Contacts of the helix formed by residues 271 - 297 (chain B) in PDB entry 6GR2
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 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 1.3 77.6 - - - +
272B LYS* 1.3 54.0 + - - +
273B GLU* 3.9 5.9 + - - +
274B GLY* 3.0 22.2 + - - -
275B PHE* 2.7 34.4 + - - +
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Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ARG* 6.6 0.2 - - + -
271B SER* 1.3 72.3 - - - +
273B GLU* 1.3 63.9 + - - +
275B PHE* 3.1 9.6 + - - +
276B ARG* 3.0 32.9 + - + +
370C GLU* 5.7 4.0 + - - -
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 5.5 1.7 - - - +
239B ARG* 5.4 0.9 + - - -
242B GLN* 3.1 28.8 + - - +
271B SER* 3.3 5.6 + - - +
272B LYS* 1.3 77.8 - - - +
274B GLY* 1.3 63.4 + - - +
275B PHE 3.3 0.3 + - - -
276B ARG* 3.3 23.7 + - - +
277B ARG* 3.1 53.1 + - - +
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLN* 4.5 8.0 + - - -
246B VAL* 3.4 30.4 - - - +
270B VAL* 4.4 0.9 - - - -
271B SER* 3.0 21.2 + - - -
273B GLU* 1.3 78.0 - - - +
275B PHE* 1.3 60.9 + - - +
277B ARG* 3.5 8.4 + - - +
278B ALA* 3.2 18.0 + - - +
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Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 6.1 0.2 - - + -
263B LEU* 3.3 48.9 - - + -
264B GLU* 4.1 13.5 - - + -
267B ARG* 3.6 56.1 - - + -
270B VAL* 3.7 16.5 - - + +
271B SER 2.7 19.7 + - - +
272B LYS* 3.1 9.6 + - - +
274B GLY* 1.3 71.8 - - - +
276B ARG* 1.3 68.9 + - + +
278B ALA* 3.3 6.3 + - - +
279B ARG* 2.9 52.0 + - - +
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LYS* 3.0 21.7 + - + +
273B GLU* 3.9 23.7 + - - +
275B PHE* 1.3 80.4 - - + +
277B ARG* 1.3 97.1 + - - +
279B ARG* 3.2 23.4 + - - +
280B HIS 3.2 8.8 + - - -
316B ASP 3.5 14.7 + - - -
317B ASP* 3.2 43.7 + - - +
319B GLU* 3.8 18.9 + - - -
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ARG* 3.2 48.2 - - - +
242B GLN* 3.4 27.1 + - + +
243B CYS* 4.8 9.4 - - - +
246B VAL* 5.7 0.9 - - + -
273B GLU* 3.1 45.4 + - - +
274B GLY* 3.7 6.7 - - - +
276B ARG* 1.3 102.0 - - - +
278B ALA* 1.3 62.2 + - - +
280B HIS* 3.2 12.0 + - - +
281B VAL* 3.3 16.4 + - - +
317B ASP 2.7 31.2 + - - -
318B TYR* 3.6 24.6 + - + +
319B GLU* 3.8 15.8 + - - -
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 3.7 24.8 - - + +
255B LEU* 3.8 24.0 - - + +
263B LEU* 3.7 17.7 - - + -
274B GLY 3.2 15.0 + - - +
275B PHE* 3.3 4.2 + - - +
277B ARG* 1.3 79.1 - - - +
279B ARG* 1.3 63.2 + - - +
281B VAL* 3.3 0.9 + - - +
282B VAL* 3.0 29.2 + - + +
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 4.2 23.1 - - + +
263B LEU* 3.5 12.7 - - + +
267B ARG* 4.4 11.3 - - - +
275B PHE* 2.9 44.0 + - + +
276B ARG* 3.2 18.3 + - - +
278B ALA* 1.3 77.9 - - - +
280B HIS* 1.3 62.1 + - - +
282B VAL* 4.3 1.8 - - - +
283B GLY* 3.1 20.3 + - - -
317B ASP* 2.8 36.4 + - - +
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Residues in contact with HIS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU 3.0 24.2 + - - -
