Contacts of the helix formed by residues 484 - 506 (chain A) 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 PHE 484 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLY* 4.7 0.2 - - - -
232A GLU* 3.7 26.9 - - + +
279A PHE* 3.5 38.8 - + - -
288A PHE* 6.3 3.8 - + - -
482A GLY 3.3 3.0 + - - -
483A GLY* 1.3 79.1 - - - +
485A MET* 1.3 66.5 + - + +
486A PRO* 3.6 1.8 - - - -
487A VAL* 3.3 6.8 + - - +
488A PHE* 2.9 56.9 + + + +
533A THR* 3.3 26.5 - - + -
537A SER* 5.9 3.4 - - - -
542A THR* 3.6 23.6 - - + -
545A ILE* 3.6 23.3 - - + -
549A LEU* 5.6 3.1 - - + -
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Residues in contact with MET 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU* 6.4 1.6 - - + -
229A VAL 3.6 16.4 - - - +
230A GLY* 3.8 8.3 - - - -
231A LYS* 4.5 13.7 - - + +
279A PHE* 3.5 37.7 - - + -
420A PRO* 5.6 7.0 - - + -
421A ARG* 4.9 20.4 - - + +
424A ILE* 6.1 4.5 - - - -
484A PHE* 1.3 84.3 - - + +
486A PRO* 1.3 70.0 - - + +
488A PHE* 3.1 21.5 + - - +
489A VAL* 3.0 32.3 + - + +
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Residues in contact with PRO 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 4.1 23.1 - - + +
229A VAL 3.8 19.5 - - - +
230A GLY* 4.0 3.4 - - - +
365A PHE* 6.2 0.4 - - + -
467A LYS* 6.2 1.8 - - - -
471A SER* 4.0 28.7 - - - +
475A THR* 6.4 1.8 - - - -
482A GLY 4.5 3.6 - - - +
483A GLY* 5.5 0.7 - - - -
484A PHE 3.8 4.7 - - - +
485A MET* 1.3 92.6 - - + +
487A VAL* 1.3 63.9 + - + +
489A VAL* 3.2 12.0 + - + +
490A LEU* 2.9 33.4 + - - +
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Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 4.0 31.4 - - + -
471A SER* 5.9 0.4 - - - +
483A GLY* 3.5 24.9 - - - +
484A PHE 3.5 6.3 - - - +
485A MET 3.2 0.6 - - - -
486A PRO* 1.3 81.5 - - + +
488A PHE* 1.3 55.9 + - - +
490A LEU* 3.2 11.3 + - + +
491A GLY* 2.9 25.6 + - - -
532A LEU* 3.7 23.5 - - + +
533A THR* 3.7 25.4 - - - +
536A VAL* 4.1 13.9 - - + -
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Residues in contact with PHE 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A PHE* 5.6 4.0 - + - -
424A ILE* 4.8 24.5 - - + -
428A PHE* 5.0 14.4 - + - -
484A PHE* 2.9 40.8 + + + +
485A MET* 3.1 26.4 + - - +
487A VAL* 1.3 76.9 - - - +
489A VAL* 1.3 63.8 + - + +
491A GLY 3.4 0.7 + - - -
492A ALA* 3.0 24.5 + - + +
529A ALA* 3.2 44.8 - - + +
533A THR* 4.1 8.9 - - + -
542A THR* 6.0 0.4 - - + -
546A CYS* 4.2 24.7 - - + -
549A LEU* 4.9 19.3 - - + -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A PRO* 4.4 22.4 - - + +
423A ALA* 5.8 2.0 - - + -
424A ILE* 3.7 29.8 - - + -
427A LEU* 5.1 2.0 - - + +
463A PHE* 4.4 24.7 - - + -
467A LYS* 4.8 14.6 - - + -
485A MET* 3.0 22.7 + - + +
486A PRO* 3.2 13.2 + - + +
488A PHE* 1.3 78.1 - - + +
490A LEU* 1.3 58.9 + - + +
492A ALA* 3.2 4.5 + - - +
493A ALA* 2.9 26.3 + - - +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 4.7 6.5 - - + -
463A PHE* 6.0 0.7 - - + -
464A PHE* 3.3 51.8 - - + +
467A LYS* 3.7 15.5 - - + +
468A PHE* 3.6 39.3 - - + +
471A SER* 3.9 16.8 - - - +
486A PRO 2.9 20.3 + - - +
487A VAL* 3.2 14.3 + - + +
489A VAL* 1.3 77.1 - - + +
491A GLY* 1.3 57.7 + - - +
493A ALA* 3.3 4.0 + - + +
494A PHE* 3.0 24.1 + - - +
532A LEU* 5.0 8.7 - - + -
