Contacts of the helix formed by residues 506 - 531 (chain A) in PDB entry 2VWK
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 CYS 506 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A PRO* 4.0 20.2 - - + -
423A LEU* 4.4 5.8 - - - -
497A TYR* 3.0 19.7 + - + +
504A TRP 3.5 3.5 + - - +
505A TYR* 1.3 79.8 - - - +
507A LYS* 1.3 61.5 + - - +
508A GLU* 3.2 19.5 - - - -
509A CYS* 2.1 58.7 + - + +
510A ALA 2.9 23.6 + - - -
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Residues in contact with LYS 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ARG* 5.8 1.2 + - - +
383A SER* 3.9 29.2 + - - +
497A TYR 4.6 0.7 - - - -
498A GLY* 5.4 1.8 - - - -
505A TYR* 3.5 31.7 - - + +
506A CYS* 1.3 71.8 - - - +
508A GLU* 1.3 67.7 + - - +
510A ALA* 3.2 9.8 + - + +
511A GLU* 2.9 55.1 + - + +
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Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 3.6 35.9 - - + +
424A ASN* 5.4 0.7 - - - +
439A HIS* 3.6 39.5 - - + +
441A PHE* 4.3 1.6 - - - -
506A CYS* 3.6 10.2 - - - -
507A LYS* 1.3 88.5 + - - +
509A CYS* 1.3 56.4 + - - +
511A GLU* 3.7 6.4 + - - +
512A SER* 2.6 35.0 + - - -
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Residues in contact with CYS 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL* 3.8 12.6 - - + -
419A SER* 3.6 10.3 - - - -
420A PRO* 3.6 21.8 - - - -
441A PHE* 4.0 12.8 - - - -
497A TYR* 3.7 19.5 - - + -
506A CYS* 2.1 54.5 - - + +
508A GLU* 1.3 72.5 - - - +
510A ALA* 1.3 67.7 + - - +
512A SER* 3.1 2.6 + - - -
513A VAL* 2.9 28.6 + - - +
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Residues in contact with ALA 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A TYR* 3.6 16.7 - - + +
497A TYR* 4.1 7.9 - - + +
498A GLY* 4.0 27.4 - - - +
506A CYS 2.9 12.4 + - - +
507A LYS* 3.2 11.6 + - + +
509A CYS* 1.3 77.0 - - - +
511A GLU* 1.3 61.3 + - - +
513A VAL* 3.3 2.1 + - - -
514A THR* 2.9 27.3 + - - +
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Residues in contact with GLU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLN* 4.6 4.3 - - - +
437A VAL* 3.8 27.1 - - + +
439A HIS* 3.7 15.4 + - - -
507A LYS* 2.9 47.5 + - + +
508A GLU* 3.7 10.3 - - - +
510A ALA* 1.3 71.4 - - - +
512A SER* 1.3 61.9 + - - +
514A THR* 3.3 8.9 + - - -
515A ALA* 2.9 29.5 + - - +
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Residues in contact with SER 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL* 4.7 1.3 - - - -
434A ALA* 3.4 13.6 - - - +
437A VAL* 3.5 8.0 - - - +
439A HIS* 3.4 14.7 - - - -
441A PHE* 3.2 31.0 - - - -
508A GLU 2.6 23.2 + - - -
509A CYS 3.5 3.6 - - - -
511A GLU* 1.3 78.1 - - - +
513A VAL* 1.3 57.0 + - - +
515A ALA* 3.2 3.2 + - - +
516A TRP* 2.9 39.0 + - - -
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Residues in contact with VAL 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TYR* 3.5 38.4 - - + +
412A ILE* 4.3 16.6 - - + +
413A ILE* 3.8 25.1 - - + -
418A VAL* 3.9 19.1 - - + -
494A TYR* 3.7 16.6 - - + -
497A TYR* 4.6 5.2 - - + -
509A CYS 2.9 22.3 + - - +
510A ALA 3.7 4.7 - - - +
512A SER* 1.3 72.1 - - - +
514A THR* 1.3 65.8 + - - +
516A TRP* 3.6 1.8 + - - +
517A GLY* 3.0 21.1 + - - -
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Residues in contact with THR 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA* 5.9 6.1 - - + -
386A GLY 5.4 6.7 - - - +
387A GLY* 5.9 2.7 - - - -
388A TYR 6.2 0.4 - - - +
409A TYR* 4.5 11.7 + - - +