44B HIS* 4.2 1.1 - - + +
276B ARG 3.2 2.8 + - - -
277B ARG 3.2 8.3 + - - +
279B ARG* 1.3 76.7 - - - +
281B VAL* 1.3 63.0 + - + +
283B GLY* 3.0 1.6 + - - -
284B GLU* 2.6 59.7 + - + +
287B ARG* 3.7 1.2 + - - +
313B SER* 2.5 39.9 + - - +
314B LEU* 3.2 32.9 - - + +
317B ASP* 4.1 14.1 + - + -
318B TYR* 3.5 33.4 - + + -
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS 3.9 8.5 - - - +
45B THR* 4.5 3.1 - - + -
48B ASN* 3.3 46.0 - - + +
243B CYS* 3.9 1.1 - - - -
255B LEU* 3.7 28.0 - - + -
277B ARG 3.3 13.1 + - - +
278B ALA 3.3 1.1 + - - +
280B HIS* 1.3 79.5 - - + +
282B VAL* 1.3 65.8 + - - +
284B GLU* 3.1 3.6 + - - +
285B ILE* 2.9 41.5 + - + +
318B TYR* 3.8 17.5 - - + -
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 3.7 20.4 - - + +
258B VAL* 3.4 40.8 - - + +
259B GLN* 3.9 1.3 - - - -
260B LEU* 3.4 33.0 - - + +
263B LEU* 4.8 6.3 - - + -
278B ALA 3.0 19.1 + - - +
279B ARG* 4.3 3.8 - - - +
281B VAL* 1.3 75.5 - - - +
283B GLY* 1.3 60.9 + - - +
285B ILE* 3.6 9.0 + - - +
286B ARG* 3.3 27.5 + - + +
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 6.0 3.8 - - - +
279B ARG 3.1 13.3 + - - -
280B HIS 3.0 5.8 + - - -
282B VAL* 1.3 77.8 - - - +
284B GLU* 1.3 59.2 + - - +
286B ARG* 3.4 6.4 + - - +
287B ARG* 2.9 47.8 + - - +
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.4 2.2 - - - -
42B GLY* 2.8 15.3 + - - -
43B GLU* 2.8 36.3 + - - +
45B THR* 3.5 19.5 - - + -
280B HIS* 2.6 33.1 + - + +
283B GLY* 1.3 69.0 - - - +
285B ILE* 1.3 61.2 + - - +
287B ARG* 2.9 32.4 + - - +
288B THR* 2.8 35.4 + - - -
310B SER* 2.6 29.4 + - - -
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 3.9 11.2 - - + -
48B ASN 4.7 1.1 - - - +
50B GLY* 3.7 27.4 - - - +
51B LEU* 3.9 19.6 - - + +
255B LEU 4.6 2.5 - - - +
256B ARG* 4.1 39.9 - - - +
281B VAL* 2.9 36.5 + - + +
282B VAL* 3.8 6.5 - - - +
284B GLU* 1.3 77.1 - - - +
286B ARG* 1.3 65.5 + - + +
288B THR* 3.4 5.8 + - - -
289B ALA* 3.2 22.0 + - - +
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLN* 5.5 5.7 + - - +
260B LEU* 4.6 31.3 - - - +
261B GLU* 4.6 11.3 + - - -
282B VAL* 3.3 17.1 + - + +
283B GLY* 3.7 9.0 - - - +
284B GLU 3.3 0.4 - - - -
285B ILE* 1.3 79.4 - - + +
287B ARG* 1.3 66.6 + - + +
288B THR 3.4 0.2 + - - -
289B ALA* 3.4 6.4 + - - +
290B GLN* 3.0 46.8 + - - +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.1 12.1 - - + -
280B HIS* 3.7 1.8 + - - +
283B GLY* 2.9 28.7 + - - +
284B GLU* 2.9 48.5 + - - +
286B ARG* 1.3 76.3 - - + +
288B THR* 1.3 53.2 + - - +
290B GLN* 3.1 12.4 + - - +
291B ALA* 2.7 36.7 + - - +
306B LEU* 3.8 26.6 - - + +
309B GLU* 3.6 37.0 + - - +
310B SER* 3.7 6.3 - - - +
313B SER* 3.3 35.0 + - - -
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Residues in contact with THR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.1 21.9 - - + +
42B GLY* 3.1 25.5 + - - -
51B LEU* 3.6 36.2 + - + -
52B VAL 4.0 11.9 - - - +
53B LEU* 4.4 1.3 - - + -
200B LEU* 4.3 8.1 - - + -
