Contacts of the helix formed by residues 494 - 519 (chain A) in PDB entry 1B3U
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 TYR 494 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A PRO 3.3 5.5 + - - +
493A ASN* 1.3 70.4 + - - +
495A LEU* 1.3 94.6 + - + +
496A HIS 3.0 1.6 - - - -
497A ARG* 3.0 28.2 + - - +
498A MET* 2.8 41.0 + - - +
532A VAL* 4.5 23.3 - - + -
534A ASN* 4.2 29.2 + - + -
535A VAL* 4.7 5.2 - - + +
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A VAL* 4.1 35.1 - - + +
493A ASN* 2.8 19.4 + - - +
494A TYR* 1.3 106.8 - - + +
496A HIS* 1.3 61.8 + - + +
498A MET* 3.4 7.5 - - + +
499A THR* 2.9 30.6 + - - -
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Residues in contact with HIS 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A MET* 3.9 21.6 - - - +
491A ASP* 2.9 34.5 + - + +
493A ASN* 3.2 41.8 + - + +
494A TYR 3.0 0.6 - - - -
495A LEU* 1.3 81.1 - - + +
497A ARG* 1.3 65.3 + - - +
499A THR* 3.0 24.2 + - - -
500A THR* 3.2 8.8 + - - -
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Residues in contact with ARG 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A MET 3.4 10.5 - - - +
489A SER* 2.8 34.3 - - - +
490A GLY 3.8 2.0 - - - -
491A ASP 2.9 24.3 + - - -
492A PRO* 3.2 24.9 + - - +
493A ASN 3.3 12.3 + - - -
494A TYR* 3.0 13.5 + - - +
496A HIS* 1.3 78.6 - - - +
498A MET* 1.3 63.1 + - - +
500A THR* 3.2 20.5 + - - -
501A LEU* 3.5 2.1 + - - +
527A MET* 3.4 25.2 - - + +
530A ASP* 2.8 38.8 + - - -
531A PRO* 5.1 3.4 - - - +
532A VAL* 3.3 20.6 - - - +
535A VAL* 4.1 6.0 - - + +
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Residues in contact with MET 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A VAL* 4.2 11.9 - - + -
494A TYR* 2.8 26.7 + - + +
495A LEU* 3.4 15.9 - - + +
496A HIS 3.1 0.2 - - - -
497A ARG* 1.3 74.1 - - - +
499A THR* 1.3 64.9 + - - +
501A LEU* 3.2 19.4 + - + +
502A PHE* 3.1 42.5 + - + -
534A ASN* 3.9 13.5 - - - +
535A VAL* 3.7 19.0 - - + +
538A ASN* 3.2 46.7 - - + +
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Residues in contact with THR 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A MET* 3.7 28.8 + - + +
448A ALA* 4.6 5.3 - - - +
450A LEU* 5.4 1.6 - - + -
451A VAL* 4.0 18.3 - - - +
488A MET* 3.6 23.3 - - + -
495A LEU 2.9 19.3 + - - -
496A HIS* 3.2 14.4 - - - -
498A MET* 1.3 74.9 - - - +
500A THR* 1.3 63.6 + - - +
502A PHE* 4.0 5.7 - - - +
503A CYS* 3.0 32.8 + - - -
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Residues in contact with THR 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 3.1 41.1 + - + +
488A MET* 3.5 11.6 - - - +
489A SER* 3.5 16.6 + - - -
496A HIS 3.2 3.7 + - - -
497A ARG 3.2 10.3 + - - -
498A MET 3.1 0.4 - - - -
499A THR* 1.3 79.2 - - - +
501A LEU* 1.3 62.8 + - - +
503A CYS* 3.5 1.7 + - - +
504A ILE* 3.1 41.0 + - + +
523A THR* 4.1 19.1 - - + -
527A MET* 4.3 11.0 - - - -
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A ARG 3.5 0.6 + - - -
498A MET* 3.2 34.4 + - + +
500A THR* 1.3 80.0 - - + +
502A PHE* 1.3 73.0 + - + +
504A ILE* 3.4 5.1 + - - +
505A ASN* 3.0 29.2 + - - +
524A VAL* 4.7 20.2 - - + -
527A MET* 3.5 37.0 - - + -
535A VAL* 3.8 11.0 - - + +
538A ASN* 3.7 26.5 - - + +
539A VAL* 3.9 12.3 - - + +
542A SER* 4.3 7.0 - - - -
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Residues in contact with PHE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LEU* 3.1 44.6 - - + -
451A VAL* 4.3 17.9 - - + -
458A ARG* 5.1 8.1 - - - -
498A MET* 3.1 28.6 + - + +
499A THR* 4.1 3.8 - - - +
501A LEU* 1.3 79.3 - - + +
503A CYS* 1.3 64.0 + - - +
