Contacts of the helix formed by residues 549 - 579 (chain A) in PDB entry 4PJW
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 THR 549 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A LEU* 1.3 93.5 - - + +
550A ALA* 1.3 67.6 + - - +
551A LYS* 3.7 6.1 + - - +
552A GLU* 2.8 47.5 + - - +
553A LYS* 3.4 13.4 + - - +
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Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A THR* 1.3 76.4 - - - +
551A LYS* 1.3 76.5 + - + +
552A GLU 3.5 0.3 + - - -
553A LYS* 3.8 13.3 + - - +
554A LYS* 3.9 8.7 + - - +
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Residues in contact with LYS 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A THR* 3.4 5.4 + - - +
550A ALA* 1.3 86.5 - - + +
552A GLU* 1.3 65.1 + - + +
554A LYS* 3.3 30.2 - - + +
555A THR* 3.3 13.2 + - - -
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Residues in contact with GLU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A CYS* 4.4 11.3 - - - -
548A LEU* 3.2 28.5 + - - +
549A THR* 2.8 36.8 + - - +
550A ALA 3.3 1.0 - - - -
551A LYS* 1.3 75.8 - - + +
553A LYS* 1.3 60.2 + - - +
554A LYS 3.1 1.8 - - - -
555A THR* 3.2 8.6 + - - +
556A GLN* 2.9 27.4 + - - +
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Residues in contact with LYS 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A CYS* 5.8 0.4 - - - -
548A LEU* 3.8 24.8 + - - +
549A THR 3.4 20.5 + - - +
550A ALA* 4.1 8.3 - - - +
551A LYS 3.5 0.4 - - - -
552A GLU* 1.3 76.2 - - - +
554A LYS* 1.3 57.7 + - - +
556A GLN* 3.4 19.5 - - - +
557A LEU* 2.9 29.3 + - - +
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Residues in contact with LYS 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ALA 3.9 5.9 + - - +
551A LYS* 3.3 26.4 + - + +
553A LYS* 1.3 77.1 - - - +
555A THR* 1.3 60.9 + - - +
557A LEU* 3.2 9.6 + - + +
558A ASP* 2.9 44.0 + - - +
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Residues in contact with THR 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LYS* 3.1 32.1 - - - +
551A LYS 3.3 11.2 + - - -
552A GLU* 3.2 11.1 + - - -
554A LYS* 1.3 78.3 - - - +
556A GLN* 1.3 52.9 + - - +
558A ASP* 3.4 10.4 + - + +
559A ASP* 2.8 43.8 + - - +
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Residues in contact with GLN 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ALA 4.1 4.3 - - - +
533A ALA 2.9 29.5 + - - +
534A GLU* 4.5 4.9 - - - +
535A CYS* 4.0 24.6 - - - +
552A GLU 2.9 13.6 + - - +
553A LYS* 3.4 24.4 - - - +
555A THR* 1.3 76.5 - - - +
557A LEU* 1.3 57.2 + - - +
559A ASP* 2.9 23.1 + - - +
560A ARG* 2.9 39.1 + - + +
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Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A LYS 2.9 17.0 + - - +
554A LYS* 3.6 7.0 - - + +
556A GLN* 1.3 76.4 - - - +
558A ASP* 1.3 54.5 + - - +
560A ARG* 3.5 12.4 + - + +
561A THR* 2.7 43.8 + - + +
596A ASP* 5.3 8.1 - - + +
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Residues in contact with ASP 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A LYS* 2.9 36.1 + - - +
555A THR* 3.4 14.0 - - + +
557A LEU* 1.3 76.0 - - - +
559A ASP* 1.3 63.9 + - - +
561A THR* 3.0 17.0 + - - -
562A LYS* 3.1 17.1 + - - +
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Residues in contact with ASP 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LYS* 3.0 40.5 + - - +
495A TRP* 3.9 21.7 - - + -
532A ALA* 3.5 26.6 - - + +
555A THR* 2.8 25.0 + - - +
556A GLN* 2.9 10.7 + - - +
558A ASP* 1.3 75.0 - - - +
560A ARG* 1.3 59.2 + - - +
562A LYS* 3.5 3.3 + - - +
563A ILE* 2.9 35.0 + - - +
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Residues in contact with ARG 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ALA* 3.7 31.1 + - - +
534A GLU* 4.7 1.2 - - - +
556A GLN* 2.9 44.1 + - + +
557A LEU* 4.0 12.3 - - + +
558A ASP 3.4 0.4 - - - -
559A ASP* 1.3 72.0 - - - +
561A THR* 1.3 52.5 + - + +
563A ILE* 3.1 9.4 + - - +
