Contacts of the helix formed by residues 520 - 546 (chain A) in PDB entry 6T8O
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 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A PRO* 6.1 0.2 - - - -
518A VAL* 3.7 3.1 - - - +
519A THR* 1.3 83.1 - - + +
521A MET* 1.3 85.3 + - - +
522A LYS* 3.5 27.7 + - - +
523A GLU* 3.3 21.5 + - + +
524A ALA* 2.8 28.7 + - - +
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Residues in contact with MET 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A PRO* 3.8 30.3 - - + +
519A THR 4.4 4.0 - - - +
520A ASP* 1.3 90.0 + - - +
522A LYS* 1.3 60.6 + - + +
524A ALA* 3.7 7.7 - - - +
525A ALA* 2.9 29.8 + - - +
599A ASP* 3.9 23.3 - - + +
600A MET* 3.9 37.0 - - + +
603A ILE* 4.0 25.8 - - + -
604A VAL* 4.9 15.5 - - + +
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Residues in contact with LYS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ASP* 3.2 22.6 - - - +
521A MET* 1.3 78.8 - - + +
523A GLU* 1.3 60.2 + - + +
525A ALA* 3.3 6.8 + - - +
526A ASN* 3.0 26.9 + - - +
529A ARG* 5.1 0.7 + - - -
603A ILE* 6.2 3.7 - - - +
604A VAL* 4.2 24.2 - - + +
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Residues in contact with GLU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A VAL* 3.8 6.9 - - + +
519A THR* 4.4 9.2 + - - -
520A ASP* 3.3 28.1 + - + +
522A LYS* 1.3 76.8 - - + +
524A ALA* 1.3 59.8 - - - +
526A ASN* 3.4 8.0 + - - +
527A ALA* 2.9 23.6 + - - +
721A LEU* 3.4 45.0 - - + +
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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
----------------------------------------------------------
497A ILE* 3.7 31.9 - - + +
518A VAL* 3.5 9.3 - - + +
520A ASP 2.8 17.7 + - - +
521A MET* 3.7 7.0 - - - +
522A LYS 3.2 0.2 - - - -
523A GLU* 1.3 74.7 - - - +
525A ALA* 1.3 59.1 + - - +
527A ALA* 3.3 5.1 + - - +
528A LEU* 2.9 34.5 + - - +
600A MET* 3.7 15.7 - - + -
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Residues in contact with ALA 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A MET 2.9 18.5 + - - +
522A LYS* 3.3 5.6 + - - +
524A ALA* 1.3 72.5 - - - +
526A ASN* 1.3 59.8 + - - +
528A LEU* 3.3 8.6 + - - +
529A ARG* 2.9 42.5 + - - +
600A MET* 5.4 1.0 - - - -
604A VAL* 5.5 0.2 - - + -
607A LYS* 3.5 28.5 - - - +
608A VAL* 4.1 17.0 - - + -
611A LEU* 4.2 2.2 - - + +
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Residues in contact with ASN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LYS 3.0 14.9 + - - +
523A GLU* 3.5 12.0 - - - +
524A ALA 3.3 0.2 - - - -
525A ALA* 1.3 76.1 - - - +
527A ALA* 1.3 56.5 + - - +
529A ARG* 3.3 17.8 + - - +
530A TRP* 3.0 26.0 + - - +
720A ILE 3.6 9.8 + - - +
721A LEU* 3.1 33.3 + - - +
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Residues in contact with ALA 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 4.9 11.2 - - + -
497A ILE* 5.1 2.9 - - + -
518A VAL* 4.8 10.3 - - + -
523A GLU 2.9 17.5 + - - +
524A ALA* 3.3 8.0 + - - +
526A ASN* 1.3 75.0 - - - +
528A LEU* 1.3 59.3 + - - +
530A TRP* 3.3 5.0 + - - +
531A SER* 2.9 30.4 + - - -
720A ILE* 3.8 30.6 + - + +
721A LEU* 4.5 6.3 - - + -
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Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 6.2 0.2 - - + -
497A ILE* 3.9 23.3 - - + -
524A ALA 2.9 19.9 + - - +
525A ALA* 3.8 4.5 - - - +
526A ASN 3.3 0.2 - - - -
527A ALA* 1.3 74.3 - - - +
529A ARG* 1.3 60.7 + - - +
531A SER* 3.2 12.3 + - - +
532A VAL* 2.9 32.3 + - + +
592A VAL* 4.6 11.0 - - + -
594A VAL* 5.7 2.5 - - + -
600A MET* 4.3 23.1 - - - -
608A VAL* 4.4 9.0 - - + -
611A LEU* 3.6 19.1 - - + -
612A ILE* 3.8 31.6 - - + -
