Contacts of the helix formed by residues 496 - 523 (chain D) in PDB entry 2HVH
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D VAL* 1.3 71.5 - - - +
497D THR* 1.3 63.5 + - - +
498D LYS* 3.4 8.7 + - - +
499D ARG* 3.4 32.9 + - - +
500D LEU* 3.2 19.1 + - - +
600D LYS* 5.7 0.9 - - - -
638D GLN 5.0 0.3 - - - +
639D ALA* 2.7 24.2 + - - +
641D VAL* 4.0 21.1 - - + +
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Residues in contact with THR 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D VAL* 3.3 14.1 + - + +
496D ASP* 1.3 70.6 + - - +
498D LYS* 1.3 66.9 + - - +
500D LEU* 3.4 7.7 - - - +
501D GLU* 2.7 42.5 + - - +
592D LEU* 3.9 22.9 - - + -
595D VAL* 4.1 29.6 - - + -
600D LYS* 3.8 25.3 - - + +
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Residues in contact with LYS 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D ASP* 3.4 8.0 + - - +
497D THR* 1.3 83.8 + - - +
499D ARG* 1.3 61.7 + - - +
501D GLU* 3.5 18.1 + - - +
502D GLN* 3.1 24.3 + - - +
600D LYS* 6.2 3.4 - - - +
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Residues in contact with ARG 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D ASP* 3.3 29.2 + - + +
497D THR 3.2 0.4 - - - -
498D LYS* 1.3 74.2 - - - +
500D LEU* 1.3 66.3 + - - +
502D GLN* 3.3 6.4 + - + +
503D MET* 3.0 39.6 + - + +
638D GLN* 3.3 53.8 + - + +
639D ALA* 4.9 1.8 - - + -
871D THR* 5.4 6.3 - - - +
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Residues in contact with LEU 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D VAL* 3.8 25.1 - - + -
496D ASP 3.2 8.7 + - - +
497D THR* 3.1 9.6 + - - +
499D ARG* 1.3 79.3 - - - +
501D GLU* 1.3 56.5 + - - +
503D MET* 3.1 27.1 + - + +
504D GLY* 2.9 23.7 + - - -
587D TYR 3.7 16.8 - - - +
588D ILE* 3.6 21.5 - - + +
591D LEU* 3.8 28.5 - - + -
592D LEU* 4.3 23.6 - - + +
595D VAL* 5.7 0.7 - - + -
636D ILE* 4.1 6.5 - - + +
639D ALA* 3.8 10.3 - - + +
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Residues in contact with GLU 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D THR* 2.7 29.7 + - - +
498D LYS* 3.8 21.3 - - - +
500D LEU* 1.3 72.8 - - - +
502D GLN* 1.3 58.4 + - - +
504D GLY* 3.1 5.3 + - - +
505D LYS* 3.0 24.4 + - - +
588D ILE* 5.3 0.2 - - - -
592D LEU* 4.1 30.1 - - + +
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Residues in contact with GLN 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D LYS 3.1 17.9 + - - +
499D ARG* 3.8 6.1 - - + +
500D LEU 3.2 0.2 - - - -
501D GLU* 1.3 73.6 - - - +
503D MET* 1.3 65.9 + - + +
504D GLY 3.1 0.4 - - - -
505D LYS* 3.2 40.3 + - - +
506D GLU* 3.2 40.0 + - - +
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Residues in contact with MET 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D ARG* 3.0 35.9 + - + +
500D LEU* 3.1 34.3 + - + +
502D GLN* 1.3 76.8 - - + +
504D GLY* 1.3 63.2 + - - +
506D GLU* 3.9 14.9 - - - +
507D LEU* 3.0 30.0 + - + +
588D ILE* 4.2 9.0 - - + -
635D LYS* 3.7 50.3 - - + +
636D ILE* 4.0 13.7 - - + +
638D GLN* 4.8 4.0 - - - +
639D ALA* 4.4 3.1 - - + +
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Residues in contact with GLY 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D LEU 2.9 13.3 + - - -
501D GLU* 3.1 7.3 + - - -
503D MET* 1.3 78.5 - - - +
505D LYS* 1.3 59.4 + - - +
507D LEU* 3.9 4.8 - - - +
508D ALA* 3.2 23.0 + - - +
584D GLN* 4.3 5.4 - - - +
588D ILE* 3.8 22.9 - - - +
