Contacts of the helix formed by residues 496 - 523 (chain A) in PDB entry 4UQG
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 ASP 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A LYS 4.3 0.2 + - - -
495A VAL* 1.3 69.8 - - - +
497A THR* 1.3 62.1 + - - +
498A LYS* 3.5 11.3 + - - +
499A ARG* 3.1 39.7 + - + +
500A LEU* 3.2 10.6 + - - +
638A GLN 4.9 1.4 - - - +
639A ALA* 2.7 23.9 + - - +
641A VAL* 4.1 21.1 - - + +
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Residues in contact with THR 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A VAL* 3.1 16.6 + - + +
496A ASP* 1.3 73.6 + - - +
498A LYS* 1.3 60.5 + - - +
500A LEU* 3.3 3.9 + - - +
501A GLU* 2.9 41.4 + - - +
592A LEU* 4.0 23.3 - - + +
595A VAL* 3.8 29.4 - - + -
600A LYS* 4.4 15.0 - - + +
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Residues in contact with LYS 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASP* 3.2 8.4 + - - +
497A THR* 1.3 82.5 + - - +
499A ARG* 1.3 61.8 + - - +
501A GLU* 3.3 14.6 + - - +
502A GLN* 3.0 29.4 + - - +
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Residues in contact with ARG 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASP* 3.1 31.4 + - + +
498A LYS* 1.3 79.3 - - - +
500A LEU* 1.3 57.4 + - - +
502A GLN* 3.2 46.4 - - - +
503A MET* 3.0 58.7 + - + +
506A GLU* 5.1 5.7 + - - -
635A LYS* 4.8 8.1 - - - +
638A GLN* 2.6 47.8 + - - +
639A ALA* 4.7 4.0 - - + -
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Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A VAL* 3.7 23.8 - - + -
496A ASP 3.2 8.8 + - - +
497A THR 3.7 6.1 - - - +
499A ARG* 1.3 73.6 - - - +
501A GLU* 1.3 62.8 + - - +
503A MET* 3.3 11.8 + - - +
504A GLY 2.8 23.6 + - - -
588A ILE* 3.7 35.0 - - + +
591A LEU* 3.9 34.8 - - + -
592A LEU* 3.8 26.9 - - + +
595A VAL* 5.3 0.2 - - + -
636A ILE* 4.6 6.3 - - + -
639A ALA* 3.6 25.6 - - + -
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Residues in contact with GLU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A THR* 2.9 27.9 + - - +
498A LYS* 3.6 17.0 - - - +
500A LEU* 1.3 77.8 - - - +
502A GLN* 1.3 57.4 + - - +
504A GLY* 3.3 3.3 + - - +
505A GLU* 3.0 32.3 + - + +
588A ILE* 5.3 0.2 - - - -
592A LEU* 4.1 25.2 - - + +
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Residues in contact with GLN 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LYS* 3.0 16.3 + - - +
499A ARG* 3.2 48.8 - - - +
501A GLU* 1.3 73.4 - - - +
503A MET* 1.3 67.5 + - - +
505A GLU* 3.2 9.2 + - + +
506A GLU* 3.1 33.2 + - - +
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Residues in contact with MET 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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499A ARG* 3.0 66.4 + - + +
500A LEU* 3.5 16.4 - - - +
502A GLN* 1.3 75.4 - - - +
504A GLY* 1.3 57.4 + - - +
506A GLU* 3.2 15.7 + - - +
507A LEU* 2.9 36.8 + - + +
588A ILE* 4.2 8.5 - - + -
635A LYS* 3.1 36.8 - - + +
636A ILE* 4.3 22.0 - - + +
638A GLN* 3.5 3.4 - - + +
639A ALA* 5.3 0.4 - - - -
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Residues in contact with GLY 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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500A LEU 2.8 14.5 + - - -
501A GLU* 3.6 4.7 - - - -
503A MET* 1.3 77.4 - - - +
505A GLU* 1.3 56.3 + - - +
507A LEU* 4.5 0.4 - - - -
508A ALA* 3.0 14.9 + - - +
584A GLN* 2.9 41.3 + - - -
588A ILE* 3.9 10.4 - - - +
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Residues in contact with GLU 505 (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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501A GLU* 3.0 19.7 + - + +
502A GLN* 3.6 11.2 - - - +
503A MET 3.2 0.4 - - - -
504A GLY* 1.3 74.3 - - - +
506A GLU* 1.3 65.0 + - + +
