Contacts of the helix formed by residues 277 - 301 (chain X) in PDB entry 1FM6
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 VAL 277 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252X MET* 4.7 17.0 - - + -
255X LEU* 3.7 30.3 - - + -
256X MET* 5.2 12.6 - - + -
272X GLU* 5.9 3.8 - - - +
274X SER* 3.0 23.3 - - - +
275X LYS 2.5 10.4 + - - +
276X GLU* 1.3 71.6 - - - +
278X ALA* 1.3 67.5 + - - +
279X ILE 3.0 2.2 - - - -
280X ARG* 2.9 23.0 + - + +
281X ILE* 3.1 18.3 + - + +
352X PHE* 5.2 0.4 - - + -
356X LEU* 5.0 7.2 - - + -
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Residues in contact with ALA 278 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275X LYS 3.5 8.0 + - - +
276X GLU* 5.1 3.1 - - - +
277X VAL* 1.3 81.5 - - - +
279X ILE* 1.3 51.3 + - - +
281X ILE* 3.1 5.4 + - - +
282X PHE* 2.7 37.1 + - - +
356X LEU* 4.1 26.8 - - + +
357X ARG* 4.4 5.8 - - + +
360X PHE* 3.5 39.4 - - + +
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Residues in contact with ILE 279 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276X GLU* 3.9 35.9 - - + +
277X VAL 3.0 1.0 - - - +
278X ALA* 1.3 79.2 - - - +
280X ARG* 1.3 59.4 + - + +
282X PHE* 3.5 8.6 + - + +
283X GLN* 2.9 55.3 + - + +
360X PHE* 4.0 23.3 - - + -
460X GLU* 6.0 3.1 - - + +
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Residues in contact with ARG 280 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263X LYS* 3.0 47.2 + - - +
265X LYS* 3.7 16.6 - - - +
266X HIS* 4.5 12.1 - - - +
267X ILE 5.9 2.5 - - - -
277X VAL* 2.9 16.5 + - + +
279X ILE* 1.3 77.8 - - + +
281X ILE* 1.3 63.5 + - + +
283X GLN* 4.2 22.3 + - - +
284X GLY* 3.0 30.1 + - - +
287X PHE* 5.1 7.5 - - - -
504X BRL 4.9 1.1 - - - -
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Residues in contact with ILE 281 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255X LEU* 4.8 13.7 - - + -
263X LYS* 5.6 4.9 - - - -
277X VAL* 3.1 21.4 + - + +
278X ALA* 3.1 10.3 + - - +
280X ARG* 1.3 76.6 - - + +
282X PHE* 1.3 66.4 + - - +
284X GLY* 3.0 11.3 + - - -
285X CYS* 3.0 19.0 + - - -
348X MET* 3.6 29.2 - - + -
352X PHE* 4.6 8.1 - - + -
353X LEU* 4.0 21.1 - - + -
356X LEU* 4.3 16.4 - - + -
363X PHE* 5.1 4.7 - - + -
504X BRL 3.8 22.1 - - + -
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Residues in contact with PHE 282 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278X ALA 2.7 20.6 + - - +
279X ILE* 3.7 9.6 - - + +
281X ILE* 1.3 74.8 - - - +
283X GLN* 1.3 62.9 + - + +
285X CYS* 3.2 6.3 + - - +
286X GLN* 3.0 47.7 + - - +
360X PHE* 3.9 30.5 - + + -
363X PHE* 4.4 25.1 - + + -
453X LEU* 4.2 13.5 - - + -
456X ILE* 5.0 7.4 - - + -
463X MET* 4.4 15.0 - - + -
464X SER 5.0 0.4 - - - -
465X LEU* 3.7 17.5 - - + -
504X BRL 3.0 35.0 - - - -
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Residues in contact with GLN 283 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279X ILE* 2.9 43.5 + - + +
280X ARG* 3.9 21.9 + - - +
282X PHE* 1.3 74.4 - - + +
284X GLY* 1.3 60.8 + - - +
286X GLN* 3.1 16.4 + - - +
287X PHE* 2.8 63.1 + - + -
464X SER 6.0 0.2 + - - -
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Residues in contact with GLY 284 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280X ARG* 3.0 17.8 + - - +
281X ILE 3.0 8.5 + - - -
283X GLN* 1.3 77.1 - - - +
285X CYS* 1.3 55.6 + - - +
287X PHE* 3.2 9.8 + - - +
288X ARG* 2.9 29.1 + - - +
504X BRL 3.5 26.6 - - - -
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Residues in contact with CYS 285 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281X ILE* 3.0 19.3 + - - -
