Contacts of the helix formed by residues 529 - 558 (chain A) in PDB entry 5E3H
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 529 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASP* 2.8 21.7 + - - +
528A LYS* 1.3 77.2 - - - +
530A GLU* 1.3 61.3 + - - +
531A GLU 3.0 3.9 + - - -
532A SER* 2.9 27.3 + - - -
533A ARG* 3.9 1.7 + - - +
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Residues in contact with GLU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASP* 3.4 14.2 + - + +
529A ASP* 1.3 78.7 - - - +
531A GLU* 1.3 58.1 + - - +
532A SER 3.3 0.2 - - - -
533A ARG* 3.2 13.7 + - + +
534A ILE* 2.9 46.8 + - + +
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Residues in contact with GLU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PHE* 3.3 29.6 - - + +
527A ASP* 5.1 2.9 + - + +
528A LYS* 3.7 43.8 + - - +
529A ASP 3.8 0.4 - - - +
530A GLU* 1.3 78.5 - - - +
532A SER* 1.3 58.2 + - - +
534A ILE* 3.2 11.0 + - + +
535A CYS* 2.8 36.5 + - - -
809A LEU* 5.4 6.2 - - - +
814A LYS* 4.7 12.9 - - + +
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Residues in contact with SER 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A LYS 4.2 6.6 + - - -
529A ASP* 2.9 19.7 + - - -
531A GLU* 1.3 78.8 - - - +
533A ARG* 1.3 59.1 + - - +
535A CYS* 4.1 2.4 - - - +
536A LYS* 2.9 33.8 + - - +
813A CYS* 3.2 31.8 - - - +
814A LYS* 4.8 2.9 - - - -
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Residues in contact with ARG 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ASP 4.8 0.9 - - - +
530A GLU* 3.2 20.3 + - + +
532A SER* 1.3 83.0 + - - +
534A ILE* 1.3 57.9 + - + +
536A LYS* 4.2 3.3 - - - +
537A ALA* 3.1 29.3 + - - +
582A ILE* 5.8 0.3 - - - +
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Residues in contact with ILE 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE* 3.7 27.6 - - + -
490A CYS* 5.1 2.9 - - - -
523A PHE* 5.4 7.0 - - + -
530A GLU* 2.9 43.1 + - + +
531A GLU* 3.2 12.5 + - + +
533A ARG* 1.3 75.4 - - + +
535A CYS* 1.3 64.2 + - - +
537A ALA* 3.2 4.7 + - - +
538A LEU* 2.9 54.1 + - + +
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Residues in contact with CYS 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A CYS* 3.7 23.4 - - - +
521A MET* 5.1 6.7 - - + -
523A PHE* 4.0 22.7 - - - -
531A GLU* 2.8 30.0 + - - +
532A SER* 4.1 4.0 - - - +
534A ILE* 1.3 75.3 - - - +
536A LYS* 1.3 54.9 + - - +
538A LEU* 3.3 6.6 + - - +
539A PHE* 2.8 36.4 + - - +
811A ARG 5.3 3.1 - - - +
812A LYS 3.8 14.8 - - - +
814A LYS* 4.9 11.0 - - + -
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Residues in contact with LYS 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A SER 2.9 20.4 + - - +
533A ARG* 4.2 4.9 - - - +
535A CYS* 1.3 76.4 - - - +
537A ALA* 1.3 57.0 + - - +
539A PHE* 3.7 4.8 - - - +
540A LEU* 2.9 31.2 + - - +
582A ILE* 4.7 5.0 - - + +
812A LYS* 3.7 14.0 + - + +
813A CYS* 4.9 7.9 - - + -
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Residues in contact with ALA 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE* 4.2 18.8 - - + -
533A ARG 3.1 20.9 + - - +
