Contacts of the helix formed by residues 260 - 286 (chain B) 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 SER 260 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PRO* 3.1 14.9 + - - -
259B ASP* 1.3 76.0 - - - +
261B ASP* 1.3 76.8 + - - +
262B ILE 4.3 1.3 - - - -
263B LYS* 3.5 7.6 + - - +
264B ALA* 3.3 19.4 + - - +
339B LEU* 4.6 14.9 - - - +
340B ALA* 5.0 0.5 - - - -
447B HIS* 3.4 25.9 - - - -
295D ALA* 5.9 4.9 - - - -
298D MET* 4.9 4.8 - - - +
299D SER* 6.1 0.9 - - - -
302D GLN* 5.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 1.3 81.5 - - - +
262B ILE* 1.3 78.2 + - + +
264B ALA* 3.4 4.2 - - - +
265B LEU* 3.2 28.2 + - + +
339B LEU* 3.5 24.3 + - - +
340B ALA* 4.0 13.5 - - - +
443B LYS* 5.0 11.6 + - - +
302D GLN* 3.7 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 3.3 1.2 + - - -
261B ASP* 1.3 87.4 + - + +
263B LYS* 1.3 55.1 + - - +
265B LEU* 3.8 12.1 - - + +
266B THR* 2.6 47.0 + - - +
443B LYS* 3.8 13.2 - - + +
444B VAL* 3.5 54.5 - - + +
447B HIS* 3.4 51.8 - - + +
448B LYS* 5.5 0.4 - - + -
302D GLN* 4.0 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 4.4 17.5 - - - +
254B ASP* 2.6 30.3 + - + +
255B PRO* 4.4 4.4 + - - +
257B VAL* 3.0 41.5 + - + -
258B PRO 3.8 10.3 - - - +
259B ASP* 3.6 21.2 + - - -
260B SER* 3.5 24.5 + - - +
261B ASP 3.4 0.4 - - - -
262B ILE* 1.3 73.4 - - - +
264B ALA* 1.3 69.7 + - - +
266B THR* 2.9 8.7 + - - -
267B THR* 2.7 32.6 + - - +
330B TYR* 5.2 5.4 - - - +
447B HIS* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER 3.3 8.3 + - - +
261B ASP 3.4 5.2 - - - +
263B LYS* 1.3 81.8 - - - +
265B LEU* 1.3 58.9 + - - +
267B THR* 3.0 2.4 + - - -
268B LEU* 3.0 35.6 + - + +
330B TYR* 3.2 23.3 - - - +
332B MET* 4.6 5.4 - - + -
339B LEU* 6.4 0.2 - - + -
340B ALA* 3.3 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ASP* 3.2 18.9 + - + +
262B ILE* 3.8 23.3 - - + +
263B LYS 3.1 0.6 - - - -
264B ALA* 1.3 76.4 - - + +
266B THR* 1.3 68.4 + - - +
268B LEU* 3.3 5.5 + - + +
269B CYS* 3.0 26.4 + - - +
340B ALA 4.2 13.7 - - - +
342B LEU* 4.1 21.3 - - + -
434B HIS* 5.4 0.9 - - - +
438B ILE* 4.0 33.2 - - + -
444B VAL* 4.5 11.2 - - + -
501B OHT 4.1 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 2.6 40.9 + - - +
263B LYS* 3.3 7.5 - - - -
265B LEU* 1.3 75.2 - - - +
267B THR* 1.3 65.8 + - - +
269B CYS* 3.3 4.9 + - - +
270B ASP* 3.2 23.1 + - + +
444B VAL* 4.5 9.0 - - - +
447B HIS* 5.4 1.4 + - - -
448B LYS* 4.7 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA* 4.0 34.4 - - + +
252B MET 5.0 0.4 - - - +
253B PRO* 4.0 23.6 - - + +
254B ASP 5.5 0.5 + - - -
263B LYS* 2.7 34.1 + - - +
264B ALA* 3.4 7.4 + - - -
266B THR* 1.3 77.5 - - - +
268B LEU* 1.3 57.5 + - - +
270B ASP* 3.6 5.5 + - - +
271B LEU* 3.2 26.2 + - - +
330B TYR* 4.2 17.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA* 3.0 20.9 + - + +
265B LEU* 3.3 7.1 + - - +
267B THR* 1.3 75.0 - - - +
269B CYS* 1.3 60.4 + - - +
271B LEU* 3.5 10.2 - - + +