494A TYR* 2.6 31.2 + - - +
510A ALA 2.9 15.9 + - - -
511A GLU* 3.6 11.2 - - - -
513A VAL* 1.3 78.2 - - - +
515A ALA* 1.3 56.6 + - - +
517A GLY* 3.3 2.9 + - - -
518A ARG* 3.1 44.6 + - + +
541A THR* 6.6 0.2 - - + -
1780A SO4 5.8 1.3 - - - +
1781A SO4 5.1 8.7 - - - +
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Residues in contact with ALA 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PRO* 3.2 35.5 - - + +
436A GLN* 3.7 16.2 - - + +
437A VAL* 4.8 0.4 - - + -
511A GLU 2.9 17.5 + - - +
512A SER* 3.6 4.9 - - - +
514A THR* 1.3 74.4 - - - +
516A TRP* 1.3 65.2 - - - +
518A ARG* 3.2 20.5 + - - +
519A GLN* 3.1 21.1 + - - +
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Residues in contact with TRP 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 3.6 29.4 - - + -
416A HIS* 3.2 51.9 + + + -
418A VAL* 3.6 22.7 - - + -
432A ASP* 3.9 12.8 - - + -
433A VAL 3.3 19.7 + - - -
434A ALA* 3.7 22.7 - - + -
435A PRO* 3.6 26.2 - - + +
441A PHE* 4.0 14.6 - + - -
512A SER* 2.9 23.4 + - - +
513A VAL 4.0 0.2 - - - +
515A ALA* 1.3 72.6 - - - +
517A GLY* 1.3 66.9 + - - +
519A GLN* 3.2 9.8 + - - +
520A TYR* 3.0 45.0 + + - -
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Residues in contact with GLY 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 4.4 8.2 - - - +
409A TYR* 4.2 16.8 - - - -
412A ILE* 3.9 10.0 - - - +
513A VAL 3.0 15.3 + - - -
514A THR 3.6 5.2 - - - -
515A ALA 3.2 0.4 - - - -
516A TRP* 1.3 76.8 - - - +
518A ARG* 1.3 60.9 + - - +
520A TYR* 3.3 1.6 + - - +
521A ILE* 3.0 34.7 + - - +
541A THR* 6.3 0.2 - - - -
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Residues in contact with ARG 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLY* 4.9 4.2 - - - -
388A TYR* 3.8 36.7 - - + +
436A GLN* 2.5 42.4 + - - +
514A THR* 3.1 32.1 + - + +
515A ALA* 3.2 20.6 + - - +
517A GLY* 1.3 73.9 - - - +
519A GLN* 1.3 53.0 + - - +
521A ILE* 3.4 8.3 + - - +
522A GLU* 2.7 59.1 + - - +
541A THR* 5.8 1.3 - - + -
1780A SO4 4.1 19.9 + - - -
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Residues in contact with GLN 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PRO* 3.1 32.4 - - + +
515A ALA 3.1 12.5 + - - +
516A TRP* 3.2 13.4 + - - +
518A ARG* 1.3 76.9 - - - +
520A TYR* 1.3 83.5 + - - +
522A GLU* 3.3 11.1 + - - +
523A THR* 2.8 50.6 + - + +
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Residues in contact with TYR 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 3.7 14.6 - - + -
408A LEU* 4.8 2.2 - - + -
412A ILE* 3.4 17.5 - - + -
416A HIS* 2.6 32.6 + - - -
516A TRP* 3.0 46.0 + + - +
517A GLY 4.0 2.5 - - - +
519A GLN* 1.3 87.6 + - - +
521A ILE* 1.3 63.8 + - - +
523A THR* 3.5 6.8 + - - -
524A THR* 2.7 32.4 + - - -
571A LEU* 4.0 15.5 - - + -
572A PRO* 3.5 30.6 - - + +
575A LEU* 3.2 31.6 - - + -
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Residues in contact with ILE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TYR* 3.7 32.3 - - + +
405A PHE* 3.8 23.6 - - + -
408A LEU* 3.9 14.6 - - + -
517A GLY 3.0 21.6 + - - +
518A ARG* 3.7 5.2 - - - +
520A TYR* 1.3 76.8 - - - +
522A GLU* 1.3 63.7 + - - +
524A THR* 3.7 1.7 - - - -
525A ILE* 3.1 33.0 + - + +
539A ALA* 4.9 1.1 - - + -
540A ASP 3.7 7.6 - - - +
541A THR* 3.6 39.7 - - + -
543A GLY* 5.8 2.0 - - - +
544A PHE* 5.2 6.7 - - + -
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Residues in contact with GLU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TYR* 3.6 27.9 - - + +
