Contacts of the helix formed by residues 525 - 554 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ARG* 4.0 31.0 - - - +
521B GLU* 3.1 42.9 + - - +
522B ALA 3.6 3.6 - - - +
524B LYS* 1.3 108.3 + - + +
526B LYS* 1.3 57.4 + - - +
528B GLU* 3.2 25.7 - - + +
529B ASP* 3.0 31.0 + - - +
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Residues in contact with LYS 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ALA 3.1 13.4 + - - +
523B GLU* 3.3 38.6 - - - +
524B LYS 3.6 1.0 + - - +
525B TYR* 1.3 77.0 - - - +
527B ALA* 1.3 62.4 + - + +
528B GLU* 3.9 0.2 + - - -
529B ASP* 3.4 6.2 + - - +
530B GLU* 2.9 28.6 + - - +
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Residues in contact with ALA 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B TYR 3.4 0.4 - - - -
526B LYS* 1.3 83.5 - - + +
528B GLU* 1.3 68.2 + - - +
530B GLU* 3.2 8.3 + - - +
531B VAL* 2.9 34.3 + - + +
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Residues in contact with GLU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LYS 4.0 4.3 - - - +
525B TYR* 3.2 40.2 - - + +
526B LYS 3.9 0.2 + - - -
527B ALA* 1.3 81.3 + - - +
529B ASP* 1.3 64.8 + - - +
531B VAL* 3.1 11.8 + - - +
532B GLN* 2.9 28.3 + - + +
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Residues in contact with ASP 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B GLU 4.9 0.7 - - - +
447B ARG* 2.7 48.1 + - - -
448B ALA* 3.3 39.3 + - + +
449B MET* 5.3 3.4 + - - +
452B ASP* 4.7 2.9 - - - +
522B ALA 4.8 2.6 - - - +
525B TYR* 3.0 22.0 + - - +
526B LYS* 3.5 7.0 - - - +
528B GLU* 1.3 78.0 - - - +
530B GLU* 1.3 56.8 + - - +
532B GLN* 3.2 10.3 + - - +
533B ARG 2.9 24.3 + - - -
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Residues in contact with GLU 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ALA* 5.4 0.4 - - - -
526B LYS 2.9 14.4 + - - +
527B ALA* 3.5 10.8 - - - +
529B ASP* 1.3 74.1 - - - +
531B VAL* 1.3 66.4 + - - +
533B ARG* 2.9 41.7 + - - -
534B GLU* 2.8 50.4 + - - +
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Residues in contact with VAL 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ALA* 2.9 20.4 + - + +
528B GLU* 3.1 11.6 + - - +
530B GLU* 1.3 76.6 - - + +
532B GLN* 1.3 68.5 + - - +
534B GLU* 3.4 6.6 + - - +
535B ARG* 2.9 42.1 + - + +
589B LYS* 5.8 0.7 - - - +
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Residues in contact with GLN 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B MET* 4.3 23.1 - - + +
451B LYS* 5.9 1.5 + - - -
528B GLU* 2.9 18.7 + - + +
529B ASP* 3.4 12.1 - - - +
530B GLU 3.2 0.2 - - - -
531B VAL* 1.3 79.9 - - - +
533B ARG* 1.3 63.4 + - - +
535B ARG* 3.2 47.8 + - - +
536B VAL* 2.9 33.2 + - - +
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Residues in contact with ARG 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B VAL* 4.6 22.7 - - + +
448B ALA* 4.4 13.2 - - + -
449B MET* 4.6 6.4 - - - -
529B ASP 2.9 14.4 + - - +
530B GLU* 2.9 44.2 + - - +
532B GLN* 1.3 75.0 - - - +
534B GLU* 1.3 71.0 + - - +
536B VAL* 3.4 6.6 + - - +
537B SER* 2.9 39.0 + - - -
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Residues in contact with GLU 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B GLU* 2.8 50.7 + - - +
531B VAL* 3.8 5.5 - - - +
533B ARG* 1.3 83.5 + - - +
535B ARG* 1.3 67.3 + - - +
537B SER* 3.3 8.2 + - - -
538B ALA* 2.9 23.9 + - - +
589B LYS* 3.2 38.5 + - + +
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Residues in contact with ARG 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B VAL* 2.9 27.1 + - + +
532B GLN* 3.2 47.2 + - - +
534B GLU* 1.3 75.9 - - - +
536B VAL* 1.3 68.4 + - + +
538B ALA* 3.2 5.2 + - - +
539B LYS* 2.9 20.8 + - - +
586B LEU* 4.9 12.7 + - - +
587B ALA 3.4 27.3 + - - +
588B GLU* 4.3 16.5 + - - +
589B LYS* 4.2 20.7 - - + +
592B PHE* 3.7 11.5 - - + -
