Contacts of the helix formed by residues 503 - 529 (chain A) in PDB entry 6HBU
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 ALA 503 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LYS* 1.3 75.7 - - - +
504A ASP* 1.3 65.8 + - - +
506A PHE* 3.5 9.8 + - - +
507A PHE* 3.2 28.9 - - + -
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Residues in contact with ASP 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LYS* 3.5 31.1 + - - +
503A ALA* 1.3 73.5 - - - +
505A ALA* 1.3 68.2 + - - +
507A PHE* 3.1 9.4 + - - +
508A VAL* 2.9 35.7 + - + +
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Residues in contact with ALA 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LYS* 3.7 38.4 - - + +
502A LYS* 4.3 7.4 + - + -
503A ALA 3.4 0.4 - - - -
504A ASP* 1.3 85.1 + - - +
506A PHE* 1.3 63.3 + - - +
508A VAL* 4.0 2.2 - - - -
509A MET* 3.3 9.7 + - - +
584A ASN* 3.1 42.0 + - - +
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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
----------------------------------------------------------
490A THR* 3.7 30.0 - - + +
491A CYS* 3.6 29.4 - - - -
494A TYR* 3.6 44.2 - + + -
500A LYS 5.1 0.6 + - - -
502A LYS 3.9 11.5 + - - +
503A ALA* 3.5 10.4 + - - +
504A ASP 3.2 0.4 - - - -
505A ALA* 1.3 78.9 - - - +
507A PHE* 1.3 85.4 + + - +
509A MET* 3.4 8.1 + - - +
510A MET* 2.9 46.8 + - + +
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Residues in contact with PHE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ALA* 3.2 29.4 - - + -
504A ASP* 3.1 8.1 + - - +
506A PHE* 1.3 99.8 - + - +
508A VAL* 1.3 61.6 + - + +
510A MET* 3.6 22.0 - - + +
511A PHE* 2.8 29.5 + - - +
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Residues in contact with VAL 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ASP* 2.9 26.2 + - + +
505A ALA* 4.6 0.7 - - - -
507A PHE* 1.3 74.6 - - + +
509A MET* 1.3 54.9 + - - +
511A PHE* 3.8 5.5 - - - +
512A THR* 2.5 43.8 + - - +
584A ASN* 3.4 26.9 - - - +
626A LEU* 3.9 28.3 - - + -
627A TRP* 4.1 26.0 - - + -
630A HIS* 4.4 1.1 + - + -
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Residues in contact with MET 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 5.2 2.9 - - + -
433A LEU* 3.7 30.7 - - + -
490A THR* 3.9 19.1 - - + +
493A VAL* 3.7 23.6 - - + -
494A TYR* 5.4 8.1 - - - -
499A LEU* 3.7 24.7 - - + -
505A ALA 3.3 16.9 + - - +
506A PHE* 3.5 5.6 - - - +
507A PHE 3.3 0.2 - - - -
508A VAL* 1.3 74.2 - - - +
510A MET* 1.3 64.2 + - - +
512A THR* 3.3 0.7 + - - -
513A LEU* 3.1 32.1 + - + +
581A LEU* 4.0 19.1 - - + -
584A ASN* 3.2 13.8 - - - +
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Residues in contact with MET 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A SER 4.1 10.0 - - - +
487A ILE* 3.8 44.6 - - + +
490A THR* 3.8 14.3 - - + +
491A CYS* 4.2 2.0 - - - -
506A PHE* 2.9 48.5 + - + +
507A PHE* 3.8 23.8 - - + +
508A VAL 3.4 0.2 - - - -
509A MET* 1.3 76.7 - - - +
511A PHE* 1.3 61.8 + - - +
513A LEU* 3.5 2.3 + - - +
514A MET* 3.2 40.2 + - + +
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Residues in contact with PHE 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A PHE 2.8 19.2 + - - +
508A VAL* 3.9 4.5 - - - +
509A MET 3.3 0.2 - - - -
510A MET* 1.3 76.9 - - - +
512A THR* 1.3 61.6 + - - +
514A MET* 3.4 16.4 + - + +
515A MET* 3.1 50.6 + - + +
627A TRP* 3.6 31.9 - + + -
630A HIS* 3.5 28.0 - + + -
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Residues in contact with THR 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 6.1 0.2 - - + -
508A VAL* 2.5 26.3 + - - +
509A MET* 3.7 4.7 - - - -
510A MET 3.3 0.4 - - - -
511A PHE* 1.3 77.3 - - - +
513A LEU* 1.3 60.5 + - - +
515A MET* 3.3 2.8 + - - +
516A VAL* 3.2 25.0 + - + +
577A GLY* 3.7 30.5 - - - +