518A ARG* 2.7 48.4 + - - +
519A GLN* 3.6 9.4 + - - +
521A ILE* 1.3 75.1 - - - +
523A THR* 1.3 59.4 + - + +
525A ILE* 3.5 6.0 + - - +
526A ARG* 3.1 27.4 + - - +
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Residues in contact with THR 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A GLN* 2.8 39.7 + - + +
520A TYR* 3.7 12.5 + - - -
522A GLU* 1.3 76.7 - - + +
524A THR* 1.3 63.2 + - - +
526A ARG* 3.7 12.4 + - - +
527A GLU* 3.2 30.9 + - - +
571A LEU* 5.3 4.2 - - - +
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Residues in contact with THR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 3.3 17.4 - - + -
520A TYR 2.7 22.2 + - - -
521A ILE 3.7 3.6 - - - -
523A THR* 1.3 75.7 + - - +
525A ILE* 1.3 58.9 + - - +
527A GLU* 3.3 6.6 + - - +
528A ILE* 2.9 25.5 + - - +
544A PHE* 4.1 11.9 - - + -
563A PHE* 3.6 23.9 - - + -
567A ILE* 4.4 11.1 - - + +
571A LEU* 4.3 12.4 - - + +
577A LEU* 3.7 25.1 - - + -
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Residues in contact with ILE 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TYR* 3.3 26.9 - - - +
390A LYS* 4.1 16.6 - - + -
521A ILE* 3.1 25.2 + - + +
522A GLU* 3.8 4.7 - - - +
524A THR* 1.3 72.3 - - - +
526A ARG* 1.3 67.4 + - - +
528A ILE* 3.1 7.4 + - - +
529A GLU* 3.1 36.5 + - - +
536A VAL* 3.8 20.9 - - + -
539A ALA* 3.6 21.3 - - + -
544A PHE* 4.0 23.3 - - + -
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Residues in contact with ARG 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A GLU 3.1 17.7 + - - +
523A THR* 3.8 13.0 - - - +
525A ILE* 1.3 78.3 - - - +
527A GLU* 1.3 62.4 + - + +
529A GLU* 3.4 4.2 + - - -
530A GLU* 3.0 59.5 + - - +
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A THR* 3.2 19.2 + - - +
524A THR* 3.5 6.5 - - - +
525A ILE 3.1 0.6 - - - -
526A ARG* 1.3 79.5 - - + +
528A ILE* 1.3 64.7 + - - +
530A GLU* 4.6 3.1 - - - +
531A LYS* 3.1 35.9 + - - +
532A PHE 3.8 0.5 + - - -
563A PHE* 4.1 13.4 - - + -
566A TYR* 2.8 32.4 + - + -
567A ILE* 4.5 9.2 - - + +
570A LYS* 2.9 21.4 + - - +
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Residues in contact with ILE 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 3.9 18.4 - - + -
524A THR 2.9 14.0 + - - +
525A ILE* 3.1 10.5 + - - +
527A GLU* 1.3 73.2 - - - +
529A GLU* 1.3 64.0 + - + +
532A PHE* 3.4 5.4 - - + +
533A GLY 3.3 6.4 + - - -
534A PHE* 3.2 60.8 + - + -
536A VAL* 3.6 25.8 - - + -
544A PHE* 4.0 13.0 - - + -
546A ALA* 4.8 1.1 - - + -
560A ALA* 5.4 0.2 - - - -
563A PHE* 3.5 47.3 - - + -
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LYS* 4.5 11.1 + - - -
525A ILE* 3.1 25.1 + - - +
526A ARG* 3.9 5.1 - - - +
528A ILE* 1.3 79.4 - - + +
530A GLU* 1.3 65.1 + - + +
533A GLY* 3.3 20.8 + - - -
534A PHE 3.7 14.9 - - - +
535A LYS* 3.8 8.5 - - - +
536A VAL* 3.1 43.4 + - + +
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Residues in contact with GLU 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ARG* 3.0 51.0 + - - +
527A GLU* 4.6 3.1 - - - +
529A GLU* 1.3 85.3 - - + +
531A LYS* 1.3 64.8 + - - +
532A PHE 3.4 0.4 + - - -
533A GLY* 4.5 1.6 + - - -
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Residues in contact with LYS 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU* 3.1 26.9 + - - +
530A GLU* 1.3 78.8 - - - +
532A PHE* 1.3 82.8 + - + +
566A TYR* 4.0 22.0 - - + +
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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