Contacts of the helix formed by residues 498 - 525 (chain A) in PDB entry 6DMY
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 498 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A PHE* 5.4 2.2 - - + -
496A ASN* 4.3 2.9 - - + +
497A ALA* 1.3 76.2 - - - +
499A THR* 1.3 59.9 + - + +
501A GLN* 4.4 4.3 - - - -
502A VAL* 2.9 36.5 + - + +
569A ALA* 6.0 3.8 - - + +
570A LEU* 6.1 4.0 - - + -
573A PHE* 4.1 12.8 - - + -
1147A PHE* 4.3 25.6 - - + -
1148A ILE* 6.6 0.2 - - - -
1152A PHE* 4.5 15.9 - - + -
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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
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485A LEU* 5.9 3.2 - - - +
495A PHE* 4.2 3.8 - - - +
496A ASN* 3.4 44.0 + - + +
498A ALA* 1.3 76.2 - - + +
500A THR* 1.3 73.3 + - - +
501A GLN 3.1 1.8 + - - -
503A LEU* 2.9 40.7 + - - +
504A PRO* 3.3 4.7 - - - +
573A PHE* 3.6 24.5 - - + -
576A GLN* 3.3 26.6 + - - +
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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
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121A LEU* 4.7 2.7 - - + -
435A SER 4.1 11.5 + - - +
437A VAL* 3.5 31.7 - - + +
442A VAL* 5.8 3.5 - - - +
495A PHE* 4.6 8.3 - - + -
496A ASN 3.6 11.1 + - - +
497A ALA 3.0 13.7 + - - -
499A THR* 1.3 90.0 + - - +
501A GLN* 1.3 71.3 + - - +
504A PRO* 4.7 8.1 - - - +
1809A Y01 4.5 33.3 - - + +
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Residues in contact with GLN 501 (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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434A PHE* 3.0 28.7 + - - +
436A ASP 2.5 32.2 + - - +
437A VAL* 5.8 0.9 - - - -
438A SER 6.1 0.9 - - - +
441A ARG* 5.7 6.5 - - - +
497A ALA 2.8 22.7 - - - +
498A ALA* 3.7 3.9 + - - +
499A THR 3.1 0.6 - - - -
500A THR* 1.3 86.9 + - - +
502A VAL* 1.3 61.2 + - + +
503A LEU 3.6 0.4 - - - -
504A PRO* 4.2 2.9 - - - +
505A PHE* 3.2 31.9 - - + -
1140A LEU* 3.3 7.8 - - + +
1145A PHE* 5.5 5.5 - - + -
1148A ILE* 3.8 30.4 - - + +
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Residues in contact with VAL 502 (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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498A ALA* 2.9 21.7 + - + +
501A GLN* 1.3 78.4 - - + +
503A LEU* 1.3 54.7 + - - +
504A PRO 3.5 0.2 - - - -
505A PHE* 3.2 5.9 + - - +
506A LEU* 2.8 45.1 + - + -
573A PHE* 3.9 17.5 - - + -
1140A LEU* 4.3 11.3 - - + +
1148A ILE* 4.8 12.1 - - + -
1152A PHE* 3.6 56.8 - - + -
1156A LEU* 5.9 1.6 - - + -
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Residues in contact with LEU 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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481A VAL* 4.6 3.8 - - + -
485A LEU* 3.8 41.7 - - + -
499A THR* 2.9 33.9 + - - +
502A VAL* 1.3 77.9 - - - +
504A PRO* 1.4 56.3 - - + +
506A LEU* 4.3 7.0 - - + -
507A ALA* 2.9 43.1 + - + +
573A PHE* 3.9 19.1 - - + -
576A GLN* 4.8 2.9 - - - +
577A ALA* 3.8 34.3 - - + +
580A VAL* 4.4 11.4 - - + -
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Residues in contact with PRO 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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442A VAL* 4.9 11.4 - - + -
446A TYR* 3.6 20.6 + - + +
481A VAL* 4.5 15.8 - - + +
485A LEU* 5.5 5.2 - - + -
499A THR 3.3 13.0 - - - +
500A THR* 4.7 7.2 - - - +
501A GLN 4.2 7.6 - - - +
502A VAL 3.8 1.8 - - - -
503A LEU* 1.4 90.1 - - + +
505A PHE* 1.3 65.5 + - + +
508A LEU* 2.9 34.8 + - - +
1809A Y01 5.1 24.5 - - + -