534A ILE* 3.5 4.5 - - - +
536A LYS* 1.3 77.8 - - - +
538A LEU* 1.3 52.5 + - - +
540A LEU* 3.4 1.9 + - - +
541A TYR* 2.7 37.2 + - - +
582A ILE* 4.3 29.4 - - + +
586A LEU* 5.7 0.3 - - - +
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Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ALA* 3.9 38.1 - - + +
489A ILE* 4.1 12.6 - - + -
490A CYS* 3.5 28.5 - - - -
520A CYS* 3.7 37.9 - - + +
523A PHE* 5.6 1.6 - - + -
534A ILE* 2.9 37.6 + - + +
535A CYS* 3.8 4.9 - - - +
537A ALA* 1.3 72.8 - - - +
539A PHE* 1.3 55.0 + - - +
541A TYR* 3.9 3.1 - - + -
542A THR* 2.7 44.5 + - + +
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Residues in contact with PHE 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A GLN* 3.8 15.9 + - + -
520A CYS* 5.6 1.0 - - - +
521A MET* 3.8 31.4 - - + -
535A CYS 2.8 22.6 + - - +
536A LYS* 3.7 7.9 - - - +
538A LEU* 1.3 74.0 - - - +
540A LEU* 1.3 57.5 + - + +
542A THR* 3.2 6.0 + - - -
543A SER* 2.6 52.8 + - - -
811A ARG 4.4 6.5 - - - +
812A LYS* 4.5 19.5 - - + +
871A HIS* 3.9 31.0 - + - -
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LYS 2.9 19.2 + - - +
537A ALA 3.8 1.6 - - - +
539A PHE* 1.3 78.9 - - + +
541A TYR* 1.3 64.9 + - - +
543A SER* 4.1 5.6 - - - -
544A HIS* 2.7 36.3 + - + +
582A ILE* 3.8 24.2 - - + -
583A GLU* 4.7 14.1 - - + +
586A LEU* 4.0 5.9 - - + +
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Residues in contact with TYR 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A THR* 3.2 29.2 - - + +
485A LEU* 5.6 4.3 - - + -
486A ALA* 4.7 18.8 - - + +
489A ILE* 6.4 0.4 - - + -
537A ALA 2.7 22.9 + - - +
538A LEU* 3.5 9.2 - - + +
540A LEU* 1.3 74.8 - - - +
542A THR* 1.3 57.7 + - + +
544A HIS* 3.6 1.2 + - - +
545A LEU* 3.0 21.7 + - - +
586A LEU* 4.3 11.2 - - + +
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Residues in contact with THR 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ALA* 5.5 7.9 - - + -
513A ILE* 3.4 12.0 - - + +
516A VAL* 3.6 31.4 - - + -
517A GLN* 3.0 35.9 + - + +
520A CYS* 5.1 3.6 - - - -
538A LEU* 2.7 31.8 + - + +
539A PHE* 3.2 2.4 + - - -
541A TYR* 1.3 72.3 - - + +
543A SER* 1.3 55.5 + - - +
545A LEU* 3.9 13.5 - - + -
546A ARG* 2.7 36.2 + - - +
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Residues in contact with SER 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A GLN* 3.5 13.8 + - - +
539A PHE* 2.6 42.9 + - - -
540A LEU* 3.7 8.7 - - - -
542A THR* 1.3 76.8 + - - +
544A HIS* 1.3 63.4 + - - +
546A ARG* 3.1 6.5 + - - +
547A LYS* 2.9 35.0 + - - +
570A PHE* 5.0 3.8 - - - -
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Residues in contact with HIS 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A THR* 5.4 2.2 - - + -
540A LEU* 2.7 29.6 + - + +
541A TYR 3.9 3.6 - - - +
543A SER* 1.3 81.7 - - - +
545A LEU* 1.3 58.4 + - - +
547A LYS* 3.2 1.4 + - - +
548A TYR* 2.8 48.3 + + + -
570A PHE* 3.6 38.3 - + + -
571A PHE* 3.6 21.4 - + - -
574A VAL* 4.0 19.6 - - + +
583A GLU* 4.6 20.3 + - + +
586A LEU* 4.1 29.5 - - + +
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Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A MET* 3.6 43.9 - - + +
