Contacts of the helix formed by residues 356 - 387 (chain B) in PDB entry 6R7Y
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 SER 356 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B SER 5.0 0.2 + - - -
353B GLU 4.4 4.4 + - - -
355B THR* 1.3 82.2 - - - +
357B VAL* 1.3 74.6 + - - +
358B LEU 3.3 2.2 - - - -
359B LEU* 3.5 14.0 + - - +
360B TYR* 3.7 27.9 - - - -
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLU 5.0 5.8 + - - +
354B TRP* 4.4 23.3 - - + -
355B THR 4.3 2.4 - - - +
356B SER* 1.3 84.9 - - - +
358B LEU* 1.3 64.9 + - - +
359B LEU 3.3 0.5 + - - -
360B TYR* 3.3 16.1 + - + +
361B VAL* 3.4 20.5 + - + +
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TRP* 5.7 5.2 - - + -
343B ALA* 4.1 23.6 - - + +
346B LEU* 4.0 39.3 - - + +
347B HIS* 4.3 11.0 - - + +
350B SER* 6.2 1.8 - - - -
354B TRP* 3.5 38.9 + - + +
355B THR 5.3 1.1 - - - +
356B SER 3.3 0.4 - - - -
357B VAL* 1.3 81.2 - - - +
359B LEU* 1.3 61.2 + - - +
361B VAL* 3.7 17.6 + - + -
362B PRO* 3.3 19.9 - - + +
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLU* 4.3 19.1 - - - +
343B ALA* 5.3 4.3 - - + +
344B LEU* 4.2 32.8 - - + +
347B HIS* 5.2 12.3 - - + +
355B THR 3.9 16.6 + - - +
356B SER* 3.5 11.7 + - - +
357B VAL 3.2 1.2 - - - -
358B LEU* 1.3 81.8 - - - +
360B TYR* 1.3 71.2 + - + +
361B VAL 3.5 0.2 - - - -
362B PRO* 3.9 11.0 - - + +
363B SER* 5.0 2.9 + - - -
428B LEU* 6.5 0.2 - - + -
431B GLN* 4.3 26.7 - - - +
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Residues in contact with TYR 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B SER* 3.7 25.2 - - - -
357B VAL* 3.3 10.0 + - + +
358B LEU 3.3 0.2 - - - -
359B LEU* 1.3 85.7 - - + +
361B VAL* 1.3 64.5 + - - +
362B PRO 3.7 0.7 - - - -
363B SER* 3.3 17.6 + - - -
364B ILE* 3.4 24.4 - - + +
431B GLN* 4.3 33.6 + - + +
435B THR* 4.4 21.3 - - + -
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B VAL* 3.4 25.8 - - + +
358B LEU* 4.0 17.7 - - + +
360B TYR* 1.3 76.3 - - + +
362B PRO* 1.3 73.0 - - + +
364B ILE* 3.1 9.0 + - + +
365B ILE* 3.0 42.2 + - + +
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Residues in contact with PRO 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.3 16.7 - - + -
339B MET* 4.1 25.8 - - + +
340B GLU* 3.5 30.3 - - - +
343B ALA* 4.5 13.7 - - + -
358B LEU* 3.3 17.5 - - + +
359B LEU* 3.9 8.5 - - + +
361B VAL* 1.3 93.1 - - + +
363B SER* 1.3 58.9 + - - +
365B ILE* 3.8 9.3 - - + +
366B TYR* 2.9 22.2 + - - +
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Residues in contact with SER 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.9 20.6 - - - -
340B GLU* 5.4 0.4 - - - -
359B LEU 5.0 2.6 + - - -
360B TYR* 3.3 13.1 + - - -
361B VAL 3.3 0.4 - - - -
362B PRO* 1.3 80.2 - - - +
364B ILE* 1.3 58.0 + - - +
366B TYR* 3.3 3.6 + - - +
367B ALA* 2.7 34.7 + - - +
432B SER* 5.0 6.7 - - - -
435B THR* 3.2 37.6 + - - +
436B LEU* 4.1 8.4 - - - +
