Contacts of the helix formed by residues 271 - 298 (chain A) in PDB entry 6Q3W
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 1.3 80.3 - - - +
272A LYS* 1.3 61.1 + - - +
273A GLU* 3.9 12.9 + - - +
274A GLY* 3.2 20.3 + - - -
275A PHE* 2.9 26.5 + - - +
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A SER* 1.3 74.9 - - - +
273A GLU* 1.3 63.6 + - - +
275A PHE* 3.3 7.5 + - - +
276A ARG* 3.3 33.0 + - - +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLN* 3.7 26.4 + - + +
271A SER* 3.9 13.1 + - - +
272A LYS* 1.3 76.2 - - - +
274A GLY* 1.3 68.5 + - - +
276A ARG* 3.0 35.4 + - - +
277A ARG* 2.9 42.3 + - - +
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Residues in contact with GLY 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLN* 5.3 7.2 - - - -
246A VAL* 3.5 28.5 - - - +
270A VAL* 4.5 0.7 - - - -
271A SER* 3.2 24.0 + - - -
273A GLU* 1.3 79.6 - - - +
275A PHE* 1.3 60.1 + - - +
277A ARG* 3.3 9.1 + - - +
278A ALA* 3.1 18.5 + - - +
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 5.2 0.2 - - + -
263A LEU* 3.5 46.7 - - + +
264A GLU* 3.6 23.1 - - + -
267A ARG* 3.2 60.3 - - + +
270A VAL* 3.9 13.8 - - + +
271A SER 2.9 12.5 + - - +
272A LYS* 3.4 11.7 - - - +
274A GLY* 1.3 76.4 - - - +
276A ARG* 1.3 58.6 + - + +
278A ALA* 3.3 5.0 + - - +
279A ARG* 2.9 58.9 + - - +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 3.3 19.0 + - - +
273A GLU* 3.0 43.2 + - - +
275A PHE* 1.3 80.5 - - + +
277A ARG* 1.3 65.6 + - - +
279A ARG* 3.5 9.4 + - - +
280A HIS 3.3 9.2 + - - -
316A ASP 4.2 7.7 + - - -
317A ASP* 3.2 53.5 + - - +
319A GLU* 2.8 33.7 + - - -
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLU* 4.9 0.6 + - - -
239A ARG* 3.0 49.2 - - - +
242A GLN* 3.1 31.4 + - + +
243A CYS* 4.8 10.1 - - - -
246A VAL* 5.7 0.2 - - + -
273A GLU* 2.9 43.3 + - - +
274A GLY* 3.6 9.4 - - - +
275A PHE 3.3 0.2 - - - -
276A ARG* 1.3 84.9 - - - +
278A ALA* 1.3 61.2 + - - +
280A HIS 3.4 2.4 + - - -
281A VAL* 3.2 26.4 + - - +
317A ASP 2.7 29.6 + - - -
318A TYR* 3.5 28.1 + - + -
319A GLU* 3.0 25.9 + - - -
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 3.7 18.2 - - + -
255A LEU* 4.0 20.4 - - + -
258A VAL* 6.2 0.2 - - + -
263A LEU* 3.7 30.3 - - + -
274A GLY 3.1 12.9 + - - +
275A PHE 3.9 0.4 - - - +
277A ARG* 1.3 77.0 - - - +
279A ARG* 1.3 61.1 + - - +
281A VAL* 3.1 1.6 + - - +
282A VAL* 2.9 35.5 + - + +
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.0 23.2 - - + +
263A LEU* 3.5 11.8 - - + +
264A GLU* 4.8 5.6 + - - -
267A ARG* 4.5 9.3 - - - +
275A PHE* 2.9 46.5 + - + +
276A ARG* 3.8 13.3 - - - +
277A ARG 3.3 0.2 - - - -
278A ALA* 1.3 76.0 - - - +
280A HIS* 1.3 63.7 + - - +
282A VAL* 4.1 2.7 - - - +
283A GLY* 3.0 20.8 + - - -
317A ASP* 2.8 37.2 + - - +
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Residues in contact with HIS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU 2.9 23.0 + - - -
44A HIS* 4.6 0.4 - - + -
276A ARG 3.3 9.8 + - - +
277A ARG 3.5 6.5 - - - +
278A ALA 3.2 0.4 - - - -
