Contacts of the helix formed by residues 286 - 311 (chain B) in PDB entry 6D6U
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 MET 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PHE* 4.0 31.5 + - + -
147B PRO* 5.8 0.2 - - - -
226B PHE* 6.0 5.4 - - - -
230B THR* 4.8 9.4 - - + -
231B TYR* 3.4 37.2 - - + +
273B ALA* 3.3 45.1 - - + +
274B ARG* 4.5 4.5 - - + +
276B SER* 5.0 1.8 - - - +
277B LEU* 5.0 4.3 - - + -
284B THR* 3.1 9.4 + - - +
285B ALA* 1.3 78.6 - - - +
287B ASP* 1.3 66.3 + - - +
288B TRP 3.2 2.2 - - - -
289B PHE* 3.2 4.1 + - - +
290B ILE* 2.9 33.7 + - + +
340B TYR* 4.6 0.2 - - - -
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Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.7 30.6 - - - +
282B TYR 4.8 1.2 - - - +
283B ALA* 3.6 17.1 - - + +
284B THR* 3.2 39.1 + - - +
286B MET* 1.3 79.4 - - - +
288B TRP* 1.3 58.3 + - + +
290B ILE* 3.4 7.1 + - - +
291B ALA* 2.8 31.5 + - - +
220C TYR* 5.5 6.6 - - - -
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Residues in contact with TRP 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ALA* 4.2 24.2 + - + +
284B THR 3.2 27.0 + - - -
285B ALA* 4.4 9.6 - - - +
286B MET 3.2 0.6 - - - -
287B ASP* 1.3 78.5 - - + +
289B PHE* 1.3 56.5 + - - +
291B ALA* 3.3 8.6 + - + +
292B VAL* 2.9 37.9 + - + +
336B PHE* 5.0 6.1 - - + -
340B TYR* 5.1 7.6 - - + -
344B TYR* 5.3 4.3 - - - -
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 6.2 0.4 - - + -
231B TYR* 3.7 44.9 - + + -
234B CYS* 3.9 16.8 - - + -
235B ILE* 3.5 29.8 - - + -
285B ALA 4.5 1.0 + - - -
286B MET* 3.2 10.5 + - - +
288B TRP* 1.3 79.6 - - - +
290B ILE* 1.3 67.0 + - + +
292B VAL* 3.2 6.0 + - + +
293B CYS* 3.0 30.1 + - - -
333B PHE* 4.8 6.3 - + - -
336B PHE* 4.3 18.6 - + - -
337B ASN* 3.9 21.8 - - - -
340B TYR* 4.4 30.1 - + + +
341B TRP* 4.7 7.6 - + - -
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 5.2 8.1 - - + -
234B CYS* 5.1 5.2 - - + -
269B LEU* 6.2 2.2 - - + -
270B SER* 3.9 30.7 - - - +
273B ALA* 3.8 29.2 - - + -
274B ARG* 4.7 11.9 - - + +
286B MET* 2.9 39.8 + - + +
287B ASP* 3.8 7.0 - - - +
289B PHE* 1.3 80.7 - - + +
291B ALA* 1.3 59.7 + - - +
293B CYS* 3.4 9.5 + - + +
294B TYR* 2.9 31.2 + - + +
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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
----------------------------------------------------------
287B ASP 2.8 19.4 + - - +
288B TRP* 3.7 12.3 - - + +
290B ILE* 1.3 76.3 - - - +
292B VAL* 1.3 59.6 + - + +
294B TYR* 3.5 10.1 - - + +
295B ALA* 2.8 30.5 + - - +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TRP* 2.9 25.5 + - + +
289B PHE* 3.2 2.9 + - + +
291B ALA* 1.3 75.9 - - + +
293B CYS* 1.3 67.9 + - - +
295B ALA* 3.9 4.7 - - - +
296B PHE* 3.0 49.1 + - + +
333B PHE* 4.8 4.5 - - + -
336B PHE* 3.3 53.4 - - + -
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Residues in contact with CYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B CYS* 2.0 51.8 - - - -
238B VAL* 3.8 22.9 - - + -
266B MET* 4.1 6.5 - - - -
289B PHE* 3.0 29.8 + - - -
290B ILE* 3.4 8.7 - - + +