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Residues in contact with PHE 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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441A ARG* 3.9 22.2 - - + -
442A VAL* 3.7 44.9 - - + -
445A GLY* 4.6 6.5 - - - -
446A TYR* 5.1 9.6 - + - -
501A GLN* 3.2 25.8 - - + -
502A VAL 3.2 5.2 + - - +
504A PRO* 1.3 81.4 - - + +
506A LEU* 1.3 62.6 - - - +
508A LEU* 4.5 2.9 - - - +
509A GLY* 3.6 12.8 + - - -
1136A GLY* 3.8 32.0 - - - +
1137A VAL* 4.3 6.7 - - - +
1139A MET* 3.9 24.5 - - + -
1140A LEU* 3.7 32.3 - - + -
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Residues in contact with LEU 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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502A VAL* 2.8 32.9 + - + +
503A LEU* 4.0 12.6 - - + +
505A PHE* 1.3 79.1 - - - +
507A ALA* 1.3 65.9 + - + +
508A LEU 3.2 0.3 + - - -
509A GLY* 3.8 0.5 - - - -
510A VAL* 3.0 48.2 + - + +
559A PHE* 4.4 22.9 - - + -
573A PHE* 5.1 6.3 - - + -
577A ALA* 5.1 2.5 - - + -
1085A ILE* 6.0 3.6 - - + -
1088A ALA* 6.3 2.7 - - + -
1092A ILE* 6.0 1.6 - - + -
1133A THR* 5.7 1.8 - - + +
1137A VAL* 5.0 8.0 - - + +
1140A LEU* 5.7 0.2 - - - +
1156A LEU* 4.0 37.5 - - + -
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Residues in contact with ALA 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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481A VAL* 4.5 7.6 - - + -
503A LEU* 2.9 35.0 + - + +
504A PRO 4.4 0.9 - - - +
506A LEU* 1.3 80.5 - - + +
508A LEU* 1.3 57.0 + - - +
510A VAL* 4.1 4.6 - - - +
511A GLY* 2.9 24.0 + - - -
577A ALA* 5.9 1.8 - - + +
580A VAL* 3.8 28.4 - - + +
581A VAL* 5.9 5.6 - - + -
584A ASN* 4.1 7.8 + - - -
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Residues in contact with LEU 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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446A TYR* 3.6 29.2 - - + +
449A MET* 3.7 37.5 - - + -
474A VAL* 4.9 7.6 - - + -
477A VAL* 3.8 27.1 - - + -
478A ALA* 4.6 13.9 - - + +
481A VAL* 4.7 6.2 - - + +
504A PRO 2.9 20.2 + - - +
505A PHE* 4.5 2.7 - - - +
507A ALA* 1.3 76.3 - - - +
509A GLY* 1.3 56.9 + - - +
511A GLY* 2.6 22.1 + - - -
512A VAL* 3.0 30.5 + - + +
1136A GLY* 5.9 2.9 - - - -
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Residues in contact with GLY 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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449A MET* 5.4 0.4 - - - -
505A PHE 3.6 8.8 + - - -
506A LEU 3.3 5.2 + - - -
508A LEU* 1.3 83.7 - - - +
510A VAL* 1.3 57.2 + - - +
512A VAL* 4.3 2.7 + - - -
513A ASP* 3.6 3.8 - - - +
1132A SER* 3.5 22.4 + - - -
1133A THR* 2.7 40.8 + - - -
1136A GLY* 5.2 2.9 - - - -
1137A VAL* 6.2 0.2 - - - -
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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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506A LEU* 3.0 40.0 + - + +
507A ALA* 4.1 6.1 - - - +
509A GLY* 1.3 77.0 - - - +
511A GLY* 1.3 64.0 + - - +
512A VAL 3.5 0.5 + - - -
513A ASP* 3.8 16.7 + - - +
514A ASP* 5.1 4.3 + - - +
555A ASN* 4.3 16.2 - - - +
559A PHE* 5.9 2.5 - - + -
581A VAL* 4.9 14.4 - - + -
1092A ILE* 3.7 34.8 - - + -
1133A THR* 4.3 12.6 - - + +
1156A LEU* 6.1 0.2 - - + -
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Residues in contact with GLY 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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477A VAL* 4.4 7.3 - - - +
507A ALA 2.9 14.0 + - - -
508A LEU 2.6 15.6 + - - -
510A VAL* 1.3 74.8 - - - +
512A VAL* 1.3 61.1 + - - -
513A ASP 3.3 0.9 + - - -
514A ASP* 4.0 14.5 + - - +
515A VAL* 4.4 8.7 - - - +
584A ASN* 3.7 19.4 + - - -