279A ARG* 1.3 78.8 - - - +
281A VAL* 1.3 60.8 + - + +
283A GLY 3.3 0.5 + - - -
284A GLU* 2.7 62.0 + - + +
287A ARG* 3.6 1.1 + - - +
313A SER* 2.6 35.6 + - - +
314A LEU* 3.3 31.0 - - + +
317A ASP* 4.0 9.7 + - + -
318A TYR* 3.5 34.5 - + + -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A HIS 3.9 7.2 - - - +
45A THR* 4.2 3.8 - - + +
48A ASN* 3.5 37.9 - - + +
243A CYS* 4.0 1.1 - - - -
255A LEU* 3.8 33.7 - - + -
277A ARG 3.2 14.1 + - - +
278A ALA 3.1 7.2 + - - +
280A HIS* 1.3 79.8 - - + +
282A VAL* 1.3 64.1 + - - +
284A GLU* 3.3 3.8 + - - +
285A ILE* 3.1 36.2 + - + +
318A TYR* 3.7 17.0 - - + -
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.1 13.5 - - + +
258A VAL* 3.3 39.5 - - + +
259A GLN* 3.8 2.9 - - - -
260A LEU* 3.3 36.8 - - + +
263A LEU* 4.9 4.9 - - + -
278A ALA* 2.9 22.4 + - + +
279A ARG* 4.1 4.3 - - - +
281A VAL* 1.3 75.9 - - - +
283A GLY* 1.3 62.9 + - - +
285A ILE* 3.7 7.7 + - - +
286A ARG* 3.4 20.1 + - - +
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG 3.0 15.0 + - - -
280A HIS 3.7 2.5 - - - -
282A VAL* 1.3 78.2 - - - +
284A GLU* 1.3 57.9 + - - +
286A ARG* 3.4 7.6 + - - +
287A ARG* 2.9 48.1 + - - +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.5 2.2 - - - -
42A GLY* 3.0 13.0 + - - -
43A GLU* 2.8 37.1 + - - +
45A THR* 3.5 17.9 - - + -
280A HIS* 2.7 35.2 + - + +
281A VAL 3.3 0.2 + - - -
283A GLY* 1.3 70.5 - - - +
285A ILE* 1.3 58.0 + - - +
287A ARG* 2.8 32.1 + - - +
288A THR* 2.6 38.2 + - - -
310A SER* 2.7 29.8 + - - -
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 4.0 10.8 - - + -
48A ASN* 4.7 1.1 - - + +
50A GLY* 3.8 26.2 - - - -
51A LEU* 3.8 22.4 - - + +
255A LEU 4.5 3.1 - - - +
256A ARG* 3.9 42.0 - - - +
281A VAL* 3.1 31.3 + - + +
282A VAL* 3.9 5.8 - - - +
284A GLU* 1.3 73.2 - - - +
286A ARG* 1.3 66.0 + - - +
288A THR* 3.3 6.8 + - - -
289A ALA* 3.1 21.7 + - - +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLN* 5.7 6.7 - - - +
282A VAL* 3.4 11.1 + - - +
283A GLY* 3.4 11.8 + - - +
284A GLU 3.3 0.2 - - - -
285A ILE* 1.3 79.1 - - - +
287A ARG* 1.3 52.6 + - + +
289A ALA* 3.0 12.1 + - - +
290A GLN* 2.8 66.5 + - - +
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.1 10.4 - - + +
280A HIS* 3.6 1.8 + - - +
283A GLY* 2.9 28.7 + - - +
284A GLU* 2.8 45.6 + - - +
286A ARG* 1.3 77.0 - - + +
288A THR* 1.3 50.8 + - - +
290A GLN* 3.5 17.3 - - - +
291A ALA* 2.6 36.0 + - - +
306A LEU* 3.8 16.7 - - + +
309A GLU* 3.6 41.8 + - - +
310A SER* 3.7 4.8 - - - +
313A SER* 3.2 34.7 + - - -
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.1 15.9 - - + +
42A GLY* 3.1 21.8 + - - -
51A LEU* 3.8 33.5 + - + +
52A VAL 4.1 13.7 - - - +
53A LEU* 4.2 2.5 - - + +
200A LEU* 4.2 7.6 - - + -
284A GLU 2.6 22.8 + - - -
285A ILE 3.7 4.5 - - - -
286A ARG 3.2 0.2 - - - -
287A ARG* 1.3 73.8 - - - +
289A ALA* 1.3 62.2 + - - +
291A ALA* 3.6 5.0 - - - +
292A ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.9 17.8 - - + +
200A LEU* 5.7 1.3 - - - -
285A ILE 3.1 12.1 + - - +