615A ILE* 5.5 5.3 - - + +
626A LEU* 5.5 6.1 - - + -
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Residues in contact with ARG 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LYS 5.1 1.0 + - - -
525A ALA* 2.9 41.1 + - - +
526A ASN* 3.3 18.5 + - - +
528A LEU* 1.3 71.8 - - - +
530A TRP* 1.3 61.1 + - - +
532A VAL* 3.3 5.9 + - - +
533A ALA* 3.0 28.9 + - - +
607A LYS* 3.6 30.8 - - - +
611A LEU* 3.7 23.6 - - + +
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Residues in contact with TRP 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 4.3 6.3 - - + -
514A LEU* 3.6 34.1 - - + -
526A ASN* 3.0 13.1 + - - +
527A ALA 3.4 7.4 - - - +
529A ARG* 1.3 75.0 - - - +
531A SER* 1.3 67.2 + - - +
533A ALA* 3.3 8.7 + - + +
534A GLU* 2.9 59.7 + - + +
590A ILE* 5.9 4.0 - - + -
624A ILE* 6.5 0.9 - - + -
717A ILE* 4.3 33.1 - - + +
719A ASP* 5.0 4.0 - - - +
720A ILE* 3.6 41.5 - - + +
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Residues in contact with SER 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE* 3.4 27.6 - - - +
527A ALA 2.9 15.4 + - - -
528A LEU* 3.2 20.0 + - - +
530A TRP* 1.3 79.7 - - - +
532A VAL* 1.3 61.7 + - - +
534A GLU* 3.4 3.6 + - - +
535A MET* 2.9 29.5 + - - +
592A VAL* 4.7 2.3 - - - +
615A ILE* 4.4 6.5 - - - +
624A ILE* 4.4 21.1 - - - +
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Residues in contact with VAL 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A LEU* 2.9 18.7 + - + +
529A ARG* 3.3 8.7 + - - +
531A SER* 1.3 75.5 - - - +
533A ALA* 1.3 57.3 + - - +
535A MET* 3.3 10.2 + - + +
536A GLU* 2.9 45.0 + - + +
611A LEU* 4.1 26.7 - - + +
614A ARG* 5.2 14.6 - - + +
615A ILE* 3.7 28.7 - - + +
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Residues in contact with ALA 533 (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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529A ARG 3.0 17.0 + - - +
530A TRP* 3.7 9.4 - - + +
531A SER 3.3 0.2 - - - -
532A VAL* 1.3 77.1 - - - +
534A GLU* 1.3 56.9 + - - +
536A GLU* 3.3 7.2 + - - +
537A ARG* 2.9 31.8 + - - +
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Residues in contact with GLU 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A TRP* 2.9 53.8 + - + +
531A SER* 3.8 4.7 - - - +
533A ALA* 1.3 75.4 - - - +
535A MET* 1.3 60.4 + - - +
537A ARG* 2.7 44.4 + - - +
538A ARG* 2.9 63.4 + - - +
587A LEU* 4.9 2.3 - - - +
590A ILE* 6.0 1.8 - - + -
624A ILE* 4.5 8.3 - - + -
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Residues in contact with MET 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A SER 2.9 18.3 + - - +
532A VAL* 3.5 11.2 - - + +
534A GLU* 1.3 77.2 - - - +
536A GLU* 1.3 77.3 + - - +
538A ARG* 3.3 4.5 + - - +
539A TYR* 2.9 39.1 + - + -
614A ARG* 3.7 21.1 - - + +
615A ILE* 3.7 22.7 - - + -
618A LYS* 4.7 8.5 - - + -
619A ALA* 3.6 32.5 - - + -
622A ALA* 3.7 18.8 - - + -
624A ILE* 4.0 14.7 - - + +
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Residues in contact with GLU 536 (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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532A VAL* 2.9 30.6 + - + +
533A ALA* 3.7 7.4 - - - +
534A GLU 3.3 0.2 - - - -
535A MET* 1.3 95.7 - - + +
537A ARG* 1.3 57.3 + - - +
539A TYR* 3.3 5.8 + - - +
540A ARG* 2.9 62.6 + - - +
618A LYS* 4.1 20.7 + - - +
501B MET* 4.6 8.7 - - - +
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Residues in contact with ARG 537 (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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533A ALA 2.9 17.0 + - - +
534A GLU* 2.7 59.2 + - - +
536A GLU* 1.3 77.2 - - - +
538A ARG* 1.3 59.1 + - - +