292B VAL* 1.3 76.7 - - - +
294B TYR* 1.3 57.1 + - - +
296B PHE* 3.3 2.6 + - - +
297B VAL* 3.0 35.8 + - - +
333B PHE* 5.1 5.1 - - - -
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Residues in contact with TYR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 6.2 0.2 - - + -
266B MET* 5.1 13.7 - - + -
267B THR* 5.2 9.6 - - - -
290B ILE* 2.9 22.5 + - + +
291B ALA* 3.5 11.4 - - + +
292B VAL 3.1 0.2 - - - -
293B CYS* 1.3 75.3 - - - +
295B ALA* 1.3 59.3 + - - +
297B VAL* 3.0 12.7 - - + +
298B PHE* 3.0 62.3 + + - +
410B Y01 2.3 83.9 - - + +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA 2.8 21.2 + - - +
292B VAL* 3.3 6.5 + - - +
294B TYR* 1.3 74.9 - - - +
296B PHE* 1.3 64.4 + - + +
298B PHE* 3.8 2.5 - - - +
299B SER* 2.9 31.0 + - - -
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Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 4.5 14.1 - - + -
292B VAL* 3.0 33.7 + - + +
293B CYS 3.8 2.9 - - - +
295B ALA* 1.3 82.3 - - + +
297B VAL* 1.3 57.6 + - - +
299B SER* 2.5 23.7 + - - -
300B ALA* 2.9 16.3 + - - +
329B PHE* 4.9 16.8 - + + -
332B LEU* 4.3 21.1 - - + -
333B PHE* 3.5 58.6 - + + -
336B PHE* 5.0 3.8 - - + -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 4.3 9.4 - - + -
241B SER* 4.6 18.4 - - - +
262B THR* 5.1 12.9 + - - +
263B VAL* 5.6 3.5 - - + +
266B MET* 3.7 39.9 - - + -
293B CYS 3.0 19.6 + - - +
294B TYR* 3.0 26.9 - - + +
296B PHE* 1.3 76.0 - - + +
298B PHE* 1.3 72.3 + - + +
300B ALA* 3.3 8.2 + - - +
301B LEU* 3.0 25.3 + - - +
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Residues in contact with PHE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 3.4 42.8 - - + -
267B THR* 5.9 0.2 - - - -
294B TYR* 3.0 62.7 + + - +
295B ALA* 4.3 2.9 - - - +
297B VAL* 1.3 86.1 - - + +
299B SER* 1.3 61.5 + - - +
301B LEU* 3.5 19.7 - - + +
302B ILE* 2.9 40.0 + - + +
410B Y01 3.9 16.4 - - + -
407C Y01 4.5 17.3 - - + -
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 2.9 16.9 + - - -
296B PHE* 2.5 30.7 + - - -
298B PHE* 1.3 73.1 - - - +
300B ALA* 1.3 57.7 + - - +
302B ILE* 3.3 8.6 + - - +
303B GLU* 2.9 29.9 + - - +
329B PHE* 4.0 22.2 - - - -
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER* 5.2 10.5 - - - +
244B SER* 6.3 1.6 - - - -
245B PHE* 3.6 34.2 - - + -
296B PHE 2.9 7.5 + - - +
297B VAL* 3.3 11.4 + - - +
299B SER* 1.3 83.3 + - - +
301B LEU* 1.3 58.6 + - - +
303B GLU* 3.4 5.0 + - - +
304B PHE* 2.9 28.9 + - - +
329B PHE* 4.2 5.6 - - + -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG 6.1 0.2 - - - +
256B THR* 6.4 1.1 - - - -
259B GLY* 4.9 17.5 - - - -
263B VAL* 4.5 9.9 - - + -
297B VAL 3.0 14.0 + - - +
298B PHE* 3.5 34.1 - - + +
299B SER 3.2 0.2 - - - -
300B ALA* 1.3 77.4 - - - +
302B ILE* 1.3 60.3 + - + +
304B PHE* 3.3 14.0 + - + +
305B ALA* 2.9 27.9 + - + +
409B Y01 3.5 43.1 - - + -
407C Y01 5.6 8.5 - - + +
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 2.9 28.1 + - + +
299B SER* 3.8 7.4 - - - +
301B LEU* 1.3 73.8 - - + +
303B GLU* 1.3 61.4 + - - +
305B ALA* 3.2 7.9 + - + +
306B THR* 2.9 32.7 + - + +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.0 26.8 - - + -