286A ARG* 3.0 13.3 + - - +
288A THR* 1.3 76.0 - - - +
290A GLN* 1.3 64.3 + - + +
292A ALA* 3.4 6.8 + - - +
293A ALA* 3.2 21.3 + - - +
296A ARG* 4.8 1.6 + - - -
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ARG* 2.8 43.1 + - - +
287A ARG* 3.5 23.1 - - - +
289A ALA* 1.3 77.8 - - + +
291A ALA* 1.3 56.7 + - - +
293A ALA* 3.4 7.1 + - - +
294A ALA* 3.0 27.5 + - - +
297A ARG* 5.0 1.2 + - - -
306A LEU* 3.6 24.9 - - + +
309A GLU* 5.2 0.5 - - - +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.6 23.8 - - + -
287A ARG 2.6 22.1 + - - +
288A THR 3.6 4.7 - - - +
289A ALA 3.2 0.2 - - - -
290A GLN* 1.3 70.8 - - - +
292A ALA* 1.3 59.7 + - - +
294A ALA* 3.2 1.7 + - - +
295A LEU 2.9 26.7 + - - -
303A PHE* 3.2 34.3 - - + -
306A LEU* 3.5 14.3 - - + +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.3 13.4 - - + +
200A LEU* 3.9 30.3 - - + -
211A VAL* 4.7 6.6 - - + +
288A THR 2.9 16.2 + - - +
289A ALA* 3.6 6.5 - - - +
290A GLN 3.4 0.2 - - - -
291A ALA* 1.3 77.3 - - - +
293A ALA* 1.3 62.1 + - - +
295A LEU* 3.4 3.9 + - - +
296A ARG* 3.1 40.9 + - - +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA 3.2 10.1 + - - +
290A GLN* 3.7 9.0 - - - +
291A ALA 3.2 0.2 - - - -
292A ALA* 1.3 78.2 - - - +
294A ALA* 1.3 63.7 + - - +
296A ARG* 3.1 23.9 + - - +
297A ARG* 3.1 35.5 + - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN 3.0 18.2 + - - +
291A ALA* 3.5 6.1 - - - +
293A ALA* 1.3 75.7 - - - +
295A LEU* 1.3 61.0 + - - +
297A ARG* 3.0 31.1 + - - +
299A ASP* 2.9 42.7 + - - +
302A ALA* 4.1 4.7 - - + -
303A PHE* 4.0 16.2 - - - +
306A LEU* 4.7 1.6 - - + -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.5 13.9 - - + -
53A LEU* 4.3 11.7 - - + -
198A ALA* 4.6 4.3 - - + -
211A VAL* 3.8 25.1 - - + -
212A PRO 4.3 10.5 - - - +
213A LEU* 3.9 29.2 - - + -
218A LEU* 5.1 0.4 - - + -
291A ALA 2.9 15.9 + - - +
292A ALA* 3.7 5.8 - - - +
294A ALA* 1.3 75.9 - - - +
296A ARG* 1.3 61.8 + - - +
298A GLY* 3.1 11.4 + - - +
299A ASP 4.8 2.0 - - - +
300A TYR* 4.1 21.9 - - + -
303A PHE* 3.8 26.1 - - + -
355A LEU* 6.0 2.5 - - + -
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 3.7 25.7 - - - +
209A SER* 4.8 10.1 + - - -
211A VAL* 4.6 19.5 - - + +
212A PRO* 6.3 1.6 - - + -
289A ALA 4.8 1.2 + - - -
292A ALA* 3.1 20.0 + - - +
293A ALA* 3.1 39.2 - - - +
295A LEU* 1.3 78.0 - - - +
297A ARG* 1.3 61.4 + - + +
298A GLY 3.1 1.8 + - - -
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN 5.0 1.0 + - - -
293A ALA* 3.3 22.4 - - + +
294A ALA* 3.0 34.9 + - - +
296A ARG* 1.3 77.2 - - + +
298A GLY* 1.3 60.1 + - - +
299A ASP* 2.8 37.6 + - + +
302A ALA* 4.0 6.1 - - - +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA 3.1 1.8 + - - -
295A LEU 3.1 10.4 + - - -
296A ARG 3.1 6.8 + - - -
297A ARG* 1.3 79.9 - - - +
299A ASP* 1.3 58.4 + - - +
300A TYR* 3.3 35.7 + - - -
----------------------------------------------------------
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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