272B ALA* 2.8 30.5 + - - +
326B TYR* 3.9 33.0 - - + -
330B TYR* 3.7 23.8 - - + -
332B MET* 4.3 11.0 - - - -
342B LEU* 3.8 29.4 - - + -
501B OHT 3.6 33.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU 3.0 17.0 + - - +
266B THR* 3.8 5.2 - - - +
268B LEU* 1.3 76.8 - - - +
270B ASP* 1.3 57.8 + - - +
272B ALA* 3.5 1.4 + - - +
273B ASP* 3.0 44.5 + - - +
435B PHE* 4.8 9.4 - - + -
439B LYS* 5.8 4.3 - - - -
501B OHT 3.9 40.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA 4.6 4.0 - - - +
252B MET 5.7 0.3 - - - +
266B THR* 3.2 15.7 + - + +
267B THR* 3.9 6.5 - - - +
269B CYS* 1.3 77.9 - - - +
271B LEU* 1.3 66.4 + - - +
273B ASP* 3.2 9.4 + - - +
274B ARG* 3.0 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ILE* 3.8 24.5 - - + +
250B TYR 4.3 9.0 - - - +
251B ALA* 4.1 22.9 - - + -
267B THR 3.2 15.4 + - - +
268B LEU* 3.5 11.9 - - + +
270B ASP* 1.3 77.8 - - - +
272B ALA* 1.3 63.8 + - - +
274B ARG* 3.0 13.3 + - - +
275B GLU* 2.8 53.8 + - + +
326B TYR* 3.8 34.5 - - + +
327B ALA* 4.6 0.4 - - + -
501B OHT 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU 2.8 22.1 + - - +
269B CYS 3.7 2.5 - - - +
271B LEU* 1.3 71.6 - - - +
273B ASP* 1.3 56.5 + - - +
275B GLU* 3.0 4.7 + - - +
276B LEU* 2.7 38.2 + - + +
305B TRP* 5.6 0.2 - - + -
309B LEU* 3.9 10.3 - - + +
501B OHT 3.4 52.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B CYS* 3.0 31.7 + - - +
270B ASP* 3.2 9.9 + - - +
272B ALA* 1.3 78.3 - - - +
274B ARG* 1.3 62.6 + - + +
276B LEU* 3.6 8.6 - - - +
277B VAL* 3.5 23.0 + - - +
501B OHT 2.8 38.3 + - - -
1323H ILE* 4.3 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ILE* 3.4 28.2 - - + +
250B TYR 3.0 29.1 + - - +
251B ALA* 3.3 17.0 + - - +
252B MET* 3.3 27.6 - - - +
270B ASP* 3.0 38.5 + - - +
271B LEU* 3.0 16.3 + - - +
273B ASP* 1.3 74.6 - - + +
275B GLU* 1.3 65.0 + - - +
277B VAL* 3.4 9.8 + - - +
278B VAL* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ILE* 4.3 17.8 - - + +
271B LEU* 2.8 44.9 + - + +
272B ALA 3.7 2.7 - - - +
274B ARG* 1.3 72.3 - - - +
276B LEU* 1.3 56.6 + - - +
278B VAL* 3.1 12.0 + - + +
279B ILE* 2.6 42.5 + - + +
309B LEU* 3.6 22.0 - - + +
316B ARG* 3.9 21.8 + - - -
326B TYR 5.2 0.4 - - - -
501B OHT 3.0 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA 2.7 21.2 + - - +
273B ASP* 3.6 8.5 - - - +
275B GLU* 1.3 71.1 - - - +
277B VAL* 1.3 57.7 + - - +
279B ILE* 3.0 15.5 + - + +
280B ILE* 2.8 52.4 + - + +
301B LEU* 6.1 2.0 - - + -
305B TRP* 4.1 34.8 - - + -
309B LEU* 4.6 4.0 - - + +
501B OHT 3.9 22.4 - - - -
1320H LEU* 3.8 23.1 - - + -
1323H ILE* 4.4 16.2 - - + -
1324H ILE* 4.5 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP 3.5 13.7 + - - +
274B ARG* 3.4 11.3 + - - +
275B GLU 3.2 0.6 - - - -
276B LEU* 1.3 78.6 - - - +
278B VAL* 1.3 67.6 + - + +
280B ILE* 3.2 13.2 + - + +
281B GLY* 3.1 18.0 + - - -
1323H ILE* 4.6 15.7 - - + -
1327H ALA* 5.1 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO* 4.3 24.5 - - + +
249B ILE* 3.5 33.9 - - + -
