Contacts of the helix formed by residues 280 - 310 (chain A) in PDB entry 6AF6
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 PHE 280 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLN* 3.8 15.0 - - + -
273A PHE* 4.0 29.8 - + + -
275A LYS* 3.8 21.3 - - + -
276A ALA 4.3 0.7 - - - -
277A ILE* 3.1 35.1 + - + +
278A GLY 3.7 0.3 - - - +
279A GLN* 1.4 75.1 - - - +
281A GLN* 1.3 66.8 + - - +
282A SER* 4.4 5.6 - - - +
283A VAL* 3.0 24.5 + - + +
284A SER* 3.0 11.9 + - - -
503A O4B 3.5 37.7 - - - -
504A CL 4.2 2.0 - - - -
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLN 3.7 4.4 + - - +
280A PHE* 1.3 73.0 - - - +
282A SER* 1.3 63.1 + - - +
284A SER* 3.4 12.1 - - - +
285A ASN* 2.8 45.4 + - - +
504A CL 3.3 25.9 - - + +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A PHE* 3.2 5.2 - - - +
281A GLN* 1.3 80.2 - - - +
283A VAL* 1.3 65.3 + - - +
285A ASN* 4.3 4.7 - - - +
286A ARG* 3.7 35.2 + - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ALA* 4.4 1.8 - - + -
277A ILE* 3.3 42.2 - - + +
278A GLY* 3.9 11.0 - - - +
280A PHE* 3.0 12.2 + - + +
282A SER* 1.3 79.0 - - - +
284A SER* 1.3 64.9 - - - +
286A ARG* 3.3 24.5 + - - +
287A ILE* 3.2 34.6 + - + +
339A THR* 4.4 17.4 + - + +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLY* 3.4 21.3 + - - -
279A GLN 5.2 0.3 - - - -
280A PHE 3.0 5.2 + - - -
281A GLN* 3.4 21.7 - - - +
283A VAL* 1.3 75.4 - - - +
285A ASN* 1.3 71.9 + - - +
287A ILE* 3.2 10.0 + - - +
288A ILE* 2.8 36.6 + - - +
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLN* 2.8 41.2 + - - +
282A SER* 4.3 4.1 - - - +
284A SER* 1.3 85.0 + - - +
286A ARG* 1.4 56.0 + - + +
288A ILE* 3.4 14.9 + - - +
289A ASP* 3.0 32.9 + - - +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A SER* 3.7 27.8 + - - +
283A VAL* 3.3 28.7 + - - +
285A ASN* 1.4 74.4 - - + +
287A ILE* 1.3 67.7 + - + +
289A ASP* 3.2 14.9 + - - +
290A MET* 3.1 25.3 + - - +
335A ASP* 3.8 35.7 + - + +
338A GLN* 3.9 45.6 + - - +
339A THR* 4.5 7.0 + - - +
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 3.9 14.4 - - + -
263A THR* 3.9 26.7 - - + +
264A LEU* 3.6 30.1 - - + -
267A ALA* 3.5 31.9 - - + -
278A GLY* 5.4 0.9 - - - -
283A VAL* 3.2 21.5 + - + +
284A SER* 3.2 10.6 + - - +
286A ARG* 1.3 76.7 - - - +
288A ILE* 1.3 66.7 + - + +
290A MET* 3.0 10.1 + - - +
291A LYS* 2.9 21.5 + - + +
339A THR* 4.2 8.3 - - + +
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER* 2.8 33.8 + - - +
285A ASN* 3.6 15.3 - - - +
287A ILE* 1.3 78.2 - - + +
289A ASP* 1.3 58.2 + - - +
291A LYS* 3.1 9.1 + - + +
292A LEU* 2.8 49.3 + - + +
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 3.0 20.1 + - - +
286A ARG* 3.2 16.4 + - - +
288A ILE* 1.3 77.3 - - - +
290A MET* 1.3 62.0 + - - +
292A LEU* 3.4 16.2 + - - +
293A ARG* 2.9 53.8 + - - +
335A ASP* 4.3 1.5 - - - +
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Residues in contact with MET 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 4.5 7.2 - - + +
259A LEU* 3.9 17.9 - - + -
260A LEU* 4.1 20.4 - - + +
263A THR* 3.7 39.5 - - - +
286A ARG 3.1 14.2 + - - +
287A ILE* 3.0 15.7 + - - +
289A ASP* 1.3 76.2 - - - +
291A LYS* 1.3 58.6 + - - +
293A ARG* 3.4 4.2 + - - +
294A LEU* 3.0 29.3 + - - +
332A SER* 3.8 36.1 - - - +
335A ASP* 3.9 26.7 - - + -
336A ALA* 4.1 3.1 - - + -
339A THR* 5.1 0.2 - - - -
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Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 3.8 29.8 - - + +
264A LEU* 6.5 0.2 - - + -
287A ILE* 2.9 12.7 + - + +
288A ILE* 3.5 12.3 - - + +
