Contacts of the helix formed by residues 260 - 285 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PRO 3.3 5.2 + - - -
259A ASP* 1.3 77.0 - - - +
261A ASP* 1.3 73.6 + - - +
262A ILE 3.3 0.3 + - - -
263A LYS* 3.4 12.3 + - - +
264A ALA* 3.2 19.6 + - - +
339A LEU* 4.0 20.3 - - - +
447A HIS* 3.0 31.7 + - - -
298E MET* 4.0 12.3 - - - -
302E GLN* 5.9 1.8 - - - -
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Residues in contact with ASP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A SER* 1.3 75.4 - - - +
262A ILE* 1.3 93.2 + - - +
264A ALA* 3.2 6.2 + - - +
265A LEU* 3.0 29.6 + - + +
339A LEU* 3.3 26.5 + - - +
340A ALA* 3.9 15.6 - - - +
443A LYS* 5.0 9.7 + - - +
302E GLN* 3.8 25.9 + - - +
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Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A SER* 3.2 1.2 + - - -
261A ASP* 1.3 100.2 + - - +
263A LYS* 1.3 56.5 + - - +
265A LEU* 3.1 12.4 + - + -
266A THR* 2.6 51.8 + - - +
443A LYS* 4.5 7.4 - - + +
444A VAL* 3.9 49.6 - - + +
447A HIS* 3.3 48.7 - - + +
448A LYS* 4.6 3.6 - - + -
302E GLN* 4.4 2.7 - - - +
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PRO* 4.0 22.2 - - - +
254A ASP* 2.5 35.6 + - - +
255A PRO* 4.2 5.5 + - - +
257A VAL* 3.1 40.9 + - + +
258A PRO 3.9 5.6 - - - +
259A ASP* 4.3 17.2 + - - +
260A SER* 3.4 23.4 + - - +
262A ILE* 1.3 78.7 - - - +
264A ALA* 1.3 56.4 + - - +
266A THR* 3.5 5.9 - - - -
267A THR* 2.7 46.2 + - - +
330A TYR* 5.2 4.5 - - + +
447A HIS* 4.6 2.1 - - - -
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER 3.2 7.8 + - - +
261A ASP 3.2 4.1 + - - +
263A LYS* 1.3 79.0 - - - +
265A LEU* 1.3 65.5 + - - +
267A THR* 3.5 2.1 + - - -
268A LEU* 3.2 28.3 + - + +
330A TYR* 3.3 21.3 + - - +
332A MET* 4.7 8.7 - - + -
336A GLN 5.1 1.3 - - - +
340A ALA* 3.4 32.1 - - + -
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASP* 3.0 26.6 + - + +
262A ILE* 3.6 21.5 - - + +
264A ALA* 1.3 73.6 - - + +
266A THR* 1.3 68.9 + - - +
268A LEU* 2.7 18.6 + - - +
269A CYS* 2.9 23.3 + - - -
340A ALA* 4.2 13.0 - - + +
342A LEU* 4.2 17.3 - - + -
434A HIS* 5.3 0.7 - - + +
438A ILE* 3.8 28.5 - - + -
444A VAL* 5.2 6.5 - - + -
500A OHT 3.8 30.5 - - + -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ILE* 2.6 39.5 + - - +
263A LYS* 3.5 6.7 - - - +
265A LEU* 1.3 72.2 - - - +
267A THR* 1.3 64.0 + - - +
269A CYS* 3.4 9.4 + - - +
270A ASP* 3.2 23.5 + - + +
444A VAL* 5.0 2.8 - - - +
448A LYS* 3.6 27.9 - - - +
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Residues in contact with THR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ALA* 4.2 23.3 - - + +
253A PRO* 4.4 21.4 - - + +
254A ASP 5.1 0.7 + - - -
263A LYS* 2.7 38.0 + - - +
264A ALA 3.8 4.5 - - - -
265A LEU 2.8 0.4 + - - -
266A THR* 1.3 75.9 - - - +
268A LEU* 1.3 61.0 + - - +
270A ASP* 3.9 3.0 + - - +
271A LEU* 3.3 21.3 + - - +
330A TYR* 3.9 31.5 + - + -
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ALA 3.2 16.0 + - - +
265A LEU* 2.7 14.2 + - - +
267A THR* 1.3 70.3 - - - +
269A CYS* 1.3 54.8 + - - +