274B ARG 3.4 6.0 + - - +
275B GLU* 3.1 19.6 + - + +
277B VAL* 1.3 79.1 - - + +
279B ILE* 1.3 63.2 + - + +
281B GLY* 3.9 2.0 - - - +
282B TRP* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO* 5.8 0.9 - - + -
275B GLU* 2.6 27.0 + - + +
276B LEU* 3.4 13.0 - - + +
278B VAL* 1.3 75.5 - - + +
280B ILE* 1.3 58.0 + - + +
282B TRP* 3.2 14.3 + - + +
283B ALA* 3.0 24.9 + - - +
301B LEU* 4.6 10.5 - - + -
305B TRP* 4.6 5.8 - - + +
308B ILE* 3.6 51.4 - - + -
309B LEU* 3.5 36.3 - - + +
370B LYS* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 2.8 47.6 + - + +
277B VAL* 3.2 9.2 + - - +
279B ILE* 1.3 71.4 - - - +
281B GLY* 1.3 64.5 + - - +
282B TRP 3.4 0.2 + - - -
283B ALA* 3.4 10.9 + - - +
284B LYS* 3.7 14.0 + - - +
301B LEU* 4.3 23.5 - - + +
1323H ILE* 4.3 8.1 - - + -
1324H ILE* 3.8 20.4 - - + +
1327H ALA* 3.5 35.9 - - + -
1328H LEU* 3.9 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL 3.1 13.3 + - - -
278B VAL* 3.9 3.1 - - - -
279B ILE 3.4 0.2 - - - -
280B ILE* 1.3 74.1 - - - +
282B TRP* 1.3 64.7 + - - +
284B LYS* 3.3 27.8 + - - +
285B HIS* 3.7 11.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.9 10.6 + - + +
244B ALA* 3.7 36.3 - - + +
245B GLU* 4.7 2.8 + - - +
246B PRO* 3.8 19.9 - - + +
278B VAL 2.8 20.1 + - - +
279B ILE* 3.4 25.1 - - + +
280B ILE 3.2 0.4 - - - -
281B GLY* 1.3 77.9 - - - +
283B ALA* 1.3 69.8 + - + +
285B HIS* 3.1 21.8 + - - +
286B ILE* 3.4 32.4 + - + -
308B ILE* 4.0 25.1 - - + -
367B VAL* 4.3 6.5 - - - +
370B LYS* 3.7 54.9 - - + +
371B ALA* 4.1 5.6 - - + -
374B LEU* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE 3.0 16.9 + - - +
280B ILE 3.4 6.5 + - - +
281B GLY 3.2 0.6 - - - -
282B TRP* 1.3 84.9 - - + +
284B LYS* 1.3 57.1 + - - +
286B ILE* 2.8 31.9 + - - +
289B PHE* 3.5 25.8 - - + +
301B LEU* 4.4 7.2 - - + -
374B LEU* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.7 10.7 + - - +
281B GLY* 3.3 19.2 + - - +
282B TRP 3.1 0.8 - - - -
283B ALA* 1.3 77.8 - - - +
285B HIS* 1.3 64.6 + - + +
286B ILE 3.4 6.8 + - - +
289B PHE* 4.1 7.8 - - + -
290B SER* 3.1 29.3 + - - +
297B GLN* 5.2 2.5 - - - +
1327H ALA 5.3 0.2 - - - -
1328H LEU* 4.1 39.8 + - + +
1330H GLY 3.6 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B HIS* 2.9 45.7 + - - +
241B LEU* 5.2 0.7 - - - -
243B VAL* 6.2 1.6 - - + +
244B ALA* 3.8 27.7 - - + +
281B GLY 3.7 16.8 - - - -
282B TRP* 3.1 12.6 + - - +
284B LYS* 1.3 77.7 - - + +
286B ILE* 1.3 64.9 + - + +
287B PRO* 3.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.2 12.8 - - + -
282B TRP* 3.4 47.6 - - + +
283B ALA* 2.8 22.9 + - - +
284B LYS 3.6 5.9 - - - +
285B HIS* 1.3 75.9 - - - +
287B PRO* 1.3 74.8 - - + +
288B GLY 3.3 0.5 + - - -
289B PHE* 3.2 22.1 + - + +
290B SER 4.3 0.7 + - - -
371B ALA* 4.1 9.9 - - + +
374B LEU* 3.8 15.3 - - + -
391B LEU* 3.9 25.6 - - + -
395B LEU* 4.1 14.8 - - + -
----------------------------------------------------------
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