290A MET* 1.3 74.7 - - - +
292A LEU* 1.3 68.3 + - + +
294A LEU* 3.2 3.0 + - - +
295A GLU* 3.0 55.2 + - + +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 2.8 42.6 + - + +
289A ASP* 3.7 16.8 - - - +
291A LYS* 1.3 74.9 - - + +
293A ARG* 1.3 63.5 + - + +
295A GLU* 3.4 4.4 + - - +
296A GLN* 3.0 43.1 + - + +
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Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 4.6 1.3 - - + -
289A ASP* 2.9 35.7 + - + +
290A MET* 3.5 12.4 - - - +
292A LEU* 1.3 77.4 - - + +
294A LEU* 1.3 63.0 + - - +
296A GLN* 3.3 3.5 + - - +
297A CYS* 2.9 28.0 + - - -
328A TYR* 3.4 55.1 - - + -
331A GLN* 3.8 21.6 - - - +
332A SER* 3.1 35.3 + - - +
335A ASP* 2.8 29.9 + - - -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL* 3.7 37.7 - - + +
256A LEU* 3.8 24.0 - - + +
257A ALA* 3.9 20.9 - - + +
260A LEU* 3.8 23.8 - - + -
290A MET 3.0 17.2 + - - +
291A LYS* 3.2 5.4 + - + +
293A ARG* 1.3 76.0 - - - +
295A GLU* 1.3 71.2 + - - +
297A CYS* 3.9 2.4 - - - -
298A ARG* 3.0 54.9 + - - +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LYS* 3.0 49.3 + - + +
292A LEU* 4.0 5.2 - - - +
294A LEU* 1.3 83.6 - - - +
296A GLN* 1.3 64.7 + - + +
298A ARG* 3.2 31.3 + - - +
299A LEU* 3.2 35.3 + - + +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.0 41.4 + - + +
293A ARG* 3.9 6.2 - - - +
295A GLU* 1.3 81.1 - - + +
297A CYS* 1.3 64.1 + - - +
299A LEU* 3.3 8.8 + - - +
300A MET* 3.1 28.1 + - + +
324A LEU* 5.8 1.8 - - + -
328A TYR* 4.0 24.4 + - + +
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Residues in contact with CYS 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL* 4.2 10.8 - - - -
256A LEU* 4.6 9.4 - - - -
293A ARG 2.9 25.7 + - - +
294A LEU* 3.9 10.8 - - - -
296A GLN* 1.3 77.8 - - - +
298A ARG* 1.3 64.8 + - - +
300A MET* 3.3 9.4 + - + +
301A LEU* 3.0 23.6 + - - +
321A SER* 5.4 0.2 - - - -
324A LEU* 4.3 5.6 - - + -
325A ILE* 3.7 38.2 - - + +
328A TYR* 3.8 22.0 - - + -
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 5.8 0.2 + - - -
74A GLU* 2.8 33.4 + - - -
253A VAL* 3.9 15.0 - - + +
257A ALA* 4.6 13.1 - - - +
294A LEU* 3.0 40.2 + - - +
295A GLU* 3.2 34.7 + - - +
297A CYS* 1.3 79.5 - - - +
299A LEU* 1.3 58.7 + - + +
301A LEU* 3.2 6.1 + - - +
302A TYR* 2.9 74.9 + - + -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.9 34.5 - - + -
295A GLU* 3.2 26.0 + - + +
296A GLN* 3.3 6.3 + - - +
298A ARG* 1.3 78.9 - - + +
300A MET* 1.3 57.3 + - + +
302A TYR* 3.3 16.9 + - + +
303A ARG* 2.9 30.8 + - - +
----------------------------------------------------------
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Residues in contact with MET 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN* 3.1 16.8 + - + +
297A CYS* 3.6 9.0 - - - +
299A LEU* 1.3 76.9 - - + +
301A LEU* 1.3 57.3 + - - +
303A ARG* 3.5 25.5 + - - +
304A ALA* 3.0 23.0 + - - +
317A ASP* 4.7 2.6 - - + +
320A MET* 3.8 46.0 - - + -
321A SER* 3.0 19.5 + - - +
324A LEU* 3.9 25.1 - - + -
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 4.5 5.6 - - + -
74A GLU* 5.6 0.7 - - - +
245A LYS 4.9 1.6 - - - +
246A GLY* 2.8 30.3 - - - +
250A ALA* 3.7 38.8 - - + +
253A VAL* 4.2 7.4 - - + -
297A CYS 3.0 17.3 + - - +
298A ARG* 3.6 5.8 - - - +
300A MET* 1.3 72.5 - - - +
302A TYR* 1.3 77.6 + - + +
304A ALA* 3.2 3.8 + - + +
305A CYS* 2.9 32.7 + - - -
321A SER* 3.4 18.6 + - - -
325A ILE* 4.1 17.3 - - + -
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Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 5.4 9.4 - - + -