505A ASN* 3.2 25.5 + - - +
506A VAL* 3.3 17.0 + - - +
538A ASN* 3.8 30.5 - - + -
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Residues in contact with CYS 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A MET* 3.7 36.8 - - - -
450A LEU* 3.6 24.2 - - - -
465A LEU* 4.8 6.1 - - + -
481A ILE* 6.0 0.2 - - - -
485A VAL* 4.0 20.0 - - + -
499A THR* 3.0 30.4 + - - +
500A THR 3.7 3.6 - - - +
502A PHE* 1.3 75.9 - - - +
504A ILE* 1.3 64.8 + - - +
506A VAL* 3.0 5.0 + - - +
507A LEU* 2.9 32.4 + - + +
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Residues in contact with ILE 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 4.1 13.0 - - + -
486A LEU* 5.0 2.0 - - + -
500A THR* 3.1 32.6 + - + +
501A LEU* 3.7 6.1 - - + +
503A CYS* 1.3 79.9 - - - +
505A ASN* 1.3 62.9 + - - +
507A LEU* 4.6 1.8 - - + -
508A SER* 3.0 24.7 + - - -
520A MET* 3.8 45.9 - - + +
523A THR* 4.5 7.2 - - + -
524A VAL* 3.6 34.3 - - + -
542A SER* 4.5 2.9 - - - +
546A ILE* 4.4 17.3 - - + -
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Residues in contact with ASN 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU* 3.0 12.9 + - - +
502A PHE* 3.3 23.7 - - - +
503A CYS 3.2 0.4 - - - -
504A ILE* 1.3 76.5 - - - +
506A VAL* 1.3 61.0 + - + +
508A SER* 3.0 18.5 + - - -
509A GLU* 3.9 1.8 + - - +
541A LYS* 5.4 1.0 - - - +
542A SER* 2.7 47.7 + - - +
545A LYS* 3.4 32.7 + - + +
546A ILE* 4.2 6.4 - - - +
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Residues in contact with VAL 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LEU* 4.6 11.2 - - + -
462A THR* 3.8 37.2 - - + +
465A LEU* 4.0 19.7 - - + -
466A LYS* 3.5 30.6 - - + +
502A PHE 3.3 13.0 + - - +
503A CYS 3.0 6.7 + - - +
505A ASN* 1.3 77.3 - - + +
507A LEU* 1.3 66.8 + - + +
508A SER 3.2 1.8 - - - -
509A GLU* 3.1 26.6 + - - +
510A VAL* 3.9 4.9 + - + +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 3.8 29.8 - - + -
469A VAL* 4.0 21.3 - - + -
477A ALA* 5.1 1.6 - - + -
481A ILE* 3.9 26.7 - - + -
482A ILE* 4.3 17.7 - - + -
485A VAL* 4.4 10.1 - - + -
503A CYS* 2.9 30.2 + - + +
504A ILE* 4.8 1.1 - - - +
506A VAL* 1.3 71.3 - - + +
508A SER* 1.3 61.2 + - - +
510A VAL* 3.0 5.3 + - + -
511A CYS* 2.8 42.4 + - - +
520A MET* 3.9 18.4 - - + -
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Residues in contact with SER 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ILE* 3.0 14.4 + - - -
505A ASN 3.0 18.7 + - - -
507A LEU* 1.3 78.5 - - - +
509A GLU* 1.3 60.0 + - - +
510A VAL 3.4 0.7 + - - -
511A CYS 4.1 3.1 + - - -
512A GLY* 4.2 3.8 + - - -
516A THR* 3.5 26.7 + - - -
520A MET* 4.2 2.6 - - - +
545A LYS* 4.2 3.6 + - - -
546A ILE* 3.4 25.2 - - - +
549A ILE* 2.9 34.9 - - - +
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Residues in contact with GLU 509 (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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466A LYS* 2.8 37.0 + - - +
505A ASN 3.9 4.6 - - - +
506A VAL* 3.1 16.7 + - - +
507A LEU 3.1 0.4 - - - -
508A SER* 1.3 82.8 + - - +
510A VAL* 1.3 66.9 + - + +
512A GLY 5.2 0.7 - - - -
545A LYS* 3.0 38.3 + - - +
549A ILE* 4.2 6.1 - - + -
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Residues in contact with VAL 510 (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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466A LYS* 4.2 35.2 - - + -
469A VAL* 3.6 39.1 - - + +
470A GLU* 4.2 21.1 - - + +
474A LYS* 3.5 18.6 + - - -
506A VAL* 4.1 2.9 - - + +
507A LEU* 3.6 17.0 - - + +
509A GLU* 1.3 85.1 - - - +
511A CYS* 1.3 64.2 + - - +
512A GLY 3.4 2.6 + - - -