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Residues in contact with GLY 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A CYS* 6.0 0.4 - - - -
487A VAL 2.9 14.7 + - - -
488A PHE 3.4 3.3 + - - -
489A VAL 3.3 0.2 - - - -
490A LEU* 1.3 76.8 - - - +
492A ALA* 1.3 56.2 + - - +
494A PHE* 3.4 3.7 + - - +
495A GLY* 3.0 23.4 + - - -
528A GLY* 3.5 17.9 - - - -
529A ALA* 3.5 15.9 + - - -
532A LEU* 4.2 17.2 - - - +
533A THR 5.7 0.2 - - - -
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE* 4.6 12.3 - - + -
427A LEU* 3.3 20.7 - - + +
428A PHE* 4.8 14.4 - - + -
488A PHE* 3.0 14.9 + - + +
489A VAL* 3.6 10.1 - - - +
491A GLY* 1.3 76.3 - - - +
493A ALA* 1.3 57.1 + - - +
495A GLY 3.3 0.2 + - - -
496A ARG* 3.0 25.5 + - - +
525A ALA* 3.6 16.1 - - - +
529A ALA* 3.5 11.5 - - + +
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Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LEU* 3.7 10.5 - - - +
460A ILE* 3.9 9.8 - - + +
463A PHE* 4.1 23.3 - - + -
464A PHE* 3.8 24.0 - - + -
489A VAL 2.9 13.6 + - - +
490A LEU* 3.4 11.7 - - + +
491A GLY 3.2 0.2 - - - -
492A ALA* 1.3 78.5 - - - +
494A PHE* 1.3 58.0 + - - +
496A ARG* 3.9 0.5 - - - +
497A LEU* 3.0 29.2 + - - +
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Residues in contact with PHE 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ILE* 4.0 19.3 - - + -
357A CYS* 4.5 21.8 - - + -
358A CYS* 3.5 33.0 - - - -
361A LEU* 4.7 11.9 - - + -
464A PHE* 4.0 27.5 - + + -
490A LEU 3.0 16.0 + - - +
491A GLY* 3.9 6.1 - - - +
493A ALA* 1.3 75.7 - - - +
495A GLY* 1.3 62.4 + - - +
497A LEU* 3.3 26.3 - - + +
498A VAL* 3.1 32.8 + - + +
532A LEU* 5.1 2.0 - - + -
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Residues in contact with GLY 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ILE* 3.9 13.2 - - - -
491A GLY 3.0 13.9 + - - -
492A ALA 3.3 0.2 + - - -
493A ALA 3.2 0.2 - - - -
494A PHE* 1.3 78.1 - - - +
496A ARG* 1.3 56.9 + - - +
498A VAL* 3.3 4.9 - - - +
499A GLY 2.9 23.0 + - - -
524A TYR* 3.4 25.9 - - - +
525A ALA* 3.7 11.7 - - - -
528A GLY* 4.7 0.2 - - - -
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Residues in contact with ARG 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LEU* 2.8 46.6 + - + +
429A ASP 2.9 20.8 + - - +
431A ASN 2.8 29.3 + - - -
433A TRP* 3.1 56.8 - - - +
460A ILE* 4.9 7.4 - - + -
492A ALA 3.0 16.8 + - - +
493A ALA 4.2 1.1 - - - +
495A GLY* 1.3 72.5 - - - +
497A LEU* 1.3 60.4 + - - +
499A GLY 4.3 0.7 - - - +
500A GLU* 2.9 45.5 + - + +
521A PRO* 3.7 20.5 - - + +
522A GLY* 4.1 6.7 - - - +
525A ALA* 3.7 12.3 - - + +
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A VAL* 3.8 33.7 - - + +
460A ILE* 3.8 26.1 - - + +
461A PHE* 4.5 24.2 - - + +
464A PHE* 5.6 6.3 - - + -
493A ALA 3.0 15.6 + - - +
494A PHE* 3.3 34.8 - - + +
496A ARG* 1.3 77.1 - - - +
498A VAL* 1.3 63.4 + - + +
500A GLU* 3.4 2.6 + - + +
501A ILE* 3.1 32.5 + - + +
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Residues in contact with VAL 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ALA* 5.8 8.1 - - + +
353A ALA* 6.3 2.7 - - + -
354A ILE* 3.7 27.8 - - + -
494A PHE* 3.1 20.8 + - + +
495A GLY 3.3 13.5 - - - +
497A LEU* 1.3 82.2 - - + +
499A GLY* 1.3 57.6 + - - +
