Contacts of the helix formed by residues 347 - 377 (chain B) in PDB entry 6QVC
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 GLU 347 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PHE* 2.9 34.3 - - - +
344B ASP* 2.9 21.4 + - - +
346B LYS* 1.3 78.1 - - - +
348B LEU* 1.3 58.3 + - - -
349B PRO* 3.4 2.2 - - - -
350B ALA* 2.9 37.3 + - + +
351B PHE* 3.2 31.0 + - - -
502B MET* 4.5 13.7 - - + -
506B PHE* 6.3 1.8 - - + -
519B ILE* 5.4 4.9 - - + -
524B TYR* 3.0 33.9 + - + +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 4.6 28.3 - - + -
329A ILE* 5.8 4.0 - - + -
343B PHE* 6.3 1.8 - - + -
344B ASP 4.0 1.8 + - - +
345B LEU* 4.1 26.2 - - + -
346B LYS 3.8 0.6 - - - +
347B GLU* 1.3 79.6 - - - +
349B PRO* 1.3 67.8 - - + +
351B PHE* 2.9 55.8 + - + +
352B ALA* 3.3 3.1 + - - +
558B PRO* 4.6 13.9 - - + -
561B VAL* 6.6 0.2 - - + -
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Residues in contact with PRO 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU 5.3 0.9 - - - +
346B LYS* 3.5 17.9 - - - +
347B GLU 3.7 0.4 - - - -
348B LEU* 1.3 94.7 - - + +
350B ALA* 1.3 59.5 + - - +
352B ALA* 2.9 31.9 + - + +
353B ALA* 3.2 5.4 + - - +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLU* 2.9 25.3 + - + +
349B PRO* 1.3 76.9 - - - +
351B PHE* 1.3 62.8 + - - +
353B ALA* 3.0 19.5 + - - +
354B ILE* 3.0 13.2 + - - +
498B VAL* 5.8 7.5 - - + +
502B MET* 4.5 24.9 - - + -
524B TYR* 5.2 4.9 - - + -
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Residues in contact with PHE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PHE* 4.1 11.4 - + - -
347B GLU* 3.2 36.7 + - - -
348B LEU* 2.9 35.3 + - + +
350B ALA* 1.3 77.9 - - - +
352B ALA* 1.3 53.5 + - - +
354B ILE* 3.1 10.6 + - + +
355B GLY* 2.8 25.8 + - - -
524B TYR* 3.5 28.3 - + - -
527B ILE* 3.8 27.1 - - + -
555B HIS* 4.4 18.8 - + - -
558B PRO* 3.6 30.7 - - + +
562B ALA* 4.3 7.3 - - + +
565B LEU* 5.7 0.4 - - - -
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU 3.3 2.8 + - - +
349B PRO* 2.9 23.8 + - + +
351B PHE* 1.3 76.6 - - - +
353B ALA* 1.3 60.2 + - - +
355B GLY* 3.0 10.7 + - - -
356B ILE* 3.1 23.2 + - + +
565B LEU* 4.5 16.8 - - + +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PRO 3.2 4.4 + - - +
350B ALA* 3.0 15.5 + - - +
352B ALA* 1.3 76.4 - - - +
354B ILE* 1.3 58.1 + - - +
356B ILE* 3.0 4.5 + - - -
357B CYS* 3.0 48.3 + - - +
494B PHE* 5.9 0.2 - - - -
498B VAL* 6.3 2.7 - - + -
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ALA 3.0 10.6 + - - +
351B PHE* 3.1 25.7 + - + +
353B ALA* 1.3 72.3 - - - +
355B GLY* 1.3 66.6 + - - +
358B CYS* 3.2 30.8 - - - +
494B PHE* 4.0 12.8 - - + -
495B GLY* 3.9 9.2 - - - -
498B VAL* 3.7 30.1 - - + -
524B TYR* 3.9 23.8 - - + +
527B ILE* 3.5 27.4 - - + -
528B GLY* 4.0 7.9 - - - -
531B ALA* 4.1 6.6 - - + +
562B ALA* 4.7 5.2 - - + -
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Residues in contact with GLY 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B PHE 2.8 13.5 + - - -
352B ALA 3.0 4.4 + - - -
354B ILE* 1.3 83.7 - - - +
356B ILE* 1.3 67.0 + - - +
358B CYS* 3.0 10.9 + - - +
359B GLY 3.3 8.8 + - - -
562B ALA* 3.8 27.8 - - - +
565B LEU* 4.4 5.8 - - - -
566B ALA* 3.8 8.9 - - - +
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA* 3.4 15.9 - - + +
353B ALA* 3.0 5.0 + - - +
355B GLY* 1.3 73.1 - - - +
357B CYS* 1.3 66.7 + - - +
359B GLY* 3.1 4.9 + - - -
360B LEU* 2.9 22.9 + - + +
565B LEU* 3.7 35.9 - - + +
566B ALA* 5.2 0.9 - - - +
568B MET* 6.0 0.4 - - + -
569B VAL* 3.9 33.1 - - + +
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Residues in contact with CYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ALA* 3.0 32.1 + - - +