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Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B GLY* 3.7 19.5 - - - +
409B VAL* 3.6 22.9 - - + -
449B MET* 3.9 23.3 - - + -
532B GLN* 2.9 24.1 + - - +
533B ARG 3.7 4.3 - - - +
535B ARG* 1.3 79.5 - - + +
537B SER* 1.3 57.9 + - - +
539B LYS* 3.2 12.1 + - + +
540B ASN* 2.9 45.5 + - - +
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Residues in contact with SER 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ARG* 2.9 28.6 + - - -
534B GLU* 3.5 9.0 - - - -
535B ARG 3.2 0.2 - - - -
536B VAL* 1.3 77.3 - - - +
538B ALA* 1.3 56.7 + - - +
540B ASN* 3.3 10.2 + - - +
541B ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B GLU 2.9 13.5 + - - +
535B ARG 3.5 7.6 - - - +
537B SER* 1.3 75.6 + - - +
539B LYS* 1.3 65.0 + - - +
541B ALA* 3.3 7.1 + - - +
542B LEU* 3.0 24.4 + - - +
589B LYS* 4.0 21.1 - - + +
592B PHE* 3.9 20.2 - - + +
593B GLU* 4.2 13.0 - - + +
596B ARG* 5.3 1.6 + - - -
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Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B GLY* 6.3 1.2 - - - -
431B TYR* 4.9 2.2 + - - -
535B ARG 2.9 8.0 + - - +
536B VAL* 3.2 15.2 + - + +
538B ALA* 1.3 77.3 - - - +
540B ASN* 1.3 62.2 + - - +
542B LEU* 3.2 3.6 + - - +
543B GLU* 2.9 50.1 + - - +
581B LEU* 4.2 23.0 - - + +
585B THR* 5.3 15.9 - - - +
592B PHE* 3.6 45.5 - - + -
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Residues in contact with ASN 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ALA* 3.0 41.5 + - - +
407B GLY* 4.6 1.7 + - - -
409B VAL* 5.2 1.0 - - - +
431B TYR* 4.6 3.1 - - - -
536B VAL* 2.9 30.3 + - - +
537B SER* 3.3 8.4 + - - +
539B LYS* 1.3 80.6 + - - +
541B ALA* 1.3 58.4 + - - +
543B GLU* 3.7 15.7 - - - +
544B SER* 2.9 35.5 + - - -
4D LEU* 4.9 12.7 - - + +
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Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B SER* 2.9 17.4 + - - +
538B ALA* 3.6 7.6 - - - +
539B LYS 3.2 0.4 - - - -
540B ASN* 1.3 76.0 - - - +
542B LEU* 1.3 63.4 + - - +
544B SER* 3.7 4.7 - - - -
545B TYR* 2.9 26.0 + - - +
596B ARG* 4.3 19.9 - - - +
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B ALA 3.0 13.1 + - - +
539B LYS 3.6 7.6 - - - +
541B ALA* 1.3 76.7 - - - +
543B GLU* 1.3 57.1 + - - +
545B TYR* 3.3 1.3 + - - +
546B ALA* 2.9 27.7 + - - +
577B VAL* 3.8 21.5 - - + -
580B TRP* 3.9 4.3 - - + -
581B LEU* 3.8 25.1 - - + -
592B PHE* 3.7 31.4 - - + +
595B LYS* 3.9 17.3 - - + +
596B ARG* 3.6 39.4 - - + +
599B LEU* 4.7 6.5 - - + -
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Residues in contact with GLU 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B TYR* 2.5 42.0 + - + -
539B LYS* 2.9 36.2 + - - +
540B ASN* 3.7 11.8 - - - +
542B LEU* 1.3 73.6 - - - +
544B SER* 1.3 66.5 + - - +
546B ALA* 3.3 2.4 + - - +
547B PHE* 2.9 55.0 + - + -
581B LEU* 4.0 21.5 - - + +
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Residues in contact with SER 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ARG* 5.0 12.0 - - - +
540B ASN 2.9 20.3 + - - -
541B ALA* 3.7 5.4 - - - -
543B GLU* 1.3 76.7 - - - +
545B TYR* 1.3 58.0 + - - +
547B PHE* 3.5 0.7 + - - +
548B ASN* 2.9 45.0 + - - +
4D LEU* 4.0 21.1 - - - +
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Residues in contact with TYR 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B ALA 2.9 17.9 + - - +
542B LEU 3.7 3.1 - - - +
544B SER* 1.3 75.7 - - - +
546B ALA* 1.3 56.8 + - - +
548B ASN* 4.0 5.1 - - + +
549B MET* 2.9 63.5 + - + +
596B ARG* 4.5 16.8 - - + -
599B LEU* 3.5 32.8 - - + -
600B GLU* 3.5 38.7 - - + +
603B CYS* 3.9 3.2 - - + +
604B ASN* 3.5 19.6 + - - -
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Residues in contact with ALA 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU 2.9 17.9 + - - +
543B GLU* 3.7 5.6 - - - +