271A LEU* 3.5 5.4 - - + +
272A ALA* 2.7 36.9 + - - +
326A TYR* 3.5 42.0 - - + -
330A TYR* 4.1 12.8 - - + -
332A MET* 4.2 15.3 - - - -
342A LEU* 3.8 29.2 - - + -
500A OHT 3.6 39.1 - - + -
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Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU* 2.9 32.2 + - - -
266A THR* 3.7 9.4 - - - +
268A LEU* 1.3 77.0 - - - +
270A ASP* 1.3 62.2 + - - +
272A ALA* 3.3 1.0 + - - +
273A ASP* 3.0 33.9 + - - +
435A PHE* 4.4 13.7 - - + -
438A ILE* 6.6 0.4 - - - -
500A OHT 3.8 27.1 - - + +
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Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ALA 6.0 0.2 - - - +
266A THR* 3.2 12.9 + - + +
267A THR* 4.5 3.1 - - - +
269A CYS* 1.3 79.2 - - - +
271A LEU* 1.3 63.7 + - - +
273A ASP* 3.3 10.9 + - - +
274A ARG* 3.2 44.9 + - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 3.9 29.8 - - + +
250A TYR 4.2 12.8 - - - +
251A ALA* 4.3 16.6 - - + -
267A THR 3.3 17.4 + - - +
268A LEU* 3.3 9.6 + - + +
269A CYS 3.2 0.2 - - - -
270A ASP* 1.3 74.7 - - - +
272A ALA* 1.3 68.2 + - - +
273A ASP 3.0 0.5 + - - -
274A ARG* 3.1 12.1 + - - +
275A GLU* 2.9 49.4 + - - +
326A TYR* 3.5 37.5 - - + +
327A ALA* 4.4 0.7 - - + -
500A OHT 4.1 8.1 - - + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU 2.7 21.8 + - - +
269A CYS 3.5 4.5 - - - +
271A LEU* 1.3 73.3 - - - +
273A ASP* 1.3 59.0 + - - +
275A GLU* 3.1 1.7 + - - +
276A LEU* 2.8 34.1 + - - +
309A LEU* 4.0 13.1 - - + +
500A OHT 3.5 52.7 - - + -
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A CYS* 3.0 23.3 + - - +
270A ASP* 3.7 11.5 - - - +
271A LEU 3.1 0.4 - - - -
272A ALA* 1.3 76.2 - - - +
274A ARG* 1.3 61.8 + - - +
276A LEU* 3.6 8.6 + - - +
277A VAL* 3.4 24.1 + - - +
500A OHT 2.6 44.0 + - - +
1323G ILE* 4.4 13.0 - - + +
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 3.5 25.8 - - + +
250A TYR 2.9 21.2 + - - +
251A ALA 3.3 23.8 + - - -
252A MET* 4.9 11.1 - - - +
270A ASP* 3.2 40.6 + - - +
271A LEU* 3.1 14.6 + - - +
273A ASP* 1.3 75.0 - - + +
275A GLU* 1.3 66.4 + - - +
277A VAL* 3.2 16.8 + - - +
278A VAL* 3.3 16.6 + - - +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 3.6 23.0 - - + +
271A LEU* 2.9 40.6 + - + +
272A ALA 3.5 3.6 - - - +
274A ARG* 1.3 73.6 - - - +
276A LEU* 1.3 53.5 + - - +
278A VAL* 3.1 10.8 - - + +
279A ILE* 2.7 41.6 + - + +
309A LEU* 3.3 26.0 - - + +
312A GLY* 5.6 0.2 - - - -
316A ARG* 3.6 21.2 + - - -
326A TYR 4.3 0.5 - - - +
500A OHT 2.8 30.0 + - - -
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ALA 2.8 22.2 + - - +
273A ASP* 3.7 6.5 - - - +
275A GLU* 1.3 71.6 - - - +
277A VAL* 1.3 58.6 + - - +
279A ILE* 3.0 14.4 + - + +
280A ILE* 2.8 42.4 + - + +
301A LEU* 6.6 0.2 - - + -
305A TRP* 3.8 37.9 - - + -
309A LEU* 4.2 9.6 - - + -
500A OHT 3.4 33.7 - - - -
1320G LEU* 4.0 17.5 - - + -
1323G ILE* 4.3 20.4 - - + -
1324G ILE* 5.9 3.1 - - + -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP 3.4 12.2 + - - +
274A ARG* 3.2 11.3 + - - +
275A GLU 3.2 1.0 - - - -