356B ILE* 1.3 79.5 - - - +
358B CYS* 1.3 57.4 + - - +
360B LEU* 3.1 18.1 - - + +
361B LEU* 2.9 34.0 + - + +
494B PHE* 4.4 19.7 - - + -
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Residues in contact with CYS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ILE* 3.2 23.8 - - - +
355B GLY 3.0 9.6 + - - +
357B CYS* 1.3 76.9 - - - +
359B GLY* 1.3 51.8 + - - +
361B LEU* 3.1 12.3 + - - +
362B GLY* 2.6 36.9 + - - -
494B PHE* 3.5 32.8 - - - -
528B GLY* 4.7 5.2 - - - -
531B ALA* 4.6 8.3 - - + -
532B LEU* 3.9 33.5 - - + +
535B ALA* 4.8 1.3 - - - -
566B ALA* 5.0 0.7 - - + -
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Residues in contact with GLY 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLY 3.3 4.4 + - - -
356B ILE 3.1 7.7 + - - -
358B CYS* 1.3 78.0 - - - +
360B LEU* 1.3 51.8 - - - +
362B GLY* 3.1 0.9 + - - -
363B ALA* 2.8 36.2 + - - +
535B ALA* 3.9 20.1 - - - +
566B ALA* 4.0 17.8 - - - +
569B VAL* 4.1 8.9 - - - +
570B ALA* 4.8 3.9 - - - +
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ILE* 2.9 14.7 + - + +
357B CYS* 3.1 19.7 - - + +
359B GLY* 1.3 76.5 - - - +
361B LEU* 1.3 66.5 + - + +
363B ALA* 3.1 13.1 + - - +
364B VAL* 3.2 23.1 + - + +
569B VAL* 3.9 9.6 - - + +
573B LEU* 4.6 15.5 - - + -
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B CYS* 2.9 28.9 + - + +
358B CYS* 3.4 17.5 - - - +
360B LEU* 1.3 77.0 - - + +
362B GLY* 1.3 61.5 + - - +
364B VAL* 3.0 22.5 + - + +
365B PHE* 3.0 12.0 + - - +
464B PHE* 3.7 26.2 - - + -
468B PHE* 4.5 18.6 - - + -
494B PHE* 4.7 21.5 - - + -
532B LEU* 3.6 24.2 - - + -
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Residues in contact with GLY 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B CYS 2.6 22.4 + - - -
359B GLY* 3.5 2.7 - - - -
361B LEU* 1.3 72.7 - - - +
363B ALA* 1.3 62.0 + - - +
365B PHE* 3.0 22.0 - - - +
366B VAL* 3.3 9.9 + - - +
532B LEU* 4.5 11.7 - - - -
535B ALA* 5.1 3.1 - - - -
536B VAL* 3.8 23.0 - - - +
570B ALA* 6.1 0.4 - - - -
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLY 2.8 12.9 + - - +
360B LEU 3.1 11.0 + - - +
362B GLY* 1.3 75.9 - - - +
364B VAL* 1.3 62.6 + - + +
366B VAL* 3.0 10.4 + - - +
367B TYR* 3.0 19.9 + - - +
570B ALA* 5.0 9.4 - - - +
573B LEU* 4.3 19.1 - - + -
574B GLN* 3.7 33.4 - - + +
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 3.3 24.7 - - + +
361B LEU* 3.0 14.1 + - - +
363B ALA* 1.3 75.5 - - + +
365B PHE* 1.3 53.6 + - - +
367B TYR* 3.0 13.5 + - + +
368B LEU* 2.7 56.4 + - + +
468B PHE* 5.1 5.6 - - + -
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU 3.0 8.1 + - - +
362B GLY* 3.0 18.8 - - - +
364B VAL* 1.3 75.5 - - - +
366B VAL* 1.3 65.3 + - - +
368B LEU* 3.1 7.3 + - - +
369B HIS* 3.0 24.1 + - + +
468B PHE* 3.5 34.1 - + + -
471B SER* 3.6 21.3 - - - -
472B ILE* 3.5 32.6 - - + +
475B THR* 5.5 5.4 - - + -
486B PRO* 6.2 0.7 - - + -
487B VAL* 4.0 26.9 - - + -
490B LEU* 4.7 6.5 - - + -
532B LEU* 5.9 3.1 - - + -
536B VAL* 4.0 26.0 - - + -
577B LEU* 5.1 12.1 - - + -
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLY 3.7 12.8 - - - +
363B ALA* 3.0 8.6 + - - +
365B PHE* 1.3 76.2 - - + +
367B TYR* 1.3 63.9 + - - +
369B HIS* 3.1 18.4 + - + +
370B ARG* 3.2 16.1 + - - +
536B VAL* 3.7 31.4 - - + +
574B GLN* 5.1 3.4 - - + -
575B PRO* 3.9 15.5 - - + +
576B SER 3.6 23.3 - - - +
577B LEU* 4.0 19.1 - - + +
580B SER* 3.8 14.1 - - - +
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ALA 3.0 11.5 + - - +
364B VAL* 3.3 16.4 - - + +
366B VAL* 1.3 76.7 - - - +
368B LEU* 1.3 69.7 + - + +
370B ARG* 3.0 48.5 + - - +
371B GLN* 3.0 63.2 + - + +