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Residues in contact with CYS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A VAL* 4.6 2.7 - - - -
474A LYS* 3.7 20.6 - - - +
477A ALA* 3.9 27.4 - - - -
482A ILE* 4.9 7.0 - - - -
507A LEU* 2.8 41.7 + - - +
510A VAL* 1.3 80.7 - - - +
512A GLY* 1.3 61.6 + - - +
514A ASP* 5.9 0.2 - - - +
515A ILE* 3.5 31.0 - - + +
516A THR* 4.6 0.2 - - - +
520A MET* 3.8 19.3 - - + -
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Residues in contact with GLY 512 (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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474A LYS* 4.2 9.8 - - - +
508A SER 4.2 5.6 + - - -
509A GLU 5.2 0.2 - - - -
510A VAL 3.4 3.8 - - - -
511A CYS* 1.3 79.6 - - - +
513A GLN* 1.3 62.9 + - - -
514A ASP 3.4 2.7 - - - -
516A THR* 2.8 32.6 + - - -
549A ILE* 4.4 5.4 - - - -
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Residues in contact with GLN 513 (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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512A GLY* 1.3 72.7 - - - -
514A ASP* 1.3 59.0 + - - +
516A THR* 3.9 0.2 - - - -
517A THR* 2.7 45.9 + - - +
549A ILE* 3.0 39.2 + - + +
550A LEU* 3.8 14.2 + - - -
551A ASP* 4.0 23.9 + - - +
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Residues in contact with ASP 514 (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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512A GLY* 3.4 1.0 - - - -
513A GLN* 1.3 80.6 + - - +
515A ILE* 1.3 61.5 + - + +
517A THR* 4.0 2.5 - - - -
518A LYS* 2.6 68.0 + - - +
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Residues in contact with ILE 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LYS* 4.0 31.9 - - + +
475A GLU* 4.4 10.5 - - - +
478A HIS* 4.2 13.5 - - + +
482A ILE* 3.5 31.2 - - + -
511A CYS* 3.5 29.2 - - + +
512A GLY 3.8 1.6 + - - -
513A GLN 3.5 0.2 - - - -
514A ASP* 1.3 77.5 - - + +
516A THR* 1.3 59.5 + - - +
519A HIS* 2.7 50.9 + - + +
520A MET* 3.6 6.7 + - + +
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Residues in contact with THR 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A SER* 3.5 31.8 + - - -
512A GLY 2.8 23.7 + - - -
513A GLN 3.9 2.9 - - - -
515A ILE* 1.3 77.4 - - - +
517A THR* 1.3 60.0 + - - +
520A MET* 3.1 31.4 + - + +
521A LEU* 3.0 27.9 + - - +
546A ILE* 4.4 17.0 - - + -
549A ILE* 4.4 9.3 - - + +
550A LEU* 4.2 17.3 - - + -
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Residues in contact with THR 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLN* 2.7 30.9 + - - +
514A ASP* 4.0 3.6 - - - -
516A THR* 1.3 78.6 - - - +
518A LYS* 1.3 65.0 + - + +
521A LEU* 3.8 9.8 - - + +
522A PRO* 3.6 15.9 - - - +
550A LEU* 3.4 21.9 - - - +
551A ASP* 5.1 2.6 + - + +
554A THR* 4.4 26.7 - - + +
558A GLU* 5.7 0.9 - - - +
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Residues in contact with LYS 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASP* 2.6 46.7 + - - +
517A THR* 1.3 83.3 - - + +
519A HIS* 1.3 86.7 + - + +
520A MET 3.8 0.2 - - - -
522A PRO* 3.6 15.5 - - - +
----------------------------------------------------------
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Residues in contact with HIS 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A HIS* 3.3 37.0 + + - -
482A ILE* 4.0 17.0 - - + +
486A LEU* 3.6 29.6 - - + +
515A ILE* 2.7 35.4 + - + +
518A LYS* 1.3 100.6 + - + +
520A MET* 1.3 61.5 + - - +
522A PRO* 4.2 3.4 - - - -
523A THR* 4.6 1.1 + - - -
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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