Contacts of the helix formed by residues 525 - 555 (chain A) in PDB entry 4PO2
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 TYR 525 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 3.7 37.2 - - - +
521A GLU* 3.2 47.4 + - + +
522A ALA 3.4 4.0 + - - +
523A GLU 3.2 0.4 - - - -
524A LYS* 1.3 109.2 + - + +
526A LYS* 1.3 63.7 + - - +
528A GLU* 3.2 25.7 - - + +
529A ASP* 3.1 24.4 + - - +
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Residues in contact with LYS 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ALA 3.5 9.0 + - - +
523A GLU* 3.6 32.0 + - - +
524A LYS 3.6 2.6 + - - -
525A TYR* 1.3 73.5 - - - +
527A ALA* 1.3 61.5 + - - +
528A GLU* 3.8 0.2 + - - -
529A ASP* 3.4 6.3 + - - +
530A GLU* 2.9 30.0 + - + +
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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
----------------------------------------------------------
525A TYR 3.5 0.6 - - - -
526A LYS* 1.3 78.4 - - - +
528A GLU* 1.3 66.8 + - - +
530A GLU* 3.2 7.8 + - - +
531A VAL* 2.9 34.3 + - + +
----------------------------------------------------------
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Residues in contact with GLU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 5.5 1.8 - - - +
524A LYS 4.2 2.7 - - - +
525A TYR* 3.2 41.9 - - + +
526A LYS 3.8 0.2 + - - -
527A ALA* 1.3 81.4 + - - +
529A ASP* 1.3 65.3 - - - +
531A VAL* 3.1 12.1 + - - +
532A GLN* 3.0 28.7 + - + +
----------------------------------------------------------
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Residues in contact with ASP 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLU 4.8 0.5 - - - +
447A ARG* 2.9 48.0 + - - +
448A ALA* 3.2 42.6 + - + +
449A MET* 5.3 2.5 + - - +
452A ASP* 4.8 3.3 - - - +
522A ALA 4.7 4.5 - - - +
525A TYR 3.1 17.9 + - - +
526A LYS* 3.6 6.7 - - - +
527A ALA 3.3 0.2 - - - -
528A GLU* 1.3 79.2 - - - +
530A GLU* 1.3 57.1 + - - +
532A GLN* 3.2 8.1 + - - +
533A ARG* 2.9 24.3 + - - +
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Residues in contact with GLU 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ALA* 5.4 0.2 - - - -
526A LYS* 2.9 20.1 + - + +
527A ALA* 3.6 7.2 - - - +
529A ASP* 1.3 71.6 - - - +
531A VAL* 1.3 66.1 + - - +
533A ARG* 2.8 48.4 + - - -
534A GLU* 2.8 48.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ALA* 2.9 20.8 + - + +
528A GLU* 3.1 12.1 + - - +
530A GLU* 1.3 75.9 - - - +
532A GLN* 1.3 69.1 + - - +
534A GLU* 3.4 6.2 + - - +
535A ARG* 2.9 30.2 + - + +
589A LYS* 5.7 1.0 - - - +
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Residues in contact with GLN 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A MET* 3.9 28.9 - - + +
451A LYS* 5.7 2.0 - - - +
528A GLU* 3.0 18.8 + - + +
529A ASP* 3.5 11.0 - - - +
531A VAL* 1.3 87.8 - - - +
533A ARG* 1.3 64.1 + - - +
535A ARG* 2.7 44.3 + - - +
536A VAL* 3.0 21.8 + - - +
----------------------------------------------------------
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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
----------------------------------------------------------