574B GLN* 4.0 16.5 + - + +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL* 2.7 42.1 + - + +
365B PHE* 3.6 4.9 - - - +
367B TYR* 1.3 83.0 - - + +
369B HIS* 1.3 62.5 + - - +
371B GLN* 3.0 30.9 + - + +
372B VAL* 3.1 13.9 + - - +
468B PHE* 4.4 20.6 - - + -
472B ILE* 5.0 18.2 - - + +
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Residues in contact with HIS 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 3.0 14.6 + + + +
366B VAL* 3.1 14.5 + - + +
368B LEU* 1.3 75.8 - - - +
370B ARG* 1.3 62.0 + - + +
372B VAL* 3.1 14.7 + - - +
373B MET* 2.9 59.8 + - + +
472B ILE* 4.6 13.4 + - + +
475B THR* 4.0 37.6 - - + +
476B THR* 5.1 2.5 - - - -
577B LEU* 4.4 21.7 - - + +
580B SER* 5.8 3.8 - - - -
581B ILE* 4.2 23.1 - - + +
584B VAL* 6.6 0.2 - - + -
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Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B VAL* 3.2 7.4 + - - +
367B TYR* 3.0 40.0 + - - +
369B HIS* 1.3 77.7 - - + +
371B GLN* 1.3 63.8 + - - +
372B VAL 3.0 1.7 + - - -
373B MET* 3.0 15.9 + - - +
374B LEU* 3.1 30.3 + - + +
574B GLN* 2.6 31.3 + - - -
575B PRO* 4.2 10.5 - - - +
580B SER* 4.0 33.3 + - - -
583B GLN* 4.3 16.4 - - - +
584B VAL* 4.2 13.0 - - + -
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Residues in contact with GLN 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B TYR* 3.0 57.4 + - + +
368B LEU* 3.0 26.2 + - + +
370B ARG* 1.3 79.4 + - - +
372B VAL* 1.3 56.1 + - - +
374B LEU* 5.1 8.2 - - - +
375B GLY* 4.0 9.8 + - - -
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU 3.1 8.3 + - - +
369B HIS* 3.1 22.3 + - - +
371B GLN* 1.3 79.1 - - - +
373B MET* 1.3 57.9 + - - +
374B LEU 3.4 0.7 - - - -
375B GLY* 3.0 7.0 + - - +
376B VAL* 2.5 35.9 + - + +
393B TYR* 5.5 1.6 - - - +
472B ILE* 4.8 10.5 - - + +
473B VAL* 5.9 6.3 - - + -
476B THR* 3.5 37.5 - - + +
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Residues in contact with MET 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B HIS* 2.9 52.5 + - + +
370B ARG* 3.0 6.4 + - - +
372B VAL* 1.3 78.9 - - - +
374B LEU* 1.3 61.1 + - - +
376B VAL* 2.9 47.9 + - + +
377B ARG* 3.3 7.4 + - - +
476B THR* 4.5 13.5 - - - +
584B VAL* 3.7 29.2 - - + +
585B LYS* 4.6 20.2 - - + -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ARG* 3.1 27.4 + - + +
371B GLN* 5.1 8.5 - - - +
373B MET* 1.3 75.7 - - - +
375B GLY* 1.3 56.4 + - - +
377B ARG* 2.9 20.5 + - - +
378B LYS* 2.9 21.7 + - + +
584B VAL* 4.9 17.7 - - + -
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Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLN 4.0 9.1 + - - -
372B VAL* 3.0 16.5 + - - -
374B LEU* 1.3 73.5 - - - +
376B VAL* 1.3 65.4 + - - +
378B LYS* 3.8 23.4 - - - +
382B LEU* 4.2 12.6 - - - +
----------------------------------------------------------
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B VAL* 2.5 20.6 + - + +
373B MET* 2.9 41.9 + - + +
375B GLY* 1.3 77.6 - - - +
377B ARG* 1.3 101.9 + - + +
382B LEU* 3.7 11.5 - - - +
393B TYR* 5.3 4.0 - - + +
476B THR* 3.9 20.0 - - + +
----------------------------------------------------------
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Residues in contact with ARG 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B MET 3.3 5.7 + - - +
374B LEU* 2.9 10.4 + - - +
376B VAL* 1.3 117.7 + - + +
378B LYS* 1.3 56.4 + - - +
379B HIS 3.8 1.8 - - - +
382B LEU* 3.7 22.3 + - - +
383B SER* 3.2 36.1 + - - +
386B LEU* 3.8 27.2 - - - +
----------------------------------------------------------
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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