67A LEU* 3.8 28.3 - - + +
70A ALA* 5.6 4.0 - - + -
71A LEU* 3.8 22.0 - - + +
74A GLU* 2.6 31.8 + - - -
253A VAL* 5.9 0.2 - - + -
298A ARG* 2.9 51.0 + - + +
299A LEU* 3.8 16.4 - - + +
301A LEU* 1.3 90.9 - - + +
303A ARG* 1.3 58.9 + - - +
305A CYS* 3.9 0.9 - - - +
306A TRP* 2.8 30.8 + - - +
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 6.5 1.1 - - - -
299A LEU 2.9 17.5 + - - +
300A MET* 4.0 31.2 + - - +
302A TYR* 1.3 78.4 - - - +
304A ALA* 1.3 56.2 + - - +
306A TRP* 3.7 12.4 - - + +
307A LYS* 2.8 52.6 + - + +
317A ASP* 4.0 19.2 + - - +
320A MET* 4.7 4.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET 3.0 18.7 + - - +
301A LEU* 3.6 6.5 - - + +
303A ARG* 1.3 76.1 - - - +
305A CYS* 1.3 65.0 + - - +
307A LYS* 3.3 1.1 + - - -
308A HIS* 3.0 19.9 + - - +
314A ALA* 3.6 10.6 - - - +
317A ASP* 3.7 41.4 - - + +
318A ILE* 3.8 15.8 - - + +
321A SER* 3.8 5.4 - - - +
----------------------------------------------------------
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Residues in contact with CYS 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 3.8 15.6 - - - +
67A LEU* 3.6 25.4 - - + +
70A ALA* 3.8 19.7 - - - -
246A GLY* 3.8 28.9 - - - -
247A CYS* 4.5 1.1 - - - -
301A LEU* 2.9 22.0 + - - +
302A TYR 3.9 2.2 - - - +
304A ALA* 1.3 76.9 - - - +
306A TRP* 1.3 65.6 + - - +
308A HIS* 3.2 6.4 + - - +
309A ASP* 3.0 28.1 + - - -
318A ILE* 5.8 1.6 - - - -
----------------------------------------------------------
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Residues in contact with TRP 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.4 18.1 - - + +
302A TYR 2.8 19.7 + - - +
303A ARG* 3.7 13.7 - - + +
305A CYS* 1.3 77.4 - - - +
307A LYS* 1.3 88.5 + - + +
309A ASP* 3.1 12.3 + - + +
310A GLN* 2.9 63.8 + - + +
312A GLN* 4.1 18.6 - - - -
----------------------------------------------------------
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ARG* 2.8 45.5 + - + +
304A ALA 3.7 4.0 - - - +
305A CYS 3.3 0.2 - - - -
306A TRP* 1.3 88.1 - - + +
308A HIS* 1.3 63.9 + - - +
310A GLN* 3.0 12.0 + - - +
312A GLN* 3.0 52.1 + - + +
313A ASP 4.8 5.3 + - - +
314A ALA* 4.1 7.6 - - + -
317A ASP* 2.9 39.7 + - - +
----------------------------------------------------------
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Residues in contact with HIS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 3.9 11.1 - - + +
102A ARG* 6.0 5.7 + - - -
239A ASP* 5.7 2.4 + - - -
242A ILE* 4.7 18.7 - - + +
243A TRP* 3.9 35.0 + + - -
304A ALA 3.0 13.9 + - - +
305A CYS* 3.4 10.3 - - - +
307A LYS* 1.3 75.7 - - - +
309A ASP* 1.3 67.2 + - - +
311A GLY* 2.9 20.1 + - - -
312A GLN 4.4 4.9 - - - -
314A ALA* 3.8 13.5 - - + +
318A ILE* 5.0 6.1 - - + -
----------------------------------------------------------
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY* 3.6 10.3 - - - -
66A ALA* 2.7 28.6 + - - +
67A LEU* 2.9 32.9 + - - +
68A ASP* 4.6 0.5 + - - -
305A CYS 3.0 10.8 + - - -
306A TRP* 3.1 11.9 + - + +
308A HIS* 1.3 81.1 + - - +
310A GLN* 1.3 63.7 + - + +
311A GLY 3.2 0.7 + - - -
----------------------------------------------------------
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Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A TRP* 2.9 63.1 + - + +
307A LYS 3.0 8.0 + - - +
309A ASP* 1.3 79.6 - - + +
311A GLY* 1.3 60.4 + - - +
312A GLN* 3.5 20.2 + - - +
----------------------------------------------------------
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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