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Residues in contact with LYS 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501D GLU 3.0 11.1 + - - +
502D GLN* 3.2 38.4 - - - +
503D MET 3.3 0.4 - - - -
504D GLY* 1.3 74.5 - - - +
506D GLU* 1.3 70.1 + - - +
507D LEU 3.3 0.3 + - - -
508D ALA* 3.3 13.3 + - - +
509D GLU* 3.0 42.4 + - - +
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Residues in contact with GLU 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D GLN* 3.2 36.0 + - - +
503D MET* 3.9 13.4 - - - +
505D LYS* 1.3 79.5 - - + +
507D LEU* 1.3 62.0 + - + +
509D GLU* 3.3 14.7 + - - +
510D GLN* 3.2 32.4 + - + +
635D LYS* 5.0 12.0 - - - -
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Residues in contact with LEU 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503D MET* 3.0 20.2 + - + +
504D GLY* 3.9 4.7 - - - +
506D GLU* 1.3 75.3 - - - +
508D ALA* 1.3 59.8 + - - +
510D GLN* 3.3 15.6 + - - +
511D LEU* 2.8 32.8 + - + +
580D LEU* 3.9 35.0 - - + +
583D LEU* 3.7 22.4 - - + -
584D GLN* 3.6 40.6 - - + +
588D ILE* 4.3 10.3 - - + -
632D GLU* 5.2 4.5 - - + +
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Residues in contact with ALA 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504D GLY 3.2 15.5 + - - +
505D LYS* 3.7 7.0 - - - +
507D LEU* 1.3 78.8 - - - +
509D GLU* 1.3 64.3 + - + +
511D LEU* 3.1 7.4 + - - +
512D GLY* 3.1 18.5 + - - -
584D GLN* 3.5 16.7 + - - +
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Residues in contact with GLU 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D LYS* 3.0 44.0 + - + +
506D GLU* 3.3 13.9 + - - +
507D LEU 3.3 0.6 - - - -
508D ALA* 1.3 77.6 - - + +
510D GLN* 1.3 61.8 + - - +
512D GLY* 3.2 10.4 + - - +
513D THR* 3.3 16.1 + - - -
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Residues in contact with GLN 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D GLU* 3.2 23.4 + - + +
507D LEU* 3.6 18.4 - - - +
508D ALA 3.3 0.2 - - - -
509D GLU* 1.3 74.9 - - - +
511D LEU* 1.3 64.1 + - - +
512D GLY 3.1 0.7 + - - -
513D THR* 3.1 8.8 + - - -
514D VAL* 3.1 29.6 + - + +
576D HIS* 4.3 8.1 - - - -
580D LEU* 3.9 19.0 - - + +
632D GLU* 3.0 29.6 + - - +
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Residues in contact with LEU 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507D LEU* 2.8 14.3 + - + +
508D ALA* 3.1 12.3 + - - +
510D GLN* 1.3 76.7 - - - +
512D GLY* 1.3 54.0 + - - +
514D VAL* 4.8 1.6 - - + -
515D GLU* 3.0 31.8 + - - +
577D TYR* 3.8 42.1 - - + +
580D LEU* 3.6 41.1 - - + +
581D GLY* 4.2 6.3 - - - +
584D GLN* 3.4 40.2 - - + +
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Residues in contact with GLY 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508D ALA 3.1 11.5 + - - -
509D GLU* 3.2 4.2 + - - -
510D GLN 3.1 0.4 - - - -
511D LEU* 1.3 75.1 - - - +
513D THR* 1.3 58.6 + - - +
515D GLU* 3.1 12.3 + - - +
516D GLN* 2.8 38.2 + - - +
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Residues in contact with THR 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D GLU 3.3 13.0 + - - -
510D GLN* 3.1 9.2 + - - -
512D GLY* 1.3 74.5 - - - +
514D VAL* 1.3 60.3 + - + +
516D GLN* 3.5 5.7 + - - +
517D ARG* 3.0 28.8 + - + +
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Residues in contact with VAL 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510D GLN* 3.1 20.8 + - + +
511D LEU* 4.2 3.8 - - - +
513D THR* 1.3 75.9 - - + +
515D GLU* 1.3 66.3 + - - +
517D ARG* 3.2 7.2 + - - +
518D ILE* 2.9 30.2 + - + +
573D ASN* 3.6 32.5 - - - +