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B TYR* 3.4 25.1 + - + +
361B VAL* 3.1 11.3 + - - +
363B SER* 1.3 82.1 + - - +
365B ILE* 1.3 66.4 + - + +
367B ALA* 3.6 5.8 - - - +
368B ILE* 2.9 41.2 + - + +
435B THR* 5.4 4.0 - - + -
439B THR* 3.9 25.6 - - + +
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Residues in contact with ILE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B MET* 4.8 20.6 - - - -
361B VAL* 3.0 36.5 + - + +
362B PRO* 3.8 7.9 - - + +
364B ILE* 1.3 78.0 - - + +
366B TYR* 1.3 62.9 + - - +
368B ILE* 3.4 7.3 + - + +
369B VAL* 3.1 32.5 + - + +
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Residues in contact with TYR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER 5.2 0.2 + - - -
332B VAL* 4.5 16.4 - - + -
333B MET* 3.9 28.3 + - - +
336B TYR* 3.6 43.7 - + + -
362B PRO 2.9 18.3 + - - +
363B SER* 3.5 3.8 - - - +
365B ILE* 1.3 78.7 - - - +
367B ALA* 1.3 56.8 + - - +
369B VAL* 3.4 6.4 + - + -
370B ILE* 3.0 57.2 + - + +
411B ASN* 3.8 16.1 + - - -
414B ALA* 5.6 0.9 - - - +
415B SER* 3.6 31.0 + - - -
432B SER* 6.1 0.2 - - - -
436B LEU* 4.3 12.6 - - + -
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B SER 2.7 20.4 + - - +
364B ILE* 3.1 5.4 + - - +
366B TYR* 1.3 73.1 - - - +
368B ILE* 1.3 64.1 + - - +
370B ILE* 3.4 6.3 + - - +
371B GLU* 3.2 23.2 + - - +
436B LEU* 3.8 21.1 - - + +
439B THR* 3.7 32.1 - - + -
440B SER* 4.8 10.4 - - - +
443B LEU* 5.0 1.4 - - - +
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ILE* 2.9 30.9 + - + +
365B ILE* 4.0 7.0 - - - +
366B TYR 3.4 0.2 - - - -
367B ALA* 1.3 76.0 - - - +
369B VAL* 1.3 63.6 + - + +
371B GLU* 3.4 2.1 + - - +
372B ILE* 3.1 39.2 + - + +
439B THR* 5.0 7.4 - - + -
443B LEU* 4.5 30.3 - - + -
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 4.0 28.3 - - + -
365B ILE* 3.1 27.2 + - + +
366B TYR* 3.9 9.6 - - + +
367B ALA 3.3 0.2 - - - -
368B ILE* 1.3 78.5 - - + +
370B ILE* 1.3 58.6 + - + +
372B ILE* 3.9 6.9 - - + +
373B MET* 3.0 35.7 + - + +
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TYR* 3.0 60.0 + - + +
367B ALA* 3.7 6.1 - - - +
368B ILE 3.3 0.2 - - - -
369B VAL* 1.3 76.8 - - + +
371B GLU* 1.3 64.0 + - - +
373B MET* 3.3 1.5 + - - +
374B ASN* 2.9 43.0 + - - +
411B ASN* 3.6 32.5 - - - +
412B CYS* 3.9 29.6 - - - +
436B LEU* 4.6 13.0 - - + -
440B SER* 5.8 3.1 - - - +
507B TYR* 5.6 1.3 - - - +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ALA 3.2 10.0 + - - +
368B ILE 3.4 0.4 + - - +
370B ILE* 1.3 84.1 - - - +
372B ILE* 1.3 61.7 + - - +
374B ASN* 4.1 21.9 + - - +
375B ARG* 3.7 46.5 + - - +
412B CYS* 5.4 1.6 - - - -
440B SER* 3.4 26.5 + - - +
443B LEU* 3.7 37.0 - - + +
444B ASN* 4.4 14.2 + - - +
447B MET* 6.1 0.7 - - + -
503B LEU* 6.2 0.3 - - - +
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Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ILE* 3.1 33.4 + - + +