508A ALA* 3.3 7.5 + - - +
509A GLU* 3.3 21.4 + - - +
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Residues in contact with GLU 506 (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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499A ARG* 5.1 4.6 + - - -
502A GLN* 3.1 24.3 + - - +
503A MET* 3.5 16.9 - - - +
505A GLU* 1.3 72.1 - - + +
507A LEU* 1.3 67.0 + - + +
509A GLU* 3.0 21.1 + - - +
510A GLN* 3.0 28.3 + - - +
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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
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503A MET* 2.9 24.5 + - + +
504A GLY 3.9 3.8 - - - +
506A GLU* 1.3 73.6 - - + +
508A ALA* 1.3 58.2 + - - +
510A GLN* 3.3 8.3 + - - +
511A LEU* 2.8 34.3 + - + +
580A LEU* 3.4 41.7 - - + +
583A LEU* 3.9 27.4 - - + -
584A GLN* 4.0 18.8 - - + +
588A ILE* 3.9 29.4 - - + -
636A ILE* 5.5 1.6 - - + -
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Residues in contact with ALA 508 (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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504A GLY 3.0 19.8 + - - +
505A GLU* 3.6 8.3 - - - +
506A GLU 3.1 0.4 - - - -
507A LEU* 1.3 75.5 - - - +
509A GLU* 1.3 61.4 + - - +
511A LEU* 3.5 7.6 + - - +
512A ARG* 3.2 34.0 + - + +
584A GLN* 3.7 11.4 - - - +
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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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505A GLU 3.3 8.8 + - - +
506A GLU* 3.0 13.3 + - - +
508A ALA* 1.3 76.5 - - - +
510A GLN* 1.3 65.4 + - + +
512A ARG* 3.2 11.6 + - - +
513A THR* 3.0 30.9 + - - +
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Residues in contact with GLN 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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506A GLU* 3.0 29.1 + - - +
507A LEU* 3.8 7.2 - - - +
509A GLU* 1.3 76.0 - - + +
511A LEU* 1.3 63.8 + - - +
513A THR* 3.4 7.7 + - - -
514A VAL* 3.0 29.1 + - + +
576A HIS* 4.8 7.8 + - - +
580A LEU* 3.8 31.7 - - + +
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Residues in contact with LEU 511 (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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507A LEU* 2.8 25.0 + - + +
508A ALA* 3.8 6.5 - - - +
509A GLU 3.3 0.2 - - - -
510A GLN* 1.3 73.9 - - - +
512A ARG* 1.4 53.3 + - + +
514A VAL* 3.5 2.3 + - - +
515A GLU* 2.9 36.9 + - - +
577A TYR* 3.6 42.4 - - + +
580A LEU* 3.6 28.9 - - + +
581A GLY* 3.7 9.6 - - - +
584A GLN* 4.1 32.5 - - + +
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Residues in contact with ARG 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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508A ALA* 3.2 24.8 + - - +
509A GLU* 3.2 10.5 + - - +
511A LEU* 1.4 74.9 - - + +
513A THR* 1.3 62.0 + - - +
515A GLU* 3.5 16.3 + - - +
516A GLN* 3.1 31.9 + - + +
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Residues in contact with THR 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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509A GLU* 3.0 18.2 + - - +
510A GLN* 3.5 11.0 - - - -
512A ARG* 1.3 74.4 - - - +
514A VAL* 1.3 68.5 + - + +
516A GLN* 3.1 7.3 + - - +
517A ARG* 3.1 22.4 + - + +
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Residues in contact with VAL 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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510A GLN* 3.0 17.9 + - + +
511A LEU 4.1 2.5 - - - +
513A THR* 1.3 77.0 - - + +
515A GLU* 1.3 56.9 + - - +
517A ARG* 3.2 8.1 + - - +
518A ILE* 2.9 29.0 + - + +
573A ASN* 3.2 45.5 - - + +
576A HIS* 3.5 29.2 - - + +
577A TYR* 4.0 17.0 - - + +
580A LEU* 4.0 7.6 - - + -
