAL* 2.8 3.5 + - - +
278V PRO* 2.6 51.8 - - - +
284V LEU* 5.5 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46V LYS* 2.2 44.6 + - - +
271V PRO* 2.6 35.9 + - + +
272V GLU* 2.9 41.1 - - + +
274V SER* 1.3 74.8 + - - +
276V SER* 1.3 54.4 + - - +
----------------------------------------------------------
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