369B VAL* 4.0 6.5 - - + +
370B ILE 3.2 0.2 - - - -
371B GLU* 1.3 80.0 - - - +
373B MET* 1.3 67.4 + - - +
375B ARG* 3.3 6.4 + - - +
376B LEU* 3.1 38.5 + - + +
443B LEU* 5.8 2.9 - - + -
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Residues in contact with MET 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 4.0 29.6 - - + -
329B SER* 4.2 15.5 - - - -
332B VAL* 4.3 18.2 - - + -
369B VAL* 3.0 23.2 + - + +
370B ILE* 4.0 2.5 - - - +
372B ILE* 1.3 79.5 - - - +
374B ASN* 1.3 58.2 + - - +
376B LEU* 3.3 10.4 + - + -
377B TYR* 2.8 30.2 + - + +
407B PHE* 3.7 17.5 - - + -
411B ASN* 3.4 30.1 - - - +
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Residues in contact with ASN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE* 2.9 21.9 + - - +
371B GLU* 4.2 21.2 + - - +
372B ILE 3.2 0.2 - - - -
373B MET* 1.3 78.2 - - - +
375B ARG* 1.3 57.8 + - + +
377B TYR* 3.4 2.6 + - - +
378B ARG* 2.9 28.2 + - - +
407B PHE* 3.3 14.4 - - - -
408B ASN* 2.7 34.2 + - - +
411B ASN* 3.1 23.3 + - - +
412B CYS* 4.0 21.8 - - - -
503B LEU* 5.2 1.6 - - - +
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Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU* 3.7 33.3 + - - +
372B ILE* 3.3 8.0 + - - +
374B ASN* 1.3 74.5 - - + +
376B LEU* 1.3 68.8 + - + +
378B ARG* 3.3 8.3 + - - +
379B TYR* 3.1 38.5 + - + -
444B ASN* 4.1 22.2 + - - +
447B MET* 3.6 38.7 + - - +
448B GLU* 4.8 4.2 - - - +
496B ASP* 5.8 2.4 + - - -
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE* 3.1 30.2 + - + +
373B MET* 3.7 13.7 - - + +
375B ARG* 1.3 81.0 - - + +
377B TYR* 1.3 61.3 + - - +
379B TYR* 3.5 12.9 + - + +
380B ALA* 3.2 22.3 + - - +
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Residues in contact with TYR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 5.1 7.4 - + - -
322B VAL* 3.5 33.9 - - + +
325B CYS* 3.6 39.0 - - + -
373B MET* 2.8 21.8 + - + +
374B ASN 3.8 3.8 - - - +
376B LEU* 1.3 73.8 - - - +
378B ARG* 1.3 61.3 + - - +
380B ALA* 3.8 4.7 - - + -
381B ALA* 2.9 41.4 + - + +
403B LYS* 3.5 23.1 + - - +
404B VAL* 4.2 6.5 - - + -
407B PHE* 3.4 50.3 - + + +
408B ASN* 5.0 2.5 - - - -
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Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASN 2.9 18.5 + - - +
375B ARG* 3.5 9.9 - - - +
376B LEU 3.2 0.4 - - - -
377B TYR* 1.3 80.6 - - - +
379B TYR* 1.3 70.0 + - + +
381B ALA* 4.1 0.3 - - - +
382B GLU* 3.0 44.2 + - - +
400B LEU* 4.4 15.1 - - - +
404B VAL* 3.9 28.7 - - + +
492B LEU* 4.9 14.1 + - - +
495B PHE* 3.5 30.3 - - - -
496B ASP* 2.4 39.0 + - - -
499B LEU* 5.6 1.6 - - - +
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Residues in contact with TYR 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ARG* 3.1 24.8 + - + +
376B LEU* 3.5 12.8 + - + +
378B ARG* 1.3 85.4 - - + +
380B ALA* 1.3 63.7 + - - +
382B GLU* 4.0 17.6 - - - +
383B PHE* 3.1 24.9 + - - +
492B LEU* 6.5 1.6 - - + -