564A THR* 2.6 44.8 + - - +
593A GLN 4.4 4.6 + - - -
594A TYR* 3.1 39.5 + - - +
595A PHE 4.0 7.7 + - - -
596A ASP* 4.3 18.7 - - + +
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Residues in contact with THR 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 2.7 29.2 + - + +
558A ASP* 3.0 13.7 + - - -
560A ARG* 1.3 78.0 - - - +
562A LYS* 1.3 55.3 + - - +
564A THR* 4.3 6.1 - - - -
565A GLU* 2.9 48.1 + - - +
596A ASP* 4.5 9.9 - - + +
599A ILE* 4.4 23.6 - - + -
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Residues in contact with LYS 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LYS* 3.7 18.3 + - - -
494A ASP* 5.0 1.4 + - - +
495A TRP* 3.7 33.7 - - + +
496A GLU* 3.4 37.3 + - + +
558A ASP 3.1 19.5 + - - +
559A ASP* 3.7 5.2 - - - +
561A THR* 1.3 75.3 + - - +
563A ILE* 1.3 63.1 - - - +
565A GLU* 4.2 5.9 - - - +
566A LEU* 3.1 30.2 + - + +
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Residues in contact with ILE 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TRP* 3.7 39.7 - - + -
529A ILE* 3.9 40.4 - - + +
532A ALA* 4.4 3.4 - - + -
533A ALA* 4.7 7.6 - - + +
559A ASP 2.9 25.7 + - - +
560A ARG* 3.4 6.7 - - - +
562A LYS* 1.3 76.7 - - - +
564A THR* 1.3 59.1 + - - +
566A LEU* 4.8 0.2 - - - -
567A PHE* 2.8 49.4 + - + +
591A LEU* 5.1 0.7 - - + -
594A TYR* 4.9 6.7 - - + +
595A PHE* 3.9 18.8 - - + -
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Residues in contact with THR 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A ARG 2.6 28.7 + - - -
561A THR* 4.0 5.8 - - - -
563A ILE* 1.3 73.4 - - - +
565A GLU* 1.3 56.2 + - - +
568A ALA* 2.8 42.0 + - + +
595A PHE* 3.4 31.2 - - + -
596A ASP* 3.2 42.2 + - - +
597A LEU* 5.3 0.4 - - - -
599A ILE* 3.8 19.7 - - + -
600A TYR* 5.4 4.3 - - + +
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Residues in contact with GLU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A THR* 2.9 36.1 + - - +
562A LYS* 4.2 5.1 - - - +
564A THR* 1.3 77.6 - - - +
566A LEU* 1.3 60.2 + - - +
568A ALA* 4.5 2.7 - - - +
569A VAL* 3.6 21.3 - - - +
599A ILE* 3.8 27.8 - - + +
605A LEU* 4.9 5.9 - - + +
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Residues in contact with LEU 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TRP* 3.5 21.8 - - + +
496A GLU* 3.4 46.2 - - + +
499A ASN* 3.7 20.9 - - + +
562A LYS* 3.1 21.7 + - + +
563A ILE 3.9 1.3 - - - +
565A GLU* 1.3 79.7 - - - +
567A PHE* 1.3 71.2 - - + +
569A VAL* 3.5 6.4 + - - +
570A ALA* 3.1 21.0 + - + +
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Residues in contact with PHE 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TRP* 3.7 31.0 - + + -
499A ASN* 4.4 9.0 - - + -
525A MSE 3.7 37.0 - - + -
529A ILE* 3.5 27.6 - - + -
563A ILE* 2.8 42.6 + - + +
566A LEU* 1.3 79.9 - - + +
568A ALA* 1.3 60.8 + - - +
569A VAL 3.1 1.1 - - - -
570A ALA* 3.7 7.4 - - + +
571A LEU* 2.9 36.9 + - + +
574A LEU* 4.2 17.3 - - + -
591A LEU* 4.3 13.2 - - + -
595A PHE* 3.8 19.5 - - + -
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Residues in contact with ALA 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A THR* 2.8 26.1 + - + +
565A GLU 4.5 1.3 - - - +
567A PHE* 1.3 76.5 - - - +
569A VAL* 1.3 59.1 + - + +
572A PRO* 3.4 17.3 - - - +
595A PHE* 4.1 5.0 - - + -
600A TYR* 3.8 37.3 + - + +
605A LEU* 4.1 20.2 - - + -
608A HIS* 3.4 15.6 - - - +
----------------------------------------------------------
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Residues in contact with VAL 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A GLU 3.6 16.6 - - - +
566A LEU 3.5 6.2 + - - +
568A ALA* 1.3 80.5 - - + +
570A ALA* 1.3 60.2 + - + +
571A LEU 3.5 0.2 - - - -
572A PRO* 3.5 9.1 - - - +
573A GLN* 3.1 23.2 - - - +
605A LEU* 4.0 18.8 - - + -
608A HIS* 3.6 34.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ASN* 3.3 37.0 - - - +
503A LEU* 5.1 2.8 - - + +
566A LEU* 3.1 19.5 + - + +
567A PHE* 4.1 8.1 - - + -