576D HIS* 4.0 27.1 - - + +
577D TYR* 3.8 23.3 - - + +
580D LEU* 4.4 6.1 - - + -
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Residues in contact with GLU 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D LEU 3.0 23.3 + - - +
512D GLY* 3.4 10.1 - - - +
514D VAL* 1.3 76.3 - - - +
516D GLN* 1.3 70.9 + - - +
518D ILE* 3.1 5.2 + - - +
519D TYR* 2.7 66.8 + - + +
528D ILE* 4.0 13.5 - - + -
577D TYR* 4.1 19.5 + - + +
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Residues in contact with GLN 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D GLY* 2.8 21.6 + - - +
513D THR* 3.9 5.8 - - - +
515D GLU* 1.3 83.5 + - - +
517D ARG* 1.3 62.2 + - - +
519D TYR* 3.2 26.2 + - - +
520D GLU* 3.0 41.1 + - - +
525D GLU* 4.4 11.8 + - - +
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Residues in contact with ARG 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513D THR* 3.0 19.9 + - + +
514D VAL* 3.4 7.6 - - - +
516D GLN* 1.3 76.1 - - - +
518D ILE* 1.3 61.7 + - - +
520D GLU* 3.5 27.5 + - - +
521D LEU* 3.1 57.5 + - + +
569D GLU* 3.1 37.8 + - - -
573D ASN* 3.4 25.4 + - - +
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Residues in contact with ILE 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D VAL* 2.9 18.6 + - + +
515D GLU 3.1 7.4 + - - +
517D ARG* 1.3 73.6 - - - +
519D TYR* 1.3 59.8 + - - +
521D LEU* 3.3 1.3 + - - -
522D ALA* 2.8 28.4 + - - +
526D PHE* 3.9 28.3 - - + -
528D ILE* 3.9 20.9 - - + -
570D ILE* 3.4 18.5 - - + +
573D ASN* 3.7 42.0 - - + +
574D ILE* 3.9 12.8 - - + +
577D TYR* 3.8 19.3 - - + -
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Residues in contact with TYR 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D GLU* 2.7 55.3 + - + +
516D GLN* 3.2 20.8 + - - +
518D ILE* 1.3 75.1 - - + +
520D GLU* 1.3 58.6 + - + +
522D ALA* 4.4 0.2 - - - -
523D GLY* 2.8 22.7 + - - -
524D GLN 3.0 29.9 + - - +
525D GLU* 3.6 37.5 - - + +
526D PHE* 3.1 42.0 + + - -
527D ASN* 5.1 0.3 - - - -
528D ILE* 3.9 18.4 + - + +
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Residues in contact with GLU 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516D GLN* 3.0 32.6 + - - +
517D ARG* 3.7 27.0 + - - +
518D ILE 3.2 0.2 - - - -
519D TYR* 1.3 75.2 - - + +
521D LEU* 1.3 65.6 + - - +
523D GLY* 3.0 14.0 + - - -
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Residues in contact with LEU 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517D ARG* 3.1 50.3 + - + +
520D GLU* 1.3 77.2 - - + +
522D ALA* 1.3 62.2 + - - +
523D GLY* 3.5 0.5 + - - -
542D LEU* 4.6 4.3 - - - +
568D HIS* 4.1 22.3 + - + -
569D GLU* 3.8 22.9 - - + +
570D ILE* 3.8 28.7 - - + +
573D ASN* 3.7 26.7 - - - +
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Residues in contact with ALA 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518D ILE 2.8 18.1 + - - +
521D LEU* 1.3 76.5 - - - +
523D GLY* 1.3 57.9 + - - +
524D GLN* 3.1 21.2 + - + +
526D PHE* 4.2 9.0 - - + -
537D ILE* 4.0 20.6 - - + -
541D LYS* 2.9 30.0 + - - +
542D LEU* 4.5 6.6 - - - +
570D ILE* 3.5 14.8 - - + +
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Residues in contact with GLY 523 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519D TYR 2.8 8.6 + - - -
520D GLU* 3.0 12.9 + - - -
521D LEU 3.2 0.2 - - - -
522D ALA* 1.3 75.6 - - - +
524D GLN* 1.3 62.0 + - - +
541D LYS* 4.7 4.9 - - - -
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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