545B TYR* 1.3 78.7 - - - +
547B PHE* 1.3 57.1 + - + +
549B MET* 3.7 1.8 - - - +
550B LYS* 2.9 29.3 + - - +
574B CYS* 3.7 8.4 - - - +
577B VAL* 3.9 19.1 - - + -
578B ILE* 4.5 16.2 - - + -
581B LEU* 5.2 0.2 - - + -
599B LEU* 3.7 22.9 - - + -
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Residues in contact with PHE 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ARG* 3.4 44.0 - - - +
543B GLU* 2.9 50.6 + - + +
544B SER 4.1 1.3 - - - +
546B ALA* 1.3 76.8 - - + +
548B ASN* 1.3 59.1 + - - +
550B LYS* 3.4 10.3 + - + +
551B SER* 2.9 33.1 + - - -
578B ILE* 3.7 44.0 - - + -
581B LEU* 5.5 2.2 - - + -
701B SO4 4.8 11.6 + - - -
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Residues in contact with ASN 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B PRO* 6.0 0.7 - - - +
469B ARG* 3.4 32.9 + - - +
544B SER* 2.9 32.8 + - - +
545B TYR* 4.0 5.1 - - + +
547B PHE* 1.3 73.8 - - - +
549B MET* 1.3 61.5 + - - +
551B SER* 3.5 6.6 + - - -
552B ALA* 2.9 28.8 + - - +
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Residues in contact with MET 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B TYR* 2.9 55.0 + - + +
546B ALA* 3.7 4.7 - - - +
548B ASN* 1.3 72.7 - - - +
550B LYS* 1.3 66.3 + - - +
552B ALA* 3.0 18.3 + - + +
553B VAL* 3.0 16.7 + - - +
570B VAL* 3.6 14.4 - - + -
574B CYS* 3.8 5.6 - - - -
599B LEU* 5.2 0.4 - - + -
603B CYS* 3.5 33.7 - - + -
604B ASN* 5.4 0.9 - - - +
607B ILE* 3.7 35.2 - - + -
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Residues in contact with LYS 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A GLU* 5.3 3.6 + - - -
546B ALA 2.9 17.9 + - - +
547B PHE* 3.4 12.3 - - + +
549B MET* 1.3 78.7 - - - +
551B SER* 1.3 61.0 + - - +
553B VAL* 3.5 7.5 - - - +
554B GLU* 3.2 44.3 + - - +
571B LEU* 4.0 11.0 - - + -
574B CYS* 3.8 17.0 - - + -
575B GLN* 5.4 8.3 - - - +
578B ILE* 4.2 22.7 - - + -
701B SO4 2.6 44.5 + - - +
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Residues in contact with SER 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A LYS* 4.8 4.4 - - - +
600A GLU* 6.2 0.2 - - - -
433B ASP* 4.1 12.3 + - - -
468B PRO* 6.4 2.0 - - - -
469B ARG* 4.7 1.6 + - - -
547B PHE 2.9 18.4 + - - -
548B ASN* 3.8 8.4 + - - -
550B LYS* 1.3 76.7 - - - +
552B ALA* 1.3 61.9 + - - +
554B GLU* 3.3 5.7 + - - +
555B ASP* 3.3 19.4 + - - +
701B SO4 3.4 25.2 + - - -
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Residues in contact with ALA 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ASN 2.9 18.4 + - - +
549B MET* 3.0 18.3 + - + +
551B SER* 1.3 77.6 - - - +
553B VAL* 1.3 61.7 + - + +
555B ASP* 3.2 22.0 - - - +
558B LEU* 3.5 11.3 - - - +
607B ILE* 5.2 5.8 - - + -
----------------------------------------------------------
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Residues in contact with VAL 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B MET 3.0 14.8 + - - +
550B LYS 3.5 11.0 - - - +
552B ALA* 1.3 76.3 - - - +
554B GLU* 1.3 61.2 + - - +
555B ASP 3.3 4.8 + - - +
558B LEU* 4.2 11.6 - - + +
562B ILE* 4.2 22.6 - - + +
567B LYS* 3.6 23.0 + - + +
570B VAL* 3.6 40.4 - - + -
571B LEU* 3.6 27.4 - - + -
607B ILE* 4.2 20.9 - - + -
----------------------------------------------------------
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Residues in contact with GLU 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A GLU* 5.0 8.9 - - - +
597A LYS* 3.3 35.0 - - + +
550B LYS* 3.2 39.2 + - - +
551B SER 3.3 2.6 + - - +
552B ALA 3.2 0.6 - - - -
553B VAL* 1.3 76.9 - - - +
555B ASP* 1.3 66.3 + - - +
556B GLU* 3.2 4.3 + - - +
567B LYS* 4.5 12.6 + - - +
571B LEU* 3.8 28.8 - - + +
701B SO4 2.9 31.7 + - - -
----------------------------------------------------------
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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