569A VAL* 1.3 79.3 - - + +
571A LEU* 1.3 59.7 + - - +
573A GLN* 3.2 15.5 + - - +
574A LEU* 2.9 29.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A PHE* 2.9 25.3 + - + +
570A ALA* 1.3 76.9 - - - +
572A PRO* 1.3 61.7 - - + +
574A LEU* 3.0 7.4 + - + +
575A LEU* 2.8 36.9 + - + +
588A LEU* 3.5 37.0 - - + +
589A LEU* 5.5 1.3 - - + -
591A LEU* 3.8 17.0 - - + -
592A PRO* 3.5 40.2 - - + -
595A PHE* 4.6 4.0 - - + -
612A LEU* 3.8 21.8 - - + -
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Residues in contact with PRO 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ALA 3.4 24.5 - - - +
569A VAL 3.5 7.9 - - - +
570A ALA 3.5 3.4 - - - -
571A LEU* 1.3 94.3 - - + +
573A GLN* 1.3 60.8 + - + +
575A LEU* 3.6 2.4 + - + -
576A ALA* 3.1 22.9 + - - +
608A HIS* 3.7 20.4 - - + +
611A ALA* 3.8 23.8 - - + +
612A LEU* 4.1 17.5 - - + +
615A GLN* 3.6 14.8 - - + +
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Residues in contact with GLN 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LEU* 4.3 28.0 - - + +
569A VAL* 3.1 32.6 - - - +
570A ALA* 3.2 12.1 + - - +
572A PRO* 1.3 78.1 - - + +
574A LEU* 1.3 58.8 + - - +
576A ALA* 3.4 7.8 + - - +
577A LYS* 3.1 28.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ASN* 3.6 22.0 - - - +
502A LEU* 4.0 23.8 - - + -
503A LEU* 4.0 12.3 - - + -
522A ILE* 5.7 0.2 - - + -
525A MSE 3.9 12.8 - - + -
567A PHE* 4.2 9.2 - - + -
570A ALA 2.9 19.2 + - - +
571A LEU* 3.0 14.1 + - + +
573A GLN* 1.3 75.3 - - - +
575A LEU* 1.3 65.0 + - - +
577A LYS 3.5 0.5 + - - -
578A TYR* 3.2 57.0 + - + +
588A LEU* 3.8 29.9 - - + +
----------------------------------------------------------
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Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU* 2.8 28.4 + - + +
572A PRO 4.0 0.4 - - - +
574A LEU* 1.3 69.8 - - - +
576A ALA* 1.3 59.0 + - - +
578A TYR 5.2 0.2 - - - -
579A SER* 2.7 39.0 + - - +
585A VAL* 4.2 9.6 - - + -
588A LEU* 3.9 25.4 - - + -
589A LEU* 4.2 24.7 - - + -
612A LEU* 3.7 30.1 - - + -
615A GLN* 4.0 27.1 - - + -
616A ILE* 4.3 4.0 - - + -
619A ILE* 3.7 24.0 - - + -
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Residues in contact with ALA 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PRO 3.1 15.2 + - - +
573A GLN* 3.4 13.5 - - - +
574A LEU 3.3 0.2 - - - -
575A LEU* 1.3 77.7 - - - +
577A LYS* 1.3 61.7 + - - +
579A SER* 3.4 12.4 + - - -
615A GLN* 3.4 25.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU 3.1 28.5 - - - +
503A LEU* 4.4 21.1 - - + +
518A GLU* 4.3 11.1 + - - -
573A GLN 3.1 12.9 + - - +
574A LEU* 3.9 4.5 - - - +
575A LEU 3.3 0.2 - - - -
576A ALA* 1.3 80.7 - - - +
578A TYR* 1.3 88.5 + - + +
579A SER* 3.8 0.5 + - - -
580A VAL* 5.1 5.9 - - - +
----------------------------------------------------------
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Residues in contact with TYR 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU* 2.3 47.8 + - + +
515A ASP* 5.0 1.6 - - - -
518A GLU* 3.2 35.5 + - + -
522A ILE* 4.3 6.3 - - + -
574A LEU* 3.2 50.0 + - + +
575A LEU 3.6 1.1 - - - -
577A LYS* 1.3 102.2 - - + +
579A SER* 1.3 64.7 + - - +
580A VAL 3.0 5.3 + - - -
581A ASP* 3.0 28.2 + - - +
584A LYS* 3.6 34.1 - - + -
585A VAL* 3.7 3.7 - - - +
588A LEU* 4.3 11.2 - - + -
----------------------------------------------------------
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Residues in contact with SER 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LEU 2.7 23.2 + - - -
576A ALA* 3.4 13.1 + - - -
577A LYS 3.5 1.4 - - - -
578A TYR* 1.3 72.2 - - - +
580A VAL* 1.3 57.9 + - - +
581A ASP 3.3 0.5 + - - -
585A VAL* 3.6 15.8 - - - +
615A GLN* 5.0 4.2 + - - -
618A ASN* 4.9 8.8 + - - -
619A ILE* 4.2 16.5 - - - +
622A LYS* 4.2 15.9 + - - +
623A HIS* 3.0 25.3 + - - -
----------------------------------------------------------
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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