282X PHE 3.5 7.2 - - - +
284X GLY* 1.3 75.3 - - - +
286X GLN* 1.3 62.5 + - - +
288X ARG* 3.2 4.0 + - - +
289X SER* 3.0 18.2 + - - -
363X PHE* 3.8 18.8 - - + -
504X BRL 3.4 89.8 - - + -
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Residues in contact with GLN 286 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282X PHE* 3.0 50.0 + - + +
283X GLN* 3.4 19.0 - - - +
285X CYS* 1.3 74.8 - - - +
287X PHE* 1.3 67.8 + - + +
289X SER* 3.0 6.1 + - - -
290X VAL* 2.9 29.4 + - - +
464X SER 4.1 7.1 + - - +
465X LEU* 3.4 16.8 - - - +
466X HIS* 2.9 32.8 + - + +
469X LEU* 3.6 21.5 - - + +
504X BRL 4.2 15.5 - - - -
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Residues in contact with PHE 287 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280X ARG* 5.1 7.6 - - - -
283X GLN* 2.8 54.7 + - + +
284X GLY* 3.7 7.6 - - - +
286X GLN* 1.3 80.5 - - + +
288X ARG* 1.3 65.6 + - - +
290X VAL* 3.3 8.2 + - + +
291X GLU* 3.2 21.5 + - - +
466X HIS* 4.1 28.5 - + + -
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Residues in contact with ARG 288 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227X PRO* 5.9 2.8 - - - +
228X LEU* 5.7 8.1 + - - +
284X GLY 2.9 14.2 + - - +
285X CYS* 3.2 11.6 + - - +
287X PHE* 1.3 77.3 - - - +
289X SER* 1.3 57.2 + - - +
291X GLU* 3.2 28.9 + - - +
292X ALA* 3.0 31.7 + - + +
295X GLU* 3.8 15.8 + - - -
326X ILE* 6.4 0.9 - - + -
333X LEU* 5.6 9.5 - - - +
504X BRL 4.4 31.4 - - + +
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Residues in contact with SER 289 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285X CYS 3.0 7.4 + - - -
286X GLN 3.0 9.2 + - - -
288X ARG* 1.3 74.0 - - - +
290X VAL* 1.3 66.4 + - - +
291X GLU 3.1 1.6 - - - -
292X ALA* 2.8 19.4 + - - +
293X VAL* 2.8 19.5 + - - +
326X ILE* 3.7 15.6 - - - +
469X LEU* 4.1 8.5 - - - -
504X BRL 3.1 50.0 + - - +
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Residues in contact with VAL 290 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286X GLN 2.9 16.4 + - - +
287X PHE* 3.3 11.2 + - - +
289X SER* 1.3 75.7 - - - +
291X GLU* 1.3 63.9 + - - +
293X VAL* 3.5 5.9 + - - +
294X GLN* 3.4 37.3 + - - +
466X HIS* 3.5 50.0 - - + +
468X LEU* 4.0 22.6 - - + +
469X LEU* 4.4 6.7 - - + +
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Residues in contact with GLU 291 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227X PRO* 5.9 2.0 - - - +
287X PHE 3.2 8.7 + - - +
288X ARG* 3.2 35.6 + - - +
289X SER 3.1 0.6 - - - -
290X VAL* 1.3 79.6 - - - +
292X ALA* 1.3 65.7 + - - +
294X GLN* 3.1 26.8 + - - +
295X GLU* 3.1 37.8 + - + +
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Residues in contact with ALA 292 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226X PHE* 6.2 0.2 - - - -
288X ARG* 3.0 27.7 + - + +
289X SER* 2.8 10.8 + - - +
291X GLU* 1.3 75.5 - - - +
293X VAL* 1.3 51.9 + - - +
295X GLU* 3.1 9.6 + - - +
296X ILE* 2.7 45.9 + - + +
326X ILE* 3.6 29.6 - - + -
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Residues in contact with VAL 293 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289X SER 2.8 20.8 + - - +
290X VAL* 3.6 7.9 - - - +
291X GLU 3.3 0.2 - - - -
292X ALA* 1.3 74.3 - - - +
294X GLN* 1.3 53.1 + - - +
296X ILE* 3.7 0.7 - - - +
297X THR* 2.6 48.0 + - - +
318X LEU* 6.2 0.2 - - + -
322X VAL* 3.8 39.2 - - + +
326X ILE* 4.6 2.9 - - + -
468X LEU* 4.1 15.7 - - + -
469X LEU* 5.0 3.4 - - + -
472X ILE* 4.0 13.0 - - + -
690Y LEU* 3.7 29.8 - - + -
693Y LEU* 4.2 4.5 - - + -