409A VAL* 4.8 19.1 - - + +
448A ALA* 4.3 12.1 - - + +
449A MET* 4.6 7.5 - - - -
529A ASP 2.9 16.3 + - - +
530A GLU* 2.8 43.4 + - - +
532A GLN* 1.3 77.7 - - - +
534A GLU* 1.3 64.8 + - - +
536A VAL* 3.3 4.6 + - - +
537A SER* 2.9 31.8 + - - -
702A PO4 3.0 48.9 + - - -
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Residues in contact with GLU 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLU* 2.8 52.4 + - - +
531A VAL* 3.8 5.5 - - - +
533A ARG* 1.3 81.1 - - - +
535A ARG* 1.3 67.2 + - - +
537A SER* 3.3 7.5 + - - -
538A ALA* 2.9 25.8 + - - +
589A LYS* 3.5 39.1 + - + +
702A PO4 4.7 3.6 - - - +
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Residues in contact with ARG 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLY* 4.9 4.0 + - - -
449A MET* 4.7 4.6 - - - +
531A VAL* 2.9 17.4 + - + +
532A GLN* 2.7 63.0 + - - +
534A GLU* 1.3 78.7 - - - +
536A VAL* 1.3 86.6 + - - +
538A ALA* 3.2 3.1 + - - +
539A LYS* 3.0 26.5 + - - +
585A THR 4.9 8.3 + - - -
586A LEU* 4.9 12.6 + - - +
587A ALA 3.5 26.1 + - - +
588A GLU* 4.1 7.4 - - + +
589A LYS* 4.0 25.3 - - + +
592A PHE* 3.9 5.9 - - + -
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ALA 3.3 26.2 - - - +
407A GLY* 3.7 23.1 - - - +
409A VAL* 3.5 23.8 - - + -
449A MET* 4.0 4.9 - - + -
532A GLN 3.0 11.2 + - - +
533A ARG 3.8 3.6 - - - +
535A ARG* 1.3 107.3 - - - +
537A SER* 1.3 63.2 + - - +
539A LYS* 3.1 11.8 + - + +
540A ASN* 2.9 31.9 + - - +
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Residues in contact with SER 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 5.7 0.2 - - - +
533A ARG* 2.9 19.1 + - - -
534A GLU 3.5 5.8 - - - -
535A ARG 3.2 0.2 - - - -
536A VAL* 1.3 79.2 - - - +
538A ALA* 1.3 57.3 + - - +
540A ASN* 3.5 7.4 + - - +
541A ALA* 2.9 30.2 + - - +
589A LYS* 6.3 0.2 - - - -
702A PO4 2.8 44.5 + - - -
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Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A GLU 2.9 17.1 + - - +
535A ARG 3.5 4.5 - - - +
537A SER* 1.3 72.7 - - - +
539A LYS* 1.3 67.2 + - - +
541A ALA* 3.3 6.8 + - - +
542A LEU* 2.9 24.6 + - - +
589A LYS* 4.0 25.8 - - + +
592A PHE* 3.9 20.1 - - + +
593A GLU* 4.4 10.3 - - + +
596A ARG* 5.3 3.3 + - - +
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Residues in contact with LYS 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLY* 6.2 4.9 - - - -
431A TYR* 3.5 14.1 + - - -
535A ARG* 3.0 13.7 + - - +
536A VAL* 3.1 14.8 + - + +
538A ALA* 1.3 77.0 - - - +
540A ASN* 1.3 65.3 + - - +
542A LEU* 3.2 4.0 + - - +
543A GLU* 2.9 50.7 + - - +
581A LEU* 4.4 16.3 - - + +
584A ASN 5.7 0.2 - - - -
585A THR* 4.7 22.4 - - - +
592A PHE* 3.6 42.7 - - + -
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Residues in contact with ASN 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ALA* 3.2 41.1 + - - +
407A GLY* 5.4 0.5 - - - -
431A TYR* 4.4 10.4 - - - -
469A ARG* 3.9 1.5 + - - +
536A VAL* 2.9 26.7 + - - +
537A SER* 3.9 6.5 - - - +
539A LYS* 1.3 83.8 + - - +
541A ALA* 1.3 57.0 + - - +
543A GLU* 3.5 7.5 + - - +
544A SER* 2.9 36.3 + - - +
3C LEU* 6.1 3.8 - - - +
