Contacts of the helix formed by residues 366 - 394 (chain A) in PDB entry 6FWF
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 366 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PRO 3.4 1.4 + - - -
365A LYS* 1.3 87.2 - - + +
367A GLN* 1.3 58.7 + - - +
368A ARG 3.5 2.0 - - - +
369A ALA* 3.7 20.6 - - + +
370A GLY* 3.1 22.2 + - - -
433A LEU* 5.9 0.2 - - - +
436A ARG* 5.4 1.0 + - - -
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 3.8 20.0 - - - +
352A LEU* 5.1 1.4 - - - +
363A ASP* 3.2 26.5 + - - +
364A PRO* 3.5 36.1 + - + +
365A LYS 3.4 0.6 - - - -
366A PHE* 1.3 74.6 - - - +
368A ARG* 1.3 60.6 + - - +
370A GLY* 3.2 2.2 + - - +
371A VAL* 2.8 39.9 + - + +
433A LEU* 3.5 44.6 + - - +
436A ARG* 3.8 5.8 + - - +
437A CYS* 3.4 24.6 - - - -
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Residues in contact with ARG 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 3.7 28.5 + - - +
278A LYS* 3.3 54.8 - - - +
279A ALA* 4.4 8.7 - - + -
363A ASP* 5.1 0.4 + - - -
366A PHE* 3.5 0.4 - - - +
367A GLN* 1.3 78.9 - - - +
369A ALA* 1.3 52.8 + - - +
371A VAL* 3.4 6.2 + - + +
372A ASN* 2.8 56.1 + - - +
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PHE* 3.6 31.7 + - + +
368A ARG* 1.3 78.1 - - - +
370A GLY* 1.3 52.7 + - - +
372A ASN* 3.5 7.3 + - - +
373A PHE* 2.8 35.4 + - - +
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PHE 3.1 15.1 + - - -
367A GLN 3.2 3.5 + - - -
369A ALA* 1.3 72.8 - - - +
371A VAL* 1.3 55.8 + - - +
373A PHE* 3.3 8.6 + - - +
374A LEU* 2.8 35.5 + - - +
429A LEU* 3.8 7.1 - - - +
433A LEU* 3.8 17.0 - - - -
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 5.1 6.7 - - - +
279A ALA* 4.3 11.2 - - + -
280A LEU* 4.2 20.2 - - + -
283A TYR* 2.7 50.2 + - + +
352A LEU* 4.4 13.2 - - + +
367A GLN* 2.8 37.4 + - + +
368A ARG* 3.7 7.0 - - - +
370A GLY* 1.3 72.2 - - - +
372A ASN* 1.3 52.5 + - - +
374A LEU* 3.5 0.5 + - - +
375A TYR* 2.8 18.4 + - - +
433A LEU* 3.7 20.9 - - + -
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Residues in contact with ASN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA* 3.1 24.2 - - - +
282A LYS* 3.8 16.5 + - - +
368A ARG* 2.8 45.2 + - - +
369A ALA* 3.8 6.5 - - - +
371A VAL* 1.3 70.8 - - - +
373A PHE* 1.3 56.6 + - - +
375A TYR* 3.4 14.3 - - + +
376A ILE* 2.8 42.9 + - + +
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Residues in contact with PHE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA 2.8 22.1 + - - +
370A GLY* 3.3 10.5 - - - +
372A ASN* 1.3 71.7 - - - +
374A LEU* 1.3 53.2 + - - +
376A ILE* 3.4 18.4 - - + +
377A ALA* 2.8 37.5 + - + +
429A LEU* 3.9 18.8 - - + -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TYR* 4.0 10.1 - - + +
348A LEU* 5.5 4.9 - - + -
352A LEU* 3.8 13.2 - - + -
370A GLY 2.8 19.5 + - - +
371A VAL 3.6 5.2 - - - +
373A PHE* 1.3 70.8 - - - +
375A TYR* 1.3 55.6 + - - +
377A ALA* 3.3 5.0 + - - +
378A LEU* 2.8 54.4 + - + +
426A GLY* 3.8 16.2 - - - +
429A LEU* 3.8 15.4 - - + +
430A TRP* 3.3 40.6 - - + +
433A LEU* 3.6 19.7 - - + -
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Residues in contact with TYR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA 4.6 0.9 - - - -
282A LYS* 3.3 38.0 + - + +
283A TYR* 3.3 61.8 + + + +
285A PHE* 5.6 2.4 - - - -
286A LEU* 4.1 23.6 + - + +
371A VAL 2.8 22.4 + - - +
372A ASN* 3.4 17.0 - - + +
374A LEU* 1.3 72.2 - - - +
376A ILE* 1.3 73.9 + - + +
378A LEU* 3.3 9.0 - - - +
379A PHE* 2.8 33.1 + + + +