482A THR* 4.0 15.8 - - + +
483A GLU* 4.3 19.1 - - + +
486A ALA* 6.1 2.5 - - + -
509A TYR* 3.5 21.7 - - - +
513A ILE* 3.6 25.1 - - + -
541A TYR 3.0 18.8 + - - +
542A THR* 3.5 15.3 - - + +
543A SER 3.2 0.2 - - - -
544A HIS* 1.3 77.5 - - - +
546A ARG* 1.3 60.3 + - - +
548A TYR* 3.6 6.4 + - + +
549A ASN* 3.3 19.2 + - - +
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Residues in contact with ARG 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLU* 5.1 3.6 - - + +
513A ILE* 3.7 20.4 - - + +
514A VAL* 6.3 2.7 - - + -
517A GLN* 5.4 2.7 - - - +
542A THR 2.7 20.9 + - - +
543A SER* 3.1 7.6 + - - +
545A LEU* 1.3 74.9 - - - +
547A LYS* 1.3 62.5 + - + +
549A ASN* 3.4 9.3 + - - +
550A ASP* 3.3 26.4 + - - +
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Residues in contact with LYS 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A SER* 2.9 22.0 + - - +
544A HIS 3.2 3.8 + - - +
546A ARG* 1.3 76.0 - - + +
548A TYR* 1.3 64.3 + - - +
550A ASP* 3.6 15.6 + - - +
551A ALA* 3.4 13.5 + - - +
566A TYR* 3.2 39.3 + - + -
567A LEU* 3.7 13.2 - - + +
570A PHE* 3.5 54.2 - - + +
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Residues in contact with TYR 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ILE* 4.3 14.6 - - + +
478A LEU* 3.5 36.8 - - + +
479A MET* 3.7 28.9 - - + -
482A THR* 4.6 12.1 - - - -
544A HIS* 2.8 36.5 + + + +
545A LEU* 3.7 7.6 - - - +
546A ARG 3.2 0.2 - - - -
547A LYS* 1.3 77.5 - - - +
549A ASN* 1.3 63.1 + - - +
550A ASP 3.1 0.2 - - - -
551A ALA* 3.2 13.9 + - + +
552A LEU* 3.3 16.5 + - - +
567A LEU* 3.9 35.2 - - + -
570A PHE* 6.2 1.1 - + - -
571A PHE* 3.3 25.5 - + - -
586A LEU* 4.5 6.0 + - + +
589A ARG* 5.8 0.3 - - - +
590A PHE* 3.6 9.6 - + - +
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Residues in contact with ASN 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A MET* 4.3 7.1 - - + -
505A GLY* 3.5 15.3 - - - -
506A THR 3.5 13.0 + - - +
509A TYR* 3.4 31.8 - - + -
510A GLU* 3.4 36.7 + - - +
513A ILE* 5.7 0.4 - - + -
545A LEU 3.3 10.8 + - - +
546A ARG* 3.4 11.6 + - - +
547A LYS 3.3 0.2 - - - -
548A TYR* 1.3 80.6 - - - +
550A ASP* 1.3 61.7 + - - +
552A LEU* 3.5 8.4 + - - +
553A ILE* 3.4 29.9 + - - +
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Residues in contact with ASP 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLU* 3.4 21.0 - - - +
546A ARG 3.3 16.2 - - - +
547A LYS* 3.6 19.9 - - - +
548A TYR 3.1 0.2 - - - -
549A ASN* 1.3 75.4 + - - +
551A ALA* 1.3 62.6 + - - +
552A LEU 3.0 5.2 + - - -
553A ILE* 3.2 10.4 + - - +
554A ILE* 3.0 30.9 + - + +
566A TYR* 3.4 29.3 + - + +
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Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A PHE* 4.4 5.7 - - + -
475A ILE* 5.7 2.9 - - + -
547A LYS 3.4 2.2 + - - +
548A TYR* 3.2 11.1 + - + +
550A ASP* 1.3 78.8 - - - +
552A LEU* 1.3 63.4 + - + +
554A ILE* 4.0 7.0 - - - -
555A SER* 3.3 9.2 + - - -
563A ALA* 3.1 36.6 - - + +
566A TYR* 4.5 2.4 - - + -
567A LEU* 3.8 39.3 - - + -
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A PHE* 5.4 3.6 - - + -