580A ALA* 3.8 13.5 + - + +
581A LEU* 3.9 17.7 - - + +
630A HIS* 2.7 32.4 + - + +
633A LEU* 5.5 2.0 - - + -
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Residues in contact with LEU 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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433A LEU* 4.3 15.3 - - + +
434A THR* 5.6 0.7 - - + -
437A GLN* 3.2 33.2 + - + +
486A SER* 4.1 6.5 - - - +
489A PHE* 3.6 35.4 - - + -
490A THR* 3.7 20.6 - - - +
509A MET* 3.1 34.7 + - + +
510A MET 4.1 3.4 - - - +
511A PHE 3.4 0.2 - - - -
512A THR* 1.3 74.3 - - - +
514A MET* 1.3 62.4 + - - +
516A VAL* 3.5 9.5 - - + +
517A ALA* 3.3 11.1 + - - +
581A LEU* 3.7 33.9 - - + -
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Residues in contact with MET 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ARG 4.7 5.4 - - - +
483A MET* 4.0 26.2 - - + +
486A SER* 3.8 17.7 - - - -
487A ILE* 3.7 31.9 - - + +
510A MET* 3.2 32.2 + - + +
511A PHE* 3.7 19.5 - - + +
512A THR 3.3 0.2 - - - -
513A LEU* 1.3 76.8 - - - +
515A MET* 1.3 60.7 + - + +
517A ALA* 3.1 3.6 + - - +
518A TYR* 2.8 51.0 + - + -
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Residues in contact with MET 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A PHE* 3.1 51.8 + - + +
512A THR 3.3 3.5 + - - +
514A MET* 1.3 76.2 - - + +
516A VAL* 1.3 59.5 + - - +
518A TYR* 4.1 12.2 - - - +
519A SER* 2.7 34.5 + - - -
630A HIS* 3.6 29.2 - - + +
633A LEU* 3.8 17.7 - - + +
634A ALA* 3.6 27.8 - - + +
637A ILE* 3.8 16.9 - - + +
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Residues in contact with VAL 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 4.8 13.7 - - + +
437A GLN* 3.7 21.7 - - + +
438A CYS* 4.4 7.5 - - - -
512A THR* 3.2 15.8 + - + +
513A LEU* 3.5 14.4 - - + +
515A MET* 1.3 74.9 - - - +
517A ALA* 1.3 64.4 + - - +
519A SER 4.0 0.4 - - - -
520A ALA* 3.3 24.4 + - - +
573A ILE* 4.0 24.6 - - + +
577A GLY* 3.6 30.3 - - - -
633A LEU* 3.7 14.1 - - + -
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Residues in contact with ALA 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLN* 3.6 29.6 - - - +
441A SER* 3.3 2.1 + - - +
482A ARG* 3.7 20.7 - - + +
486A SER* 4.0 5.6 - - - +
513A LEU 3.3 18.8 + - - +
514A MET 3.1 5.9 + - - +
516A VAL* 1.3 77.6 - - - +
518A TYR* 1.3 57.9 + - - +
521A SER* 2.7 35.5 + - - -
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Residues in contact with TYR 518 (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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478A LEU* 3.4 35.3 - - + +
482A ARG* 3.6 31.9 - - + -
483A MET* 3.3 42.8 - - + +
514A MET* 2.8 36.9 + - + +
515A MET* 4.1 10.1 - - - +
517A ALA* 1.3 76.8 - - - +
519A SER* 1.3 58.3 + - - +
521A SER* 3.4 3.7 + - - -
522A SER* 2.8 35.4 + - - +
637A ILE* 3.7 26.0 - - + -
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Residues in contact with SER 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A MET 2.7 22.7 + - - -
518A TYR* 1.3 76.3 - - - +
520A ALA* 1.3 59.0 + - - +
522A SER* 3.6 4.0 + - - -
523A MET* 3.2 19.6 + - - +
573A ILE* 3.5 22.4 - - - +
633A LEU* 3.0 45.6 + - - +
636A MET* 4.6 7.4 - - - -
637A ILE* 3.3 9.8 - - - +
640A PHE* 3.9 4.5 - - - -
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Residues in contact with ALA 520 (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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438A CYS* 3.8 10.8 - - + +
441A SER* 3.6 17.2 - - - +
516A VAL 3.3 18.6 + - - +
518A TYR 3.3 0.2 - - - -
519A SER* 1.3 77.6 - - - +
521A SER* 1.3 59.8 + - - +
523A MET* 3.9 2.2 - - - +
524A ALA* 3.2 17.8 + - - +
541A MET* 3.3 12.5 - - - +
545A PHE* 3.6 27.4 - - + -
573A ILE* 3.9 12.1 - - + +