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Residues in contact with GLU 515 (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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511A LEU 2.9 17.2 + - - +
512A ARG* 3.6 20.9 - - - +
513A THR 3.2 0.2 - - - -
514A VAL* 1.3 75.3 - - - +
516A GLN* 1.3 71.9 + - - +
518A ILE* 3.3 5.2 + - - +
519A TYR* 3.1 62.4 + - + +
528A ILE* 4.1 13.7 - - + -
577A TYR* 4.1 16.1 - - + +
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Residues in contact with GLN 516 (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 ARG* 3.1 20.9 + - + +
513A THR* 3.1 6.5 + - - +
515A GLU* 1.3 87.6 + - - +
517A ARG* 1.3 57.5 + - - +
519A TYR* 3.3 29.9 + - - +
520A GLU* 2.9 29.8 + - - +
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Residues in contact with ARG 517 (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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513A THR* 3.1 13.0 + - + +
514A VAL* 3.3 12.3 - - - +
516A GLN* 1.3 74.8 - - - +
518A ILE* 1.3 57.8 + - - +
520A GLU* 3.0 41.3 + - - +
521A LEU* 2.8 50.2 + - + +
569A GLU* 3.0 34.2 + - - -
573A ASN* 3.3 28.0 - - - +
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Residues in contact with ILE 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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514A VAL 2.9 17.4 + - - +
515A GLU 3.5 7.2 - - - +
517A ARG* 1.3 76.2 - - - +
519A TYR* 1.3 56.6 + - - +
521A LEU* 4.7 0.7 - - - -
522A ALA* 2.9 28.6 + - - +
526A PHE* 3.7 28.3 - - + -
528A ILE* 3.9 22.9 - - + -
570A ILE* 3.7 17.2 - - + +
573A ASN* 3.6 40.8 - - + +
574A ILE* 3.9 14.6 - - + +
577A TYR* 3.8 19.5 - - + -
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Residues in contact with TYR 519 (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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515A GLU* 3.1 49.9 + - + +
516A GLN* 3.3 26.9 + - - +
518A ILE* 1.3 73.1 - - + +
520A GLU* 1.3 60.3 + - - +
523A GLY* 2.9 24.1 + - - -
524A GLN 3.1 31.5 + - - +
525A GLU* 3.7 17.0 - - + +
526A PHE* 3.1 41.6 + + - -
527A ASN* 5.1 0.3 - - - -
528A ILE* 3.8 21.1 + - + +
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Residues in contact with GLU 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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516A GLN 2.9 12.6 + - - +
517A ARG* 3.0 43.6 + - - +
519A TYR* 1.3 77.9 - - - +
521A LEU* 1.3 62.4 + - - +
523A GLY* 3.1 14.3 + - - -
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Residues in contact with LEU 521 (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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517A ARG* 2.8 56.7 + - + +
518A ILE 4.0 3.1 - - - +
520A GLU* 1.3 73.5 - - - +
522A ALA* 1.3 59.8 + - - +
542A LEU* 4.7 2.9 - - - +
568A HIS* 3.8 24.7 + - + -
569A GLU* 3.6 34.3 - - + +
570A ILE* 3.6 16.8 - - + +
573A ASN* 3.4 29.8 - - + +
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Residues in contact with ALA 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ILE 2.9 19.9 + - - +
521A LEU* 1.3 77.2 - - - +
523A GLY* 1.3 58.1 + - - +
524A GLN 3.6 8.7 + - - +
526A PHE* 3.8 20.0 - - + -
537A ILE* 3.9 14.3 - - + +
541A LYS* 2.9 32.4 + - - -
542A LEU* 4.6 7.0 - - - +
570A ILE* 3.8 17.9 - - + +
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Residues in contact with GLY 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A TYR 2.9 9.0 + - - -
520A GLU 3.1 10.7 + - - -
521A LEU 3.6 0.2 + - - -
522A ALA* 1.3 77.2 - - - +
524A GLN* 1.3 64.0 + - - +
541A LYS* 4.7 6.6 - - - -
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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
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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