472A LYS* 4.1 30.3 - - + +
475A ILE* 3.8 22.4 - - + -
476A ALA* 6.0 2.0 - - + +
479A MET* 3.9 22.7 - - - -
504A PHE 4.5 1.1 - - - -
505A GLY* 3.4 33.9 - - - +
548A TYR 3.3 10.9 + - - +
549A ASN* 3.5 8.5 - - - +
550A ASP 3.0 0.2 - - - -
551A ALA* 1.3 76.4 - - - +
553A ILE* 1.3 67.8 + - - +
554A ILE 3.1 1.3 - - - -
555A SER* 2.5 27.3 + - - +
556A GLU* 3.2 10.1 + - - +
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Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A GLY 3.3 21.1 + - - +
506A THR* 4.8 8.5 - - - +
507A GLN* 5.1 2.9 - - - +
510A GLU* 4.5 9.0 - - - +
549A ASN* 3.4 26.9 + - - +
550A ASP* 3.2 10.9 + - - +
552A LEU* 1.3 77.8 - - - +
554A ILE* 1.3 63.8 + - + +
556A GLU* 3.4 17.5 + - - +
557A HIS* 3.5 34.0 + - + +
635A LYS* 6.3 2.5 - - - -
636A THR* 6.1 5.8 - - + -
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Residues in contact with ILE 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ASP* 3.0 19.7 + - + +
551A ALA* 4.0 6.3 - - - +
553A ILE* 1.3 75.2 - - + +
555A SER* 1.3 61.8 + - - +
556A GLU 3.0 2.2 - - - -
557A HIS* 3.1 5.3 + - - +
558A ALA* 2.8 34.1 + - + +
559A ARG 4.6 0.2 - - - +
562A ASP* 4.1 15.0 - - + +
563A ALA* 4.0 20.9 - - + +
566A TYR* 3.6 46.2 - - + -
636A THR* 5.8 2.5 - - - +
638A ALA* 4.5 15.5 - - + +
639A LEU* 5.1 8.1 - - + +
642A ALA* 4.7 6.7 - - + -
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Residues in contact with SER 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG* 2.2 41.8 + - - -
471A PHE* 4.2 22.7 - - - -
472A LYS* 5.6 3.5 - - - +
551A ALA 3.3 11.7 + - - -
552A LEU* 2.5 27.2 + - - +
554A ILE* 1.3 78.1 - - - +
556A GLU* 1.3 59.4 + - - +
558A ALA 2.9 11.1 - - - +
559A ARG 4.1 7.0 - - - -
560A MET* 4.8 6.3 - - - -
563A ALA* 4.3 4.9 - - - -
----------------------------------------------------------
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Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A SER* 4.2 21.3 - - - -
466A ARG* 4.2 19.7 + - - +
472A LYS* 5.9 3.3 - - - +
552A LEU 3.2 14.1 + - - +
553A ILE* 3.5 10.8 - - - +
554A ILE 3.0 0.6 - - - -
555A SER* 1.3 83.4 + - - +
557A HIS* 1.3 68.5 - - + +
558A ALA 3.4 0.2 - - - -
608A ASN* 2.6 23.4 + - - +
610A LYS* 3.6 10.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ILE* 3.5 27.5 + - + +
554A ILE* 3.1 3.3 + - - +
556A GLU* 1.3 90.6 - - + +
558A ALA* 1.3 60.0 + - - +
608A ASN* 3.7 1.8 - - - -
610A LYS* 3.2 25.1 + - - +
611A LEU* 4.2 1.7 - - - +
635A LYS* 4.8 18.5 + - + -
639A LEU* 3.8 32.5 - - + +
643A LEU* 4.6 0.5 - - - +
715A TYR* 2.6 32.8 + - + -
716A GLU* 4.6 17.8 - - + +
743A SER* 5.8 0.2 - - - -
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Residues in contact with ALA 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG* 3.4 5.9 + - - -
554A ILE* 2.8 13.4 + - + +
555A SER 2.9 20.1 - - - +
556A GLU 3.4 0.8 - - - -
557A HIS* 1.3 82.5 - - - +
559A ARG* 1.3 66.8 + - - +
562A ASP* 3.4 14.4 - - - +
608A ASN* 3.5 5.1 + - - +
611A LEU* 3.7 15.9 - - + -
639A LEU* 3.7 17.7 - - + -
642A ALA* 4.2 7.4 - - + -
643A LEU* 4.7 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