Contacts of the helix formed by residues 293 - 317 (chain U) 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 PRO 293 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292U LEU* 1.3 99.3 - - + +
294U LEU* 1.3 60.1 + - - +
295U ASP* 3.3 3.4 - - + +
296U ASP* 2.9 33.2 - - - +
297U GLN* 2.9 25.3 + - - +
384U SER* 3.9 9.2 - - - +
385U ASN* 6.3 1.1 - - + -
388U GLU* 4.4 11.2 - - - +
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Residues in contact with LEU 294 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292U LEU 3.6 0.8 + - - -
293U PRO* 1.3 70.8 - - - +
295U ASP* 1.3 68.6 + - - +
297U GLN* 3.4 14.0 + - - +
298U VAL* 3.4 18.3 + - + +
634V HIS* 3.5 36.6 - - + +
637V LEU* 4.2 24.9 - - + +
638V GLN* 3.9 30.3 - - + +
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Residues in contact with ASP 295 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293U PRO* 3.3 3.4 - - + +
294U LEU* 1.3 83.7 - - - +
296U ASP* 1.3 69.2 + - - +
298U VAL* 3.3 8.8 + - - +
299U ILE* 3.3 29.9 + - + +
628V GLU* 5.4 7.5 - - - +
629V ARG* 5.6 1.7 + - - -
634V HIS* 4.7 10.7 + - - -
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Residues in contact with ASP 296 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292U LEU* 4.4 12.1 - - + +
293U PRO* 2.9 29.1 + - + +
294U LEU 3.3 0.4 - - - -
295U ASP* 1.3 77.4 - - - +
297U GLN* 1.3 66.2 + - - +
299U ILE* 3.3 3.9 + - - +
300U LEU* 3.0 30.1 + - + +
382U GLY 4.2 1.9 - - - +
383U LEU* 3.4 22.2 - - + +
384U SER* 2.6 50.8 + - - -
385U ASN* 4.6 3.8 + - - +
389U VAL* 5.6 2.7 - - + -
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Residues in contact with GLN 297 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284U LYS* 4.9 2.6 - - - +
289U PHE* 3.6 32.2 - - + -
290U SER* 3.1 32.2 + - - +
292U LEU* 3.2 21.8 - - + +
293U PRO 2.9 20.7 + - - +
294U LEU* 3.4 16.0 - - - +
295U ASP 3.2 0.2 - - - -
296U ASP* 1.3 77.9 - - - +
298U VAL* 1.3 61.7 + - - +
300U LEU* 3.5 0.6 + - - +
301U LEU* 3.2 23.2 + - - +
637V LEU* 3.1 44.9 + - + +
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Residues in contact with VAL 298 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294U LEU* 3.4 10.1 + - + +
295U ASP* 3.3 13.2 + - - +
296U ASP 3.2 0.4 - - - -
297U GLN* 1.3 80.0 - - - +
299U ILE* 1.3 61.0 + - + +
301U LEU 3.5 0.7 + - - -
302U ARG* 2.9 30.2 + - - +
630V HIS* 4.0 22.9 - - + +
633V LEU* 3.2 29.2 - - + +
634V HIS* 4.3 28.5 - - + +
637V LEU* 3.5 18.4 - - + -
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Residues in contact with ILE 299 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295U ASP* 3.3 19.6 + - + +
296U ASP* 3.3 6.3 + - - +
298U VAL* 1.3 77.7 - - + +
300U LEU* 1.3 61.6 + - - +
302U ARG* 3.0 7.2 + - - +
303U ALA* 2.8 31.5 + - + +
380U SER* 3.5 28.9 - - - -
381U LYS 3.8 12.1 - - - +
382U GLY* 3.6 34.1 - - - +
383U LEU* 3.9 12.6 - - + +
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Residues in contact with LEU 300 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289U PHE* 3.9 20.0 - - + -
292U LEU* 4.3 9.0 - - + -
296U ASP* 3.0 21.6 + - + +
297U GLN 3.8 3.8 - - - +
299U ILE* 1.3 76.8 - - - +
301U LEU* 1.3 57.8 + - - +
303U ALA* 3.4 3.5 + - - +
304U GLY* 2.9 27.5 + - - -
375U LEU* 3.6 36.0 - - + +
376U PHE* 3.9 18.2 - - + -
377U ASN* 3.6 25.4 - - + +
380U SER* 4.8 2.9 - - - +
383U LEU* 4.0 20.2 - - + -
389U VAL* 4.1 15.9 - - + -
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Residues in contact with LEU 301 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279U LEU* 4.0 30.5 - - + -
280U VAL* 4.4 14.1 - - + -
282U TRP* 5.6 0.4 - - + -
283U ALA* 4.0 23.1 - - + -
289U PHE* 4.1 8.1 - - + -
297U GLN 3.2 13.2 + - - +
298U VAL 4.0 3.1 - - - +
300U LEU* 1.3 77.7 - - - +