588A VAL* 4.7 4.5 - - - +
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Residues in contact with VAL 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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449A MET* 4.1 15.0 - - + -
474A VAL* 4.8 15.3 - - + -
477A VAL* 4.2 9.4 - - + -
508A LEU* 3.0 44.8 + - + +
509A GLY* 4.3 0.8 + - - +
510A VAL 3.4 0.8 - - - -
511A GLY* 1.3 76.2 - - - +
513A ASP* 1.3 64.3 + - - +
514A ASP 3.3 0.2 - - - -
515A VAL* 3.0 23.2 + - + +
516A PHE* 3.0 45.0 + - + +
1132A SER* 4.7 7.0 - - - -
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Residues in contact with ASP 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 GLY 3.6 13.0 - - - +
510A VAL* 3.8 11.6 - - - +
511A GLY 3.3 1.6 - - - -
512A VAL* 1.3 77.0 - - - +
514A ASP* 1.3 62.2 + - - +
516A PHE* 3.4 8.3 + - - +
517A LEU* 2.9 27.8 + - - +
1095A GLU* 4.3 22.4 - - + +
1125A PRO 5.3 4.1 - - - +
1128A ASP 3.4 1.4 - - - +
1129A GLY* 3.3 23.0 - - - +
1132A SER* 2.3 31.0 + - - -
1133A THR* 3.6 8.3 + - - -
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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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510A VAL 5.1 4.3 - - - +
511A GLY* 4.0 10.2 + - - +
512A VAL 3.3 0.2 - - - -
513A ASP* 1.3 80.0 - - - +
515A VAL* 1.3 61.4 + - - +
517A LEU* 3.3 7.2 + - - +
518A LEU* 3.0 33.1 + - - +
548A VAL* 4.1 28.4 - - + +
551A THR* 3.4 26.6 + - - +
552A SER* 5.1 6.1 - - - -
585A PHE* 5.5 5.4 - - - -
588A VAL* 4.3 15.2 - - + +
1095A GLU* 5.4 2.8 - - - +
1099A HIS* 5.7 1.7 + - - -
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Residues in contact with VAL 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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457A MET* 6.2 0.4 - - + -
470A GLY* 5.7 3.1 - - - +
473A GLY* 4.5 13.0 - - - -
474A VAL* 5.4 0.9 - - + +
476A LEU* 5.1 0.2 - - + -
477A VAL* 3.7 28.9 - - + -
511A GLY 4.4 3.1 - - - +
512A VAL* 3.0 14.9 + - + +
514A ASP* 1.3 75.7 - - - +
516A PHE* 1.3 66.7 + - + +
518A LEU* 3.4 1.0 + - - -
519A ALA* 3.0 28.7 + - + +
588A VAL* 3.8 24.5 - - + -
592A PHE* 3.6 39.1 - - + -
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Residues in contact with PHE 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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449A MET* 5.1 1.1 - - + -
452A TYR* 4.3 15.0 - + - -
453A ALA* 3.9 20.0 - - + -
456A THR* 3.6 37.7 - - + -
457A MET* 3.6 19.9 - - + +
470A GLY 5.8 2.0 - - - -
474A VAL* 5.7 0.7 - - + -
512A VAL* 3.0 37.3 + - + -
513A ASP* 3.8 8.5 - - - +
514A ASP 3.3 0.2 - - - -
515A VAL* 1.3 83.1 - - + +
517A LEU* 1.3 57.0 + - - +
519A ALA* 3.5 4.4 + - - +
520A HIS* 3.0 27.0 + - - +
1125A PRO* 4.6 4.8 - - - +
1128A ASP* 3.5 41.8 - - + +
1132A SER* 4.5 9.2 - - - -
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Residues in contact with LEU 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 ASP 2.9 17.5 + - - +
514A ASP* 3.6 8.1 - - - +
515A VAL 3.2 0.4 - - - -
516A PHE* 1.3 78.1 - - - +
518A LEU* 1.3 57.6 + - - +
520A HIS* 3.1 10.3 + - - +
521A ALA* 3.0 23.4 + - - +
544A THR* 3.7 33.2 - - + +
547A SER* 4.7 3.4 - - - +
548A VAL* 3.7 20.4 - - + -
1099A HIS* 4.1 30.3 - - + +
1122A MET* 4.6 11.4 - - - -
1125A PRO* 3.8 32.0 - - + +
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Residues in contact with LEU 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 ASP 3.0 19.1 + - - +
515A VAL 4.1 3.1 - - - +
517A LEU* 1.3 73.0 - - - +
519A ALA* 1.3 61.1 + - - +
521A ALA* 3.3 3.9 + - - +
522A PHE* 2.9 28.6 + - - +
540A CYS* 3.9 12.5 - - - +
541A LEU* 4.5 24.2 - - + -