501A ILE* 3.2 20.4 - - + +
502A MET* 2.9 39.1 + - + +
524A TYR* 4.7 8.1 - - + -
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Residues in contact with GLY 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A GLY 2.9 15.6 + - - -
497A LEU 3.2 0.2 - - - -
498A VAL* 1.3 78.9 - - - +
500A GLU* 1.3 55.9 + - - +
502A MET* 3.3 3.2 + - - +
503A ALA* 2.9 27.2 + - - +
519A ILE* 4.5 3.3 - - - +
521A PRO* 3.6 15.6 - - - +
524A TYR* 3.7 30.1 - - - -
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A THR* 3.7 6.4 - - - +
433A TRP* 2.9 29.6 + - + +
434A VAL* 3.1 39.4 + - + +
456A VAL* 5.7 2.7 - - + -
457A VAL* 6.0 4.7 - - + -
460A ILE* 4.6 14.4 - - + -
496A ARG* 2.9 49.8 + - + +
497A LEU* 3.9 4.3 - - + +
499A GLY* 1.3 75.7 - - - +
501A ILE* 1.3 61.3 + - + +
503A ALA* 3.3 5.2 + - - +
504A MET* 2.9 26.3 + - - +
521A PRO* 3.3 11.1 - - + +
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Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A VAL* 3.8 28.9 - - + -
497A LEU* 3.1 18.7 + - + +
498A VAL* 3.2 33.2 - - + +
500A GLU* 1.3 77.5 - - + +
502A MET* 1.3 62.6 + - + +
504A MET* 3.4 23.1 + - + +
505A LEU* 2.9 26.2 + - - +
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Residues in contact with MET 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLU* 4.5 15.7 - - + -
350A ALA* 4.5 21.8 - - + -
498A VAL* 2.9 33.0 + - + +
499A GLY* 3.7 6.5 - - - +
500A GLU 3.2 0.2 - - - -
501A ILE* 1.3 80.9 - - + +
503A ALA* 1.3 58.8 + - - +
505A LEU* 3.6 14.0 - - + +
506A PHE* 2.9 56.2 + - + +
519A ILE* 3.5 19.6 - - + +
524A TYR* 4.7 13.0 - - + +
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Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A THR* 3.7 34.9 - - + +
434A VAL* 6.0 0.4 - - - -
499A GLY 2.9 13.8 + - - +
500A GLU* 3.3 11.9 + - - +
502A MET* 1.3 77.2 - - - +
504A MET* 1.3 61.2 + - - +
506A PHE 3.2 18.3 - - - +
507A PRO* 3.5 7.3 - - - +
519A ILE* 3.6 20.1 - - + +
521A PRO* 5.4 3.6 - - + -
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Residues in contact with MET 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A VAL* 4.8 25.3 - - + +
455A ASN* 5.1 12.6 - - - -
457A VAL* 5.9 5.6 - - + -
500A GLU 2.9 13.3 + - - +
501A ILE* 3.6 24.2 - - + +
502A MET 3.2 0.2 - - - -
503A ALA* 1.3 75.8 - - - +
505A LEU* 1.3 64.3 + - + +
507A PRO* 3.4 16.9 - - - +
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Residues in contact with LEU 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ILE 2.9 18.1 + - - +
502A MET* 3.2 21.0 + - + +
504A MET* 1.3 79.5 - - + +
506A PHE* 1.3 92.1 + - + +
507A PRO* 3.3 8.5 - - - +
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Residues in contact with PHE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LYS* 6.1 6.7 - - + -
347A GLU* 6.3 2.0 - - + -
502A MET* 2.9 34.5 + - + +
503A ALA* 3.2 12.4 - - - +
505A LEU* 1.3 101.3 - - + +
507A PRO* 1.3 63.2 - - - +
508A ASP* 3.3 7.7 + - + +
509A GLY* 4.2 10.4 + - - +
518A LYS* 5.7 1.6 - - - +
519A ILE* 4.7 17.5 + - + +
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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) + - + + + + + -
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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