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Residues in contact with GLN 294 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290X VAL* 3.4 34.9 + - - +
291X GLU* 3.1 17.0 + - - +
293X VAL* 1.3 78.4 - - + +
295X GLU* 1.3 63.8 + - + +
297X THR* 3.3 4.8 + - - -
298X GLU* 3.0 34.3 + - - +
468X LEU* 5.1 3.3 - - + +
692Y ARG* 5.1 9.9 - - - +
693Y LEU* 4.2 26.5 - - + -
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Residues in contact with GLU 295 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225X SER* 3.2 33.2 - - - +
226X PHE* 3.8 17.6 - - + -
227X PRO* 3.3 26.8 - - - +
288X ARG* 3.8 17.1 + - - -
291X GLU* 3.2 38.6 - - + +
292X ALA* 3.1 7.6 + - - +
294X GLN* 1.3 77.3 - - + +
296X ILE* 1.3 57.0 + - - +
298X GLU* 3.3 8.2 + - - +
299X TYR* 2.9 23.2 + - - +
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Residues in contact with ILE 296 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226X PHE* 3.9 19.7 - - + -
292X ALA* 2.7 28.3 + - + +
293X VAL* 3.7 4.3 - - - +
295X GLU* 1.3 69.0 - - - +
297X THR* 1.3 56.1 + - - +
299X TYR* 3.0 1.8 + - + +
300X ALA* 2.6 34.1 + - - +
318X LEU* 4.8 7.0 - - + -
322X VAL* 3.8 34.8 - - + +
325X ILE* 3.4 48.9 - - + -
326X ILE* 4.0 15.3 - - + -
329X MET* 5.2 1.3 - - - -
388X ILE* 5.6 0.4 - - + -
392X ILE* 4.4 9.6 - - + -
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Residues in contact with THR 297 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293X VAL* 2.6 35.3 + - - +
294X GLN* 3.6 5.4 - - - -
296X ILE* 1.3 77.2 - - - +
298X GLU* 1.3 63.4 + - - +
300X ALA* 3.3 7.3 + - - +
301X LYS* 3.1 25.7 + - - +
318X LEU* 3.9 18.3 - - + +
322X VAL* 5.4 0.5 - - - +
690Y LEU* 5.1 1.8 - - - +
693Y LEU* 3.9 34.9 - - + +
694Y LEU* 3.9 26.2 - - + +
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Residues in contact with GLU 298 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221X SER* 5.0 0.2 + - - -
225X SER* 3.8 13.8 + - - +
294X GLN* 3.0 30.3 + - - +
295X GLU* 3.5 11.0 - - - +
296X ILE 3.2 0.2 - - - -
297X THR* 1.3 78.6 - - - +
299X TYR* 1.3 62.5 + - - +
301X LYS* 2.7 48.3 + - - +
302X SER* 3.8 6.4 + - - -
693Y LEU* 4.2 8.9 - - - +
696Y GLU* 4.4 16.4 - - - +
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Residues in contact with TYR 299 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218X LEU* 3.4 29.8 + - + +
221X SER* 3.5 15.0 - - - -
222X TYR* 3.3 44.6 - + + -
225X SER* 3.6 7.8 + - - +
226X PHE* 3.7 21.8 - + + -
295X GLU 2.9 13.4 + - - +
296X ILE* 3.5 5.8 - - - +
298X GLU* 1.3 74.0 - - - +
300X ALA* 1.3 65.2 + - - +
301X LYS 3.0 2.0 - - - -
302X SER* 2.6 24.5 + - - -
303X ILE* 3.7 20.2 - - + +
385X ALA* 2.6 34.8 + - - -
388X ILE* 4.3 14.1 - - + -
389X ALA* 4.1 3.4 - - + +
392X ILE* 4.3 11.9 - - + -
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Residues in contact with ALA 300 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296X ILE 2.6 20.7 + - - +
297X THR 3.6 5.4 - - - +
299X TYR* 1.3 74.3 - - - +
301X LYS* 1.3 60.9 + - - +
303X ILE* 3.4 18.8 + - - +
306X PHE* 3.1 38.8 - - + +
318X LEU* 3.9 26.0 - - + -
392X ILE* 3.9 14.8 - - + -
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Residues in contact with LYS 301 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297X THR* 3.1 17.4 + - - +
298X GLU* 2.7 37.7 + - - +
299X TYR 3.0 1.0 - - - -
300X ALA* 1.3 78.6 - - - +
302X SER* 1.3 59.9 + - - +
303X ILE 3.3 3.6 + - - +
306X PHE* 4.0 1.3 - - + -
307X VAL* 3.4 38.1 - - + +
693Y LEU 3.1 22.9 + - - -
694Y LEU* 3.4 37.1 + - + +
696Y GLU 3.7 13.7 + - - -
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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