544A THR* 3.3 25.8 - - - +
545A GLY* 5.7 0.7 - - - -
548A VAL* 4.1 22.7 - - + -
588A VAL* 4.3 19.5 - - + +
589A LEU* 4.9 6.3 - - + -
592A PHE* 4.1 26.0 - - + -
593A PRO* 5.1 3.6 - - + -
596A LEU* 4.8 7.4 - - + +
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Residues in contact with ALA 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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457A MET* 3.8 30.5 - - + -
466A GLN* 3.7 14.7 - - - +
515A VAL* 3.0 18.7 + - + +
516A PHE 3.8 4.7 - - - +
517A LEU 3.3 0.2 - - - -
518A LEU* 1.3 77.0 - - - +
520A HIS* 1.3 56.5 + - - +
522A PHE* 3.3 6.8 + - - +
523A SER* 2.9 29.1 + - - -
592A PHE* 4.6 10.4 - - + -
596A LEU* 5.6 2.7 - - + -
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Residues in contact with HIS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PHE 3.0 14.0 + - - +
517A LEU* 3.3 16.1 + - - +
519A ALA* 1.3 74.5 - - - +
521A ALA* 1.3 63.7 + - - +
523A SER* 3.0 7.1 + - - +
524A GLU* 3.0 63.4 + - + +
543A ARG* 5.6 2.5 - - - -
1120A GLU 5.8 0.2 + - - -
1121A HIS* 3.5 27.6 + + - -
1122A MET* 5.1 4.2 - - + -
1124A ALA* 5.1 6.0 - - + +
1125A PRO* 3.7 34.8 - - + +
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Residues in contact with ALA 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 LEU 3.0 9.0 + - - +
518A LEU* 3.3 8.0 + - - +
520A HIS* 1.3 80.5 + - - +
522A PHE* 1.3 60.2 + - - +
523A SER 3.6 0.2 + - - -
524A GLU* 3.9 4.0 + - - +
525A THR* 3.7 13.0 + - - -
536A ARG* 3.7 8.8 + - - -
540A CYS* 3.8 18.9 - - - +
543A ARG* 4.3 16.2 - - + +
544A THR* 3.7 37.7 - - + +
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Residues in contact with PHE 522 (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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464A LYS* 4.9 2.3 - - + +
466A GLN* 3.3 20.5 + - + +
518A LEU 2.9 17.1 + - - +
519A ALA* 3.7 5.6 - - - +
520A HIS 3.2 0.2 - - - -
521A ALA* 1.3 77.4 - - - +
523A SER* 1.3 59.2 + - - +
526A GLY* 3.6 8.6 - - - -
536A ARG* 2.7 40.8 + - + +
537A THR* 5.2 6.1 - - - -
540A CYS* 3.6 21.5 - - + -
596A LEU* 4.0 34.8 - - + -
599A ASP* 3.9 19.1 - - - -
600A LEU* 3.6 43.7 - - + -
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Residues in contact with SER 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ARG* 4.9 12.3 + - - -
464A LYS* 3.9 22.6 + - - +
466A GLN* 3.9 16.2 - - - +
519A ALA 2.9 16.2 + - - -
520A HIS* 3.0 9.6 + - - -
522A PHE* 1.3 79.8 - - - +
524A GLU* 1.3 64.2 + - - +
525A THR 3.5 0.2 - - - -
526A GLY* 3.6 10.1 + - - -
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Residues in contact with GLU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS* 5.6 0.2 + - - -
520A HIS* 3.0 53.7 + - + +
521A ALA* 3.9 1.5 + - - +
523A SER* 1.3 81.3 - - - +
525A THR* 1.3 60.0 + - - +
526A GLY 3.1 4.1 + - - -
543A ARG* 4.2 23.5 + - - +
1120A GLU* 5.7 1.4 - - - +
1121A HIS* 5.4 7.5 - - + -
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Residues in contact with THR 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ALA 3.7 6.3 + - - -
524A GLU* 1.3 73.3 - - - +
526A GLY* 1.3 55.5 + - - +
527A GLN 3.4 3.0 + - - -
528A ASN* 3.4 37.9 + - + +
536A ARG* 2.7 39.4 + - - +
539A GLU* 3.5 26.1 + - - +
543A ARG* 2.7 28.9 + - - +
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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
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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) + - + + + + + -
------------------------------------------------------------
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