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Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ASN* 2.8 30.3 + - + +
373A PHE* 3.4 24.5 - - + +
375A TYR* 1.3 85.2 - - + +
377A ALA* 1.3 62.7 + - - +
379A PHE* 3.3 14.4 - - + +
380A ILE* 2.8 35.6 + - + +
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 2.8 25.1 + - + +
374A LEU* 3.5 8.5 - - - +
376A ILE* 1.3 72.1 - - - +
378A LEU* 1.3 55.5 + - + +
380A ILE* 3.3 11.8 - - + +
381A VAL* 2.8 44.6 + - + +
422A LEU 5.6 2.0 - - - +
426A GLY* 5.3 9.2 - - - -
429A LEU* 5.6 4.5 - - + -
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TYR* 5.8 2.9 - - + -
286A LEU* 5.4 2.5 - - + -
341A PHE* 4.3 23.6 - - + -
344A ALA* 5.7 2.9 - - + -
345A THR* 3.9 30.1 - - + +
348A LEU* 5.3 14.1 - - + -
374A LEU* 2.8 38.9 + - + +
375A TYR* 3.3 12.3 - - - +
377A ALA* 1.3 72.5 - - - +
379A PHE* 1.3 56.9 + - - +
381A VAL* 3.3 5.8 + - + +
382A VAL* 2.8 39.8 + - + +
423A LEU* 5.1 14.8 - - + +
426A GLY* 4.3 18.6 - - - -
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Residues in contact with PHE 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 4.7 23.9 - - + +
375A TYR* 2.8 26.1 + + + +
376A ILE* 3.2 19.5 + - + +
378A LEU* 1.3 73.4 - - - +
380A ILE* 1.3 71.0 + - + +
382A VAL* 3.5 6.0 - - + +
383A GLY* 2.8 27.9 + - - -
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Residues in contact with ILE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 2.8 24.3 + - + +
377A ALA* 3.3 16.4 - - + +
379A PHE* 1.3 80.5 - - + +
381A VAL* 1.3 64.2 + - + +
383A GLY* 4.5 1.1 - - - +
384A GLY* 2.8 30.7 + - - +
418A PHE* 6.3 0.2 - - + -
419A TRP* 3.8 11.1 - - + -
422A LEU* 4.7 19.3 - - + -
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PHE* 3.7 22.9 - - + -
377A ALA* 2.8 27.6 + - + +
378A LEU* 3.7 7.2 - - + +
380A ILE* 1.3 71.3 - - + +
382A VAL* 1.3 52.0 + - - +
385A SER* 2.8 42.3 + - - -
415A LEU* 5.9 0.2 - - + -
419A TRP* 3.7 26.1 - - + +
422A LEU* 3.4 46.4 - - + +
423A LEU* 3.7 13.9 - - + +
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Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 5.7 4.7 - - + -
290A LEU* 4.0 22.0 - - + -
341A PHE* 3.3 45.1 - - + -
345A THR* 5.6 2.2 - - + -
378A LEU* 2.8 38.5 + - + +
379A PHE* 3.5 6.5 - - + +
381A VAL* 1.3 71.4 - - - +
383A GLY* 1.3 63.0 + - - +
385A SER* 2.7 18.0 + - - -
386A TYR* 3.3 41.1 - - + +
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Residues in contact with GLY 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PHE* 2.8 19.8 + - - -
380A ILE* 4.1 0.7 - - - -
382A VAL* 1.3 75.2 - - - +
384A GLY* 1.3 52.3 + - - +
386A TYR* 3.4 16.4 + - - -
387A ALA* 2.8 37.2 + - - +
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Residues in contact with GLY 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ILE* 2.8 22.0 + - - +
383A GLY* 1.3 70.7 - - - -
385A SER* 1.3 55.4 + - - +
387A ALA* 3.7 7.5 - - - +
388A GLY 2.8 24.8 + - - -
419A TRP* 3.3 32.2 - - - -
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLN* 4.5 0.7 - - - +
341A PHE* 3.5 15.6 - - - -
381A VAL 2.8 21.4 + - - -
382A VAL 2.7 22.9 + - - -
384A GLY* 1.3 72.8 - - - +
386A TYR* 1.3 62.0 + - - +
388A GLY* 3.3 2.1 + - - -
389A ASN* 2.9 29.6 + - - +
405A PHE 4.2 0.3 - - - +
415A LEU* 3.5 28.6 - - - +
416A GLY 4.3 0.5 + - - -
419A TRP* 3.4 24.1 - - - -
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Residues in contact with TYR 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 4.2 13.3 - - + +