302U ARG* 1.3 60.6 + - - +
304U GLY 4.4 0.2 - - - +
305U TRP* 3.0 32.7 + - - +
308U LEU* 4.6 4.7 - - + -
375U LEU* 4.0 17.0 - - + -
454U MET* 3.7 13.3 - - + +
633V LEU* 4.1 13.9 - - + -
637V LEU* 4.1 23.3 - - + -
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Residues in contact with ARG 302 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298U VAL* 2.9 24.2 + - - +
299U ILE* 3.6 7.2 - - - +
301U LEU* 1.3 78.2 - - - +
303U ALA* 1.3 61.9 + - - +
305U TRP* 4.3 13.5 - - - -
306U ASN* 5.5 0.3 - - - +
453U GLU 3.5 18.2 + - - -
454U MET* 3.7 27.5 - - + +
456U GLU* 3.1 11.1 + - - +
457U ALA* 2.8 67.4 - - + +
458U PRO* 3.9 8.5 - - - +
630V HIS* 3.1 52.3 + - + +
633V LEU* 4.0 2.7 - - + -
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Residues in contact with ALA 303 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299U ILE* 2.8 15.0 + - + +
300U LEU* 4.1 2.0 - - - +
302U ARG* 1.3 78.4 - - - +
304U GLY* 1.3 57.5 + - - +
306U ASN* 4.1 10.3 - - - +
307U GLU* 4.7 6.9 - - - +
377U ASN* 5.6 8.1 + - + +
380U SER* 3.3 28.9 - - - +
381U LYS* 6.0 2.2 - - - +
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Residues in contact with GLY 304 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300U LEU 2.9 16.2 + - - -
303U ALA* 1.3 79.5 - - - +
305U TRP* 1.3 64.1 + - - +
306U ASN* 3.2 4.0 + - - -
307U GLU* 3.3 8.1 + - - +
308U LEU* 3.0 36.5 + - - +
374U VAL* 4.4 15.7 - - - +
377U ASN* 6.5 0.2 - - - -
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Residues in contact with TRP 305 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272U ALA* 5.1 1.4 - - - +
276U LEU* 2.9 35.2 - - + +
279U LEU* 3.8 18.4 - - + -
301U LEU 3.0 21.1 + - - +
302U ARG 4.3 11.9 + - - -
303U ALA 3.8 1.4 - - - -
304U GLY* 1.3 74.4 - - - +
306U ASN* 1.3 70.0 + - + +
308U LEU* 3.4 2.1 + - - +
309U LEU* 3.0 40.9 + - + +
433U LEU* 3.3 34.8 - - + -
436U LEU* 4.0 2.7 - - + -
451U LEU* 3.6 23.9 - - + +
454U MET* 3.6 40.2 - - + -
455U LEU* 3.9 15.0 - - + -
457U ALA* 5.3 2.5 - - + -
502U 9CR 3.9 22.9 - - + +
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Residues in contact with ASN 306 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302U ARG 5.5 0.2 - - - +
303U ALA 4.1 14.9 - - - +
305U TRP* 1.3 104.1 + - + +
307U GLU* 1.3 65.0 + - - +
309U LEU* 3.3 2.7 + - - +
310U ILE* 2.5 38.1 + - + +
429U GLY* 2.8 43.4 + - - -
430U LEU* 6.0 0.4 - - - +
432U CYS* 5.7 1.1 - - + -
433U LEU* 3.4 29.4 - - + +
502U 9CR 4.3 12.7 - - + +
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Residues in contact with GLU 307 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303U ALA 4.7 7.7 - - - +
304U GLY* 3.3 6.3 + - - +
306U ASN* 1.3 86.6 + - - +
308U LEU* 1.3 63.9 + - - +
310U ILE* 3.5 7.8 - - - +
311U ALA* 3.0 26.7 + - - +
374U VAL* 3.9 20.0 - - + +
422U LEU 5.0 0.9 - - - +
425U LEU* 3.6 33.0 - - + +
426U ARG* 2.8 61.6 + - - +
429U GLY* 4.4 8.1 - - - -
430U LEU* 5.8 0.5 + - - +
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Residues in contact with LEU 308 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279U LEU* 4.0 22.9 - - + -
282U TRP* 4.0 8.7 - - + -
301U LEU* 4.6 5.2 - - + -
304U GLY* 3.0 35.5 + - - +
305U TRP* 3.6 6.3 - - - +
307U GLU* 1.3 78.4 - - - +
309U LEU* 1.3 60.2 + - - +
311U ALA* 3.6 2.5 + - + +
312U SER* 3.3 6.4 + - - -
371U ARG* 2.9 80.2 + - + +
374U VAL* 3.8 12.1 - - + -
375U LEU* 4.3 23.1 - - + -
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Residues in contact with LEU 309 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272U ALA* 3.6 23.6 - - - +
275U GLN* 3.9 29.6 - - + -
276U LEU* 3.4 28.9 - - + -
279U LEU* 4.0 25.1 - - + -
305U TRP* 3.0 29.9 + - + +
306U ASN 4.0 2.2 - - - +
308U LEU* 1.3 73.5 - - - +
310U ILE* 1.3 65.7 + - - +