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 4.4 25.1 - - + -
376B LEU 3.2 16.8 + - - +
377B TYR* 3.9 7.2 - - + +
379B TYR* 1.3 76.9 - - - +
381B ALA* 1.3 58.9 + - - +
383B PHE* 3.5 9.4 + - + +
384B LEU* 2.9 30.8 + - - +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 5.7 1.1 - - - -
377B TYR* 2.9 39.5 + - + +
378B ARG 4.1 2.2 - - - +
380B ALA* 1.3 74.3 - - - +
382B GLU* 1.3 60.3 + - - +
384B LEU* 3.8 7.1 - - - +
385B THR* 2.8 35.9 + - - -
400B LEU* 3.7 3.9 - - + +
403B LYS* 4.3 16.4 - - + -
404B VAL* 4.2 14.8 - - + -
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ARG* 3.0 33.7 + - - +
379B TYR* 4.0 20.5 - - - +
381B ALA* 1.3 75.4 - - - +
383B PHE* 1.3 57.7 + - - +
385B THR 3.4 1.0 + - - -
386B SER* 2.9 30.9 + - - -
396B TYR* 3.8 18.5 + - - +
400B LEU* 3.7 19.6 - - + +
492B LEU* 5.1 11.2 - - - +
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Residues in contact with PHE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TYR 3.1 18.9 + - - +
380B ALA* 3.8 8.3 - - + +
382B GLU* 1.3 79.6 - - - +
384B LEU* 1.3 77.1 + - + +
386B SER* 3.4 7.3 + - - +
387B TRP* 3.2 39.1 + + + +
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B VAL* 4.7 9.9 - - + +
318B SER* 3.8 33.8 + - - +
321B PHE* 3.7 35.0 - - + -
322B VAL* 5.5 1.6 - - + -
380B ALA 2.9 17.6 + - - +
381B ALA* 3.9 7.0 - - - +
382B GLU 3.3 0.2 - - - -
383B PHE* 1.3 93.8 - - + +
385B THR* 1.3 59.6 + - - +
387B TRP* 3.8 22.4 - - + +
388B GLU* 3.1 23.0 - - - +
403B LYS* 5.1 6.3 - - + -
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Residues in contact with THR 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 5.2 0.2 + - - -
381B ALA 2.8 17.6 + - - -
382B GLU 4.2 0.2 - - - -
384B LEU* 1.3 76.9 - - - +
386B SER* 1.3 59.6 + - - +
387B TRP 3.1 5.4 + - - -
388B GLU* 3.4 32.1 + - - +
389B ASN 4.4 1.7 + - - -
390B HIS* 3.7 20.0 + - + -
396B TYR* 4.0 21.8 - - + -
399B HIS* 3.8 18.8 - - + -
400B LEU* 4.2 11.7 - - - +
403B LYS* 3.5 21.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 4.5 19.3 + - - +
287B GLY 4.8 6.8 + - - +
382B GLU* 2.9 21.4 + - - -
383B PHE* 3.4 9.3 + - - -
385B THR* 1.3 75.7 - - - +
387B TRP* 1.3 57.0 + - - +
388B GLU 3.5 0.2 - - - -
389B ASN* 4.3 11.0 + - - +
396B TYR* 4.0 11.8 - - - -
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Residues in contact with TRP 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B HIS* 6.1 0.2 - - - -
313B ARG* 3.3 80.9 + - + +
317B VAL* 4.3 25.6 - - + -
318B SER* 5.3 0.7 - - - -
383B PHE* 3.2 34.8 + + + +
384B LEU* 3.8 23.3 - - + +
385B THR 3.1 0.8 - - - -
386B SER* 1.3 76.3 - - - +
388B GLU* 1.3 65.8 + - + +
389B ASN* 3.2 10.7 + - - +
----------------------------------------------------------
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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).
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