284B GLU* 2.8 27.4 + - - +
285B ILE 3.7 4.7 - - - -
286B ARG 3.3 0.2 - - - -
287B ARG* 1.3 72.9 - - - +
289B ALA* 1.3 62.5 + - - +
291B ALA* 3.1 2.3 + - - +
292B ALA* 3.0 23.7 + - - +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.7 23.9 - - + +
200B LEU* 5.6 1.8 - - - -
285B ILE 3.2 10.3 + - - +
286B ARG* 3.8 5.4 - - - +
288B THR* 1.3 80.1 - - - +
290B GLN* 1.3 62.8 + - + +
292B ALA* 3.7 6.9 + - - +
293B ALA* 3.4 19.1 + - - +
296B ARG* 5.4 0.9 + - - -
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ARG* 3.0 41.8 + - - +
287B ARG* 3.4 12.7 - - - +
289B ALA* 1.3 75.5 - - + +
291B ALA* 1.3 64.0 + - - +
293B ALA* 3.3 8.4 + - - +
294B ALA* 3.1 21.3 + - - +
297B ARG* 5.2 1.4 + - - -
306B LEU* 3.6 28.6 - - + +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 3.8 26.9 - - + -
53B LEU* 4.7 0.2 - - + -
287B ARG 2.7 19.5 + - - +
288B THR 3.1 4.2 + - - +
290B GLN* 1.3 71.4 - - - +
292B ALA* 1.3 65.2 + - - +
294B ALA* 3.3 2.1 + - - +
295B LEU 3.0 10.6 + - - -
303B PHE* 3.0 44.3 - - + -
306B LEU* 3.5 14.1 - - + +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.3 16.4 - - + +
200B LEU* 4.0 33.2 - - + -
211B VAL* 4.9 3.8 - - + +
288B THR 3.0 15.1 + - - +
289B ALA* 3.9 6.1 - - - +
291B ALA* 1.3 78.3 - - - +
293B ALA* 1.3 61.3 - - - +
295B LEU* 3.1 7.5 + - - +
296B ARG* 3.1 38.3 + - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ALA 3.4 10.4 + - - +
290B GLN* 3.3 11.1 + - - +
291B ALA 3.2 0.6 - - - -
292B ALA* 1.3 79.6 - - - +
294B ALA* 1.3 61.1 + - - +
296B ARG* 3.3 25.4 + - - +
297B ARG* 3.4 30.0 + - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN 3.1 12.2 + - - +
291B ALA* 3.3 8.9 + - - +
293B ALA* 1.3 75.2 - - - +
295B LEU* 1.3 55.0 + - - +
297B ARG* 3.4 22.7 - - - +
298B GLY 3.0 7.4 + - - -
299B ASP* 2.7 52.7 + - + +
302B ALA* 4.2 4.7 - - + -
303B PHE* 4.0 16.4 - - + +
306B LEU* 5.1 2.5 - - + -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 5.2 1.6 - - + -
53B LEU* 4.6 17.0 - - + -
198B ALA* 4.6 7.4 - - + -
211B VAL* 3.4 29.4 - - + -
212B PRO 4.5 6.9 - - - +
213B LEU* 4.0 37.9 - - + -
218B LEU* 5.1 1.3 - - + -
291B ALA 3.0 12.6 + - - +
292B ALA* 3.1 9.8 + - - +
294B ALA* 1.3 76.0 - - - +
296B ARG* 1.3 65.9 + - - +
298B GLY* 3.0 14.2 + - - +
299B ASP 4.9 0.2 - - - +
300B TYR* 4.2 19.9 - - + -
303B PHE* 4.2 18.6 - - + -
355B LEU* 5.4 3.4 - - + -
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.7 23.8 - - - +
209B SER* 4.5 10.7 + - - -
211B VAL* 4.3 28.9 - - + +
289B ALA 5.4 1.2 + - - -
292B ALA* 3.1 34.1 + - - +
293B ALA* 3.3 15.5 + - - +
295B LEU* 1.3 76.7 - - - +
297B ARG* 1.3 57.6 + - + +
298B GLY 3.7 0.2 + - - -
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN 5.2 1.4 + - - -
293B ALA* 3.4 28.1 + - - +
294B ALA* 3.4 28.2 - - - +
296B ARG* 1.3 78.8 - - - +
298B GLY* 1.3 58.8 + - - +
299B ASP* 3.6 28.6 + - + +
302B ALA* 4.8 4.0 - - - +
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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