540A ARG* 3.4 11.9 + - - +
541A LEU* 2.9 49.2 + - - +
584A LEU* 6.1 0.8 - - - +
587A LEU* 4.8 14.1 - - - +
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Residues in contact with ARG 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A GLU* 2.9 43.9 + - - +
535A MET* 3.6 5.6 - - - +
537A ARG* 1.3 78.1 - - - +
539A TYR* 1.3 59.4 + - - +
541A LEU* 3.4 4.8 + - - +
542A MET* 2.9 39.7 + - + +
550A LEU* 5.2 0.2 - - - +
587A LEU* 3.6 38.6 + - + +
588A PRO* 2.9 44.8 + - - +
590A ILE* 4.0 7.3 - - - +
622A ALA* 3.6 19.9 + - - +
623A GLY* 2.8 38.8 + - - -
624A ILE* 3.6 13.7 - - - +
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Residues in contact with TYR 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A MET* 2.9 38.7 + - + +
536A GLU* 3.7 7.9 - - - +
538A ARG* 1.3 75.8 - - - +
540A ARG* 1.3 58.2 + - - +
542A MET* 3.4 16.8 + - + +
543A ALA* 2.9 29.5 + - - +
618A LYS* 2.3 71.8 + - + +
621A ALA* 4.1 8.4 + - + +
622A ALA* 3.6 29.6 + - + -
500B LYS* 5.8 1.4 - - + +
501B MET* 4.5 23.7 - - + +
502B LEU* 4.5 28.5 - - + -
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Residues in contact with ARG 540 (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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536A GLU* 2.9 58.2 + - - +
537A ARG* 3.8 9.0 - - - +
538A ARG 3.3 0.2 - - - -
539A TYR* 1.3 75.5 - - - +
541A LEU* 1.3 58.2 + - - +
543A ALA* 3.3 7.0 + - - +
544A ALA* 2.9 27.0 + - - +
501B MET* 4.9 20.0 - - + +
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Residues in contact with LEU 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ARG* 2.9 36.7 + - - +
538A ARG* 4.0 5.2 - - - +
540A ARG* 1.3 77.2 - - - +
542A MET* 1.3 58.9 - - + +
544A ALA* 3.3 7.0 + - + +
545A MET* 2.9 38.8 + - + +
553A PHE* 3.6 35.0 - - + -
569A ASP* 5.0 1.3 - - - +
570A PRO* 4.3 18.8 - - + +
584A LEU* 3.8 30.5 - - + -
587A LEU* 5.3 9.2 - - + -
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Residues in contact with MET 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ARG* 2.9 31.3 + - + +
539A TYR* 3.8 23.8 - - + +
541A LEU* 1.3 76.8 - - + +
543A ALA* 1.3 59.1 + - - +
545A MET* 4.3 1.6 - - - +
546A GLY* 2.8 23.9 + - - -
547A VAL* 3.0 37.5 + - + +
549A ASN* 3.4 26.7 - - - +
550A LEU* 4.4 4.5 - - - -
553A PHE* 4.5 16.6 - - + -
587A LEU* 5.9 3.6 - - + -
621A ALA* 3.3 23.6 - - + +
622A ALA* 4.2 13.5 - - - +
502B LEU* 5.8 3.6 - - + -
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A TYR 2.9 19.0 + - - +
540A ARG* 3.7 6.7 - - - +
542A MET* 1.3 75.6 - - - +
544A ALA* 1.3 62.5 + - - +
546A GLY* 3.7 7.5 + - - -
501B MET* 3.9 31.2 - - + +
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ARG 2.9 16.1 + - - +
541A LEU* 3.6 11.2 - - + +
542A MET 3.2 0.2 - - - -
543A ALA* 1.3 80.9 - - - +
545A MET* 1.3 66.0 + - + +
546A GLY 3.7 0.3 + - - -
570A PRO* 5.6 10.5 - - + -
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Residues in contact with MET 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 2.9 37.2 + - + +
542A MET* 3.3 0.9 + - - +
544A ALA* 1.3 80.0 - - + +
546A GLY* 1.3 64.3 + - - +
547A VAL* 3.6 21.0 - - + +
553A PHE* 4.2 8.5 - - + -
556A LYS* 3.9 31.8 + - + +
567A LEU* 5.2 11.2 - - + -
570A PRO* 3.7 27.6 - - + -
584A LEU* 4.8 7.6 - - + -
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Residues in contact with GLY 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A MET 2.8 9.4 + - - -
543A ALA* 3.7 6.8 + - - -
544A ALA 3.4 3.2 + - - -
545A MET* 1.3 78.8 - - - +
547A VAL* 1.3 57.7 + - - +
548A ARG* 4.4 6.1 + - - +
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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