4C LEU* 4.5 14.6 - - + +
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A SER* 2.9 19.1 + - - +
538A ALA* 3.6 7.2 - - - +
539A LYS 3.2 0.2 - - - -
540A ASN* 1.3 76.9 - - - +
542A LEU* 1.3 57.5 + - - +
544A SER* 3.9 3.9 - - - -
545A TYR* 2.9 30.3 + - - +
596A ARG* 4.3 18.5 - - - +
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Residues in contact with LEU 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ALA 2.9 16.7 + - - +
539A LYS* 3.6 4.5 - - - +
541A ALA* 1.3 77.0 - - - +
543A GLU* 1.3 62.5 - - - +
545A TYR* 3.2 3.0 + - + +
546A ALA* 2.9 20.3 + - - +
577A VAL* 3.7 20.6 - - + -
580A TRP* 3.9 8.3 - - + -
581A LEU* 3.8 25.4 - - + -
592A PHE* 3.7 24.0 - - + +
595A LYS* 3.8 19.3 - - + +
596A ARG* 3.6 40.5 - - + +
599A LEU* 4.9 7.0 - - + -
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Residues in contact with GLU 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A TYR* 3.1 33.6 + - - -
469A ARG* 3.9 15.4 + - - +
539A LYS* 2.9 31.4 + - - +
540A ASN* 3.9 5.5 - - - +
542A LEU* 1.3 76.8 - - - +
544A SER* 1.3 65.2 + - - +
546A ALA* 3.1 4.0 + - - +
547A PHE* 3.0 55.0 + - + -
581A LEU* 3.7 27.1 - - + +
582A ASP* 5.0 6.9 - - - +
----------------------------------------------------------
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Residues in contact with SER 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 2.9 31.8 + - - +
540A ASN* 2.9 18.2 + - - +
541A ALA* 3.9 4.3 - - - -
543A GLU* 1.3 76.0 - - - +
545A TYR* 1.3 57.8 + - - +
547A PHE* 3.8 1.5 - - - +
548A ASN* 2.9 45.6 + - - -
4C LEU* 4.5 9.5 - - - +
----------------------------------------------------------
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Residues in contact with TYR 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ALA 2.9 19.2 + - - +
542A LEU* 3.2 4.9 + - + +
544A SER* 1.3 75.4 - - - +
546A ALA* 1.3 55.3 + - - +
548A ASN* 3.5 4.8 + - + +
549A MET* 2.9 40.1 + - + +
596A ARG* 4.1 22.0 - - + -
599A LEU* 3.5 40.6 - - + -
600A GLU* 3.5 30.0 - - + +
603A CYS* 3.4 22.9 - - - +
604A ASN* 3.7 8.0 + - - -
434B ASN* 3.4 42.0 - - + +
466B PRO* 3.7 19.1 + - + -
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU 2.9 12.7 + - - +
543A GLU* 3.1 9.4 + - - +
545A TYR* 1.3 77.7 - - - +
547A PHE* 1.3 63.4 + - + +
549A MET* 3.3 2.8 + - - +
550A LYS* 3.0 25.4 + - - +
574A CYS* 3.7 9.3 - - - +
577A VAL* 4.2 11.7 - - + -
578A ILE* 4.2 26.5 - - + -
581A LEU* 5.2 0.2 - - + -
599A LEU* 3.9 21.3 - - + -
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Residues in contact with PHE 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A TYR 5.6 0.7 - - - -
432A SER* 6.1 1.1 - - - -
433A ASP* 4.0 28.5 - - - -
469A ARG* 3.9 31.4 - - + +
543A GLU* 3.0 55.8 + - + +
544A SER* 3.8 6.3 - - - +
546A ALA* 1.3 79.6 - - + +
548A ASN* 1.3 62.3 + - - +
550A LYS* 3.5 8.1 + - + +
551A SER* 2.9 29.6 + - - -
578A ILE* 4.9 23.1 - - + -
----------------------------------------------------------
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Residues in contact with ASN 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG 5.6 2.3 - - - +