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Residues in contact with SER 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A SER* 3.1 8.7 + - - -
444A ALA* 4.1 11.3 - - - +
477A ASP* 4.5 4.5 - - - -
482A ARG* 2.9 30.9 + - - +
517A ALA 2.7 23.6 + - - -
518A TYR* 3.8 5.6 - - - -
520A ALA* 1.3 77.2 - - - +
522A SER* 1.3 58.1 + - - +
523A MET 3.2 0.2 - - - -
524A ALA* 3.1 7.3 + - - +
525A LEU* 3.0 34.8 + - - +
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Residues in contact with SER 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 2.8 24.0 + - - +
519A SER 3.9 4.5 - - - -
521A SER* 1.3 76.8 - - - +
523A MET* 1.3 56.5 + - - +
525A LEU* 3.4 2.4 + - - +
526A ALA 3.0 20.8 + - - -
636A MET 4.3 6.3 - - - -
637A ILE* 3.8 12.2 - - - +
640A PHE* 3.3 30.1 - - - +
641A LEU* 3.4 35.3 - - - +
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Residues in contact with MET 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A SER 3.2 12.9 + - - +
520A ALA* 4.0 2.2 - - - +
521A SER 3.2 0.4 - - - -
522A SER* 1.3 74.6 - - - +
524A ALA* 1.3 63.5 + - - +
526A ALA* 4.3 2.7 - - + +
527A ILE* 3.3 36.4 + - + +
541A MET* 3.6 26.5 - - + -
544A CYS* 4.1 21.8 - - + -
545A PHE* 3.9 15.7 - - + -
548A MET* 3.6 33.7 - - + -
573A ILE* 4.5 2.5 - - + -
640A PHE* 3.6 40.1 - - + -
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Residues in contact with ALA 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A SER 3.3 26.0 - - - +
444A ALA* 3.9 10.8 - - + -
445A VAL* 3.8 21.3 - - + +
520A ALA 3.2 9.0 + - - +
521A SER 3.1 10.1 + - - +
523A MET* 1.3 77.6 - - - +
525A LEU* 1.3 61.2 + - - +
527A ILE* 4.3 1.0 - - - +
528A ALA* 3.3 26.7 + - - +
541A MET* 3.4 13.7 - - + +
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ALA* 3.3 23.3 - - + +
445A VAL 5.5 0.9 - - - +
447A LEU* 3.8 20.4 - - + -
448A PHE* 3.8 27.4 - - + +
474A LEU* 3.7 30.3 - - + -
477A ASP* 5.0 5.4 - - - +
521A SER* 3.0 17.8 + - - +
522A SER* 3.4 6.3 + - - +
524A ALA* 1.3 78.5 - - - +
526A ALA* 1.3 58.9 + - - +
527A ILE 3.2 0.4 - - - -
528A ALA* 4.5 1.6 - - + +
529A ALA* 3.0 35.5 + - - +
641A LEU* 3.8 11.0 - - + -
644A ALA* 3.5 14.2 - - + +
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Residues in contact with ALA 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A SER 3.0 11.7 + - - +
523A MET* 3.5 7.6 + - + +
524A ALA 3.4 0.2 - - - -
525A LEU* 1.3 76.9 - - - +
527A ILE* 1.3 60.3 + - + +
640A PHE* 3.3 33.0 - - + +
643A ILE* 4.0 18.9 - - + +
644A ALA* 3.8 11.4 - - - +
647A LYS* 2.9 28.1 + - - +
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Residues in contact with ILE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A MET* 3.3 34.3 + - + +
524A ALA 4.4 2.7 - - - +
525A LEU 3.2 0.2 - - - -
526A ALA* 1.3 80.9 - - + +
528A ALA* 1.3 56.8 + - - +
531A GLN* 3.2 15.0 - - - +
536A VAL* 6.3 0.7 - - + -
537A ALA* 3.9 27.8 - - + +
540A LEU* 4.2 35.9 - - + +
541A MET* 3.7 20.0 - - - -
544A CYS* 5.3 4.3 - - - -
647A LYS* 2.9 17.6 + - - +
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Residues in contact with ALA 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A VAL* 3.4 38.6 - - + +
448A PHE* 4.5 4.3 - - + +
449A VAL* 3.4 22.3 - - + +
524A ALA 3.3 19.4 + - - +
525A LEU* 3.4 2.2 + - + +
527A ILE* 1.3 78.5 - - - +
529A ALA* 1.3 63.3 + - - +
530A GLY 3.4 1.7 + - - -
531A GLN* 3.7 13.5 + - - +
537A ALA* 3.7 7.0 - - + -
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Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PHE* 4.1 14.4 - - + -
525A LEU 3.0 18.6 + - - +
527A ILE 3.6 1.2 - - - -
528A ALA* 1.3 78.5 - - - +
530A GLY* 1.3 62.9 + - - +
531A GLN* 3.6 1.6 + - - +
644A ALA* 3.4 26.5 - - - +
647A LYS* 3.3 37.8 + - + +
648A LEU* 4.0 9.9 - - + -
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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