299B SER 2.9 16.8 + - - +
300B ALA* 3.5 7.9 - - - +
302B ILE* 1.3 76.9 - - - +
304B PHE* 1.3 75.0 + - - +
306B THR* 3.1 12.3 - - + +
307B VAL* 2.9 36.3 + - - +
321B ILE* 3.1 28.3 - - + +
322B ASP* 3.4 13.2 - - - +
325B SER* 3.9 16.9 + - - +
329B PHE* 4.8 7.0 - - + -
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Residues in contact with PHE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B SER* 4.6 9.2 - - - +
251B SER 4.4 0.2 - - - -
252B VAL* 3.8 22.9 - - - -
255B ARG* 3.2 62.1 - - + -
256B THR* 3.6 23.6 - - + -
300B ALA 2.9 14.4 + - - +
301B LEU* 3.3 18.1 + - + +
303B GLU* 1.3 83.9 + - - +
305B ALA* 1.3 60.9 + - - +
307B VAL* 3.3 4.7 + - + +
308B ASN* 2.9 49.1 + - + +
409B Y01 4.6 15.9 - - + -
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 2.9 17.4 + - + +
302B ILE* 3.2 10.7 + - + +
304B PHE* 1.3 81.7 - - - +
306B THR* 1.3 61.7 + - - +
308B ASN* 3.5 11.9 + - - +
309B TYR* 3.6 11.1 + - - +
409B Y01 4.6 33.6 - - + +
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ILE* 2.9 20.7 + - + +
303B GLU* 3.1 21.5 - - + +
305B ALA* 1.3 73.8 - - - +
307B VAL* 1.3 66.0 + - + +
309B TYR* 3.2 6.5 + - - +
310B PHE* 2.9 56.1 + - + -
321B ILE* 5.3 5.4 - - + -
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 5.0 8.5 - - + +
255B ARG* 5.1 11.2 - - - +
303B GLU* 2.9 43.9 + - - +
304B PHE* 3.8 7.0 - - + +
306B THR* 1.3 75.0 - - + +
308B ASN* 1.3 65.2 + - - +
310B PHE* 4.3 5.6 - - - +
311B THR* 2.9 29.0 + - - +
318B ALA* 3.7 23.6 - - + -
321B ILE* 3.7 26.5 - - + -
322B ASP* 4.7 11.0 - - - +
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Residues in contact with ASN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG 5.7 2.3 + - - -
252B VAL* 3.3 43.8 - - - +
255B ARG* 5.8 4.0 - - - +
304B PHE* 2.9 28.7 + - + +
305B ALA* 3.7 7.4 - - - +
306B THR 3.3 0.2 - - - -
307B VAL* 1.3 77.3 - - - +
309B TYR* 1.3 58.5 + - - +
311B THR* 3.8 14.7 - - - +
312B LYS* 4.5 10.4 - - - +
409B Y01 3.9 27.6 - - + +
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Residues in contact with TYR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ALA 3.6 8.6 + - - +
306B THR* 3.2 9.7 + - - +
307B VAL 3.0 0.6 - - - -
308B ASN* 1.3 79.5 - - - +
310B PHE* 1.3 88.8 + + - +
311B THR 3.4 1.0 + - - -
312B LYS* 3.8 33.9 + - - +
313B SER* 4.7 2.4 + - - -
409B Y01 5.5 10.1 - - + +
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B THR* 2.9 38.0 + - + +
307B VAL* 4.3 4.5 - - - +
309B TYR* 1.3 100.4 - + - +
311B THR* 1.3 64.7 + - - +
312B LYS 3.1 4.4 + - - -
313B SER* 3.3 19.9 + - - -
314B GLN 3.3 10.0 - - - +
317B ARG* 4.8 28.6 - - + +
318B ALA* 5.1 2.5 - - - +
321B ILE* 4.1 22.4 - - + -
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 3.9 32.4 - - - +
307B VAL* 2.9 23.7 + - - +
308B ASN* 3.8 18.4 - - - +
310B PHE* 1.3 76.8 - - - +
312B LYS* 1.3 69.5 + - + +
314B GLN 3.9 16.8 - - - +
315B PRO* 4.2 10.6 - - - +
318B ALA* 3.9 16.4 - - - +
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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