311U ALA 3.1 1.8 - - - -
312U SER* 3.2 5.8 + - - +
313U PHE* 3.2 25.0 + - - +
371U ARG* 4.2 11.2 - - - +
502U 9CR 4.1 17.2 - - + +
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Residues in contact with ILE 310 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306U ASN* 2.5 38.4 + - + +
307U GLU* 3.5 8.7 - - - -
309U LEU* 1.3 75.2 - - - +
311U ALA* 1.3 58.5 + - - +
313U PHE* 3.2 31.5 - - + -
314U SER* 2.7 37.5 + - - +
349U VAL* 4.6 6.3 - - + -
353U LEU* 3.3 25.6 - - + -
425U LEU* 2.9 28.0 - - + +
428U ILE* 4.6 7.9 - - + -
429U GLY* 4.9 11.4 - - - -
432U CYS* 5.7 6.5 - - + -
502U 9CR 5.0 6.7 - - + +
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Residues in contact with ALA 311 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307U GLU 3.0 18.0 + - - +
308U LEU* 3.7 6.7 - - - +
309U LEU 3.1 0.2 - - - -
310U ILE* 1.3 83.8 - - - +
312U SER* 1.3 56.2 + - - +
314U SER* 3.8 4.4 - - - -
315U HIS* 3.1 28.1 + - - +
357U MET* 3.9 8.9 - - + +
367U LEU* 3.7 11.6 - - + +
371U ARG* 4.2 18.6 - - + -
425U LEU* 4.1 17.9 - - + -
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Residues in contact with SER 312 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239U GLU* 4.2 3.2 + - - -
275U GLN* 5.9 3.8 - - - -
308U LEU 3.4 1.3 + - - -
309U LEU* 3.2 11.9 + - - -
311U ALA* 1.3 78.9 - - - +
313U PHE* 1.3 59.6 + - - +
315U HIS* 4.1 3.5 - - - +
316U ARG* 3.1 39.2 + - - +
367U LEU* 4.9 6.2 - - - +
371U ARG* 2.7 44.9 + - - +
502U 9CR 5.6 0.9 - - - -
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Residues in contact with PHE 313 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309U LEU 3.2 22.3 + - - -
310U ILE* 3.2 31.6 - - + -
312U SER* 1.3 75.4 - - - +
314U SER* 1.3 63.9 + - - +
316U ARG* 3.6 25.1 - - - +
317U SER* 2.7 37.8 + - - -
324U ILE* 3.9 24.2 - - + -
325U LEU 3.9 6.0 - - - +
349U VAL* 3.7 26.5 - - + -
502U 9CR 3.4 70.7 - - + +
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Residues in contact with SER 314 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310U ILE* 2.7 31.4 + - - +
311U ALA* 3.8 4.0 - - - -
313U PHE* 1.3 89.1 - - - +
315U HIS* 1.3 64.9 + - - +
317U SER* 3.2 8.5 + - - -
318U ILE* 3.6 6.6 + - - +
349U VAL* 3.8 9.9 - - - +
353U LEU* 3.9 8.5 - - - +
354U VAL* 3.5 33.4 - - - +
357U MET* 3.9 18.4 - - - -
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Residues in contact with HIS 315 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311U ALA 3.1 15.6 + - - +
312U SER 4.1 1.8 - - - +
314U SER* 1.3 77.0 - - - +
316U ARG* 1.3 68.9 + - - +
318U ILE* 2.9 39.7 + - + +
357U MET* 3.5 12.5 - - + -
362U MET* 3.1 49.2 + - + +
363U ASP* 3.8 10.4 + - - -
364U LYS* 4.5 25.5 + - + -
367U LEU* 3.7 33.0 - - + +
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Residues in contact with ARG 316 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243U GLU* 5.8 3.6 - - - +
244U PRO* 4.9 23.1 - - + +
275U GLN* 4.5 8.5 + - - -
312U SER* 3.1 32.0 + - - +
313U PHE* 3.6 7.7 - - - +
315U HIS* 1.3 81.3 + - - +
317U SER* 1.3 58.3 + - - +
318U ILE* 3.0 8.0 + - - +
319U ALA* 3.5 11.8 + - - +
325U LEU* 2.6 62.9 + - + +
326U LEU 4.6 3.8 - - - -
327U ALA* 3.0 25.7 - - - +
502U 9CR 2.8 31.3 + - - -
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Residues in contact with SER 317 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313U PHE 2.7 23.4 + - - -
314U SER 3.5 8.1 - - - -
315U HIS 3.1 1.0 - - - -
316U ARG* 1.3 74.2 - - - +
318U ILE* 1.3 62.6 + - - +
319U ALA 3.2 1.5 + - - +
320U VAL* 3.0 21.6 + - - +
323U GLY 3.8 5.7 - - - +
324U ILE* 2.9 18.7 - - - +
325U LEU* 2.7 34.8 + - - +
354U VAL* 3.6 18.2 - - - +
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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