544A SER* 2.9 33.5 + - - +
545A TYR* 3.9 5.5 - - - +
547A PHE* 1.3 76.6 - - - +
549A MET* 1.3 62.0 + - - +
551A SER* 3.7 6.4 - - - -
552A ALA* 2.9 29.8 + - - +
434B ASN* 5.9 2.8 + - - +
436B PRO* 6.3 0.8 - - - +
466B PRO* 3.9 17.5 - - + +
----------------------------------------------------------
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Residues in contact with MET 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A TYR* 2.9 44.5 + - + +
546A ALA 3.7 3.6 - - - +
548A ASN* 1.3 74.3 - - - +
550A LYS* 1.3 66.3 + - - +
552A ALA* 3.1 4.1 + - + +
553A VAL* 2.9 33.3 + - + +
570A VAL* 3.8 15.7 - - + -
574A CYS* 3.7 15.0 - - - -
599A LEU* 4.9 0.4 - - + -
603A CYS* 3.6 35.2 - - + -
607A ILE* 4.0 20.9 - - + -
466B PRO* 3.6 34.5 - - + +
----------------------------------------------------------
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Residues in contact with LYS 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ALA 3.0 17.9 + - - +
547A PHE* 3.7 7.0 - - + +
549A MET* 1.3 77.0 - - - +
551A SER* 1.3 63.4 + - - +
553A VAL* 3.3 9.9 - - - +
554A GLU* 2.9 56.3 + - - +
571A LEU* 3.6 20.6 - - + -
574A CYS* 4.0 12.4 - - + -
575A GLN* 5.9 2.2 - - - -
578A ILE* 4.9 15.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE 2.9 18.3 + - - -
548A ASN* 3.7 9.4 - - - -
550A LYS* 1.3 75.7 - - - +
552A ALA* 1.3 58.3 + - - +
554A GLU* 3.2 7.2 + - - +
555A ASP* 2.9 30.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ASN 2.9 19.9 + - - +
549A MET* 3.1 8.3 + - + +
551A SER* 1.3 79.6 - - - +
553A VAL* 1.3 63.5 + - + +
555A ASP* 3.4 14.9 + - - +
558A LEU* 3.2 22.9 - - + +
607A ILE* 5.3 0.9 - - + -
465B PRO* 4.3 13.9 - - + -
466B PRO* 3.7 22.9 - - + -
----------------------------------------------------------
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Residues in contact with VAL 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A MET* 2.9 23.5 + - + +
550A LYS 3.3 13.2 - - - +
552A ALA* 1.3 78.0 - - + +
554A GLU* 1.3 59.7 + - + +
555A ASP 3.4 3.6 + - - +
558A LEU* 4.7 8.2 - - + +
562A ILE* 3.8 30.6 - - + +
567A LYS* 3.5 28.2 + - + +
570A VAL* 3.6 29.8 - - + -
571A LEU* 3.6 28.9 - - + -
607A ILE* 5.0 6.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LYS* 2.9 59.3 + - - +
551A SER* 4.0 5.4 - - - +
553A VAL* 1.3 77.4 - - - +
555A ASP* 1.3 65.1 + - - +
556A GLU* 3.4 2.8 + - - -
559A LYS* 6.0 0.7 - - - +
567A LYS* 4.5 12.5 + - - +
571A LEU* 4.0 24.1 - - + +
----------------------------------------------------------
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Residues in contact with ASP 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A SER* 2.9 12.9 + - - +
552A ALA* 3.5 16.6 - - - +
553A VAL 3.4 3.5 - - - +
554A GLU* 1.3 77.4 - - - +
556A GLU* 1.3 84.0 + - - +
557A GLY* 3.0 16.9 + - - -
558A LEU* 3.0 18.6 + - + +
559A LYS* 3.6 8.0 + - - +
463B GLY* 5.2 8.7 - - - +
495B THR* 5.9 2.1 - - - +
497B LYS* 5.7 2.4 + - - -
----------------------------------------------------------
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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