293A VAL* 5.6 2.3 - - + +
334A TRP* 2.8 57.4 + + + -
337A GLN* 3.9 24.5 - - + -
338A SER* 4.5 15.4 + - - -
341A PHE* 4.6 3.6 - + - -
382A VAL* 3.3 44.6 - - + +
383A GLY* 3.4 15.8 + - - -
385A SER* 1.3 78.9 + - - +
387A ALA* 1.3 56.4 + - - +
389A ASN* 3.7 13.0 - - - +
390A PHE* 2.8 25.5 + - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A TRP* 5.4 0.4 - - - -
383A GLY 2.8 20.7 + - - +
384A GLY* 3.7 9.2 - - - +
386A TYR* 1.3 76.3 - - - +
388A GLY* 1.3 59.4 + - - +
390A PHE* 3.0 11.8 - - + +
391A PHE* 2.8 45.1 + - + -
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Residues in contact with GLY 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLY 2.8 17.3 + - - -
385A SER 3.3 2.0 + - - -
387A ALA* 1.3 68.7 - - - +
389A ASN* 1.3 54.5 + - - +
391A PHE* 3.2 9.4 + - - +
392A ALA 2.8 31.0 + - - -
397A LEU* 6.0 0.4 - - - -
405A PHE* 3.5 20.9 - - - -
406A GLY* 3.2 18.0 - - - -
419A TRP* 4.7 1.6 - - - -
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Residues in contact with ASN 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.5 2.7 - - - -
333A THR* 3.4 37.6 + - - +
334A TRP* 4.0 1.3 - - - +
337A GLN* 5.0 1.8 - - - +
385A SER 2.9 15.6 + - - +
386A TYR* 3.5 17.1 - - - +
388A GLY* 1.3 73.0 - - - +
390A PHE* 1.3 58.6 + - - +
393A LEU* 2.8 41.4 + - + +
406A GLY 3.7 2.8 - - - +
407A HIS* 3.4 19.8 + - - +
414A ASP* 3.1 37.2 + - - +
415A LEU* 3.8 2.3 - - - +
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Residues in contact with PHE 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TRP* 3.5 52.5 - + + -
326A PHE* 3.7 20.9 - + - -
330A LEU* 3.5 24.7 - - + +
334A TRP* 3.8 15.7 - + + -
386A TYR 2.8 18.6 + - - +
387A ALA* 3.0 15.7 - - + +
389A ASN* 1.3 74.8 - - - +
391A PHE* 1.3 81.9 + + - +
394A THR* 2.7 35.3 + - - +
396A ILE* 4.8 3.4 - - + -
----------------------------------------------------------
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Residues in contact with PHE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ALA* 2.8 40.1 + - + +
388A GLY* 3.2 8.0 + - - +
390A PHE* 1.3 96.7 - + - +
392A ALA* 1.3 59.3 + - - +
394A THR* 3.5 7.3 + - - -
396A ILE* 2.8 53.1 + - + +
397A LEU* 4.7 14.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.7 18.0 - - - +
64A THR* 5.1 1.6 - - - +
388A GLY 2.8 9.9 + - - -
391A PHE* 1.3 70.5 - - - +
393A LEU* 1.3 60.3 + - - +
394A THR 3.2 2.0 - - - -
395A HIS* 2.8 23.5 + - - +
397A LEU* 3.7 18.2 - - + -
402A ASN* 3.7 12.6 - - + +
406A GLY* 3.5 11.2 - - - -
407A HIS 3.4 27.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR 3.1 33.1 - - - +
65A GLY* 3.9 16.4 - - - +
327A PRO* 5.1 5.6 - - + +
329A ALA* 3.8 28.3 - - + +
330A LEU* 3.4 28.9 - - + -
333A THR* 3.5 33.4 - - + +
389A ASN* 2.8 26.5 + - + +
392A ALA* 1.3 72.3 - - - +
394A THR* 1.3 58.1 + - - +
395A HIS* 3.3 1.2 + - - +
407A HIS* 3.8 13.2 - - + +
----------------------------------------------------------
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Residues in contact with THR 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ASP 3.1 27.1 - - - +
325A TRP* 3.6 21.1 - - + +
327A PRO* 4.2 11.0 - - + -
330A LEU* 4.6 1.6 - - + -
390A PHE* 2.7 24.5 + - + +
391A PHE 3.5 0.7 + - - -
393A LEU* 1.3 77.0 - - - +
395A HIS* 1.3 69.1 + - - +
396A ILE* 3.2 28.6 - - + +
----------------------------------------------------------
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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