276A LEU* 1.3 78.3 - - - +
278A VAL* 1.3 67.1 + - + +
280A ILE* 3.6 9.5 + - - +
281A GLY* 3.2 17.0 + - - -
1323G ILE* 3.9 19.1 - - + -
1327G ALA* 4.7 13.1 - - + +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO* 4.4 24.3 - - + +
249A ILE* 3.3 32.8 - - + -
274A ARG 3.3 6.9 + - - +
275A GLU* 3.1 18.4 - - + +
277A VAL* 1.3 79.5 - - + +
279A ILE* 1.3 58.4 + - + +
280A ILE 3.1 1.8 - - - -
281A GLY* 3.2 2.9 + - - +
282A TRP* 2.7 36.1 + - - +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO* 5.7 0.9 - - - -
275A GLU* 2.7 26.7 + - + +
276A LEU* 3.0 17.4 + - + +
278A VAL* 1.3 74.3 - - + +
280A ILE* 1.3 59.2 + - + +
282A TRP* 3.2 15.0 - - + +
283A ALA* 2.8 24.1 + - - +
301A LEU* 4.2 13.7 - - + -
305A TRP* 4.5 3.1 - - - +
308A ILE* 3.9 46.7 - - + +
309A LEU* 3.8 39.3 - - + +
370A LYS* 6.1 1.8 - - - +
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 2.8 28.3 + - + +
277A VAL 3.7 4.0 - - - +
279A ILE* 1.3 75.0 - - + +
281A GLY* 1.3 67.6 + - - +
283A ALA* 2.9 22.6 + - - +
284A LYS* 3.4 10.0 + - - +
301A LEU* 3.9 23.3 - - + -
1323G ILE* 4.0 5.6 - - + +
1324G ILE* 3.4 40.6 - - + +
1327G ALA* 3.7 31.6 - - + +
1328G LEU* 4.1 26.2 - - + +
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL 3.2 9.6 + - - -
278A VAL* 3.2 7.5 + - - -
280A ILE* 1.3 79.9 - - - +
282A TRP* 1.3 61.4 + - - +
284A LYS* 3.5 20.5 + - - +
285A HIS* 3.4 18.6 + - - -
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Residues in contact with TRP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 4.6 17.3 + - + +
244A ALA* 3.7 29.7 - - + +
245A GLU* 4.7 2.2 + - - -
246A PRO* 4.0 22.4 - - + +
278A VAL 2.7 16.4 + - - +
279A ILE* 3.2 34.1 - - + +
281A GLY* 1.3 70.5 - - - +
283A ALA* 1.3 74.7 + - + +
285A HIS* 2.8 27.8 + - - +
286A ILE* 3.5 33.9 + - + +
308A ILE* 4.2 20.9 - - + -
367A VAL* 4.2 7.4 - - - +
370A LYS* 3.8 39.7 - - + +
371A ALA* 3.7 22.2 - - + -
374A LEU* 4.1 10.5 - - + -
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ILE 2.8 16.0 + - - +
280A ILE* 2.9 15.0 + - - +
282A TRP* 1.3 81.4 - - + +
284A LYS* 1.3 57.3 + - - +
286A ILE* 2.8 33.3 + - - +
289A PHE* 3.5 36.3 - - + +
301A LEU* 4.3 8.3 - - + -
374A LEU* 4.2 11.7 - - + -
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.4 12.3 + - - +
281A GLY* 3.6 14.8 - - - +
282A TRP 3.0 0.8 + - - -
283A ALA* 1.3 76.5 - - - +
285A HIS* 1.3 63.7 + - + +
286A ILE 3.3 7.5 + - - +
289A PHE* 4.1 6.7 - - + -
290A SER* 3.3 29.8 + - - +
297A GLN* 5.4 2.2 - - - +
1327G ALA 4.3 9.2 - - - -
1328G LEU* 3.3 46.2 + - + -
1329G MET 5.2 0.6 + - - -
1330G GLY 4.3 9.3 + - - -
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Residues in contact with HIS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS* 2.9 38.4 + - - +
241A LEU* 5.4 1.3 - - + -
244A ALA* 3.8 32.7 - - + +
281A GLY 3.4 24.0 + - - -
282A TRP* 2.8 15.2 + - + +
284A LYS* 1.3 78.4 - - + +
286A ILE* 1.3 62.0 + - - +
287A PRO* 3.5 1.6 - - - +
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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