Contacts of the helix formed by residues 522 - 554 (chain B) in PDB entry 4JWE
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 ASN 522 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LYS 2.9 23.2 + - - -
578A GLY* 3.6 21.5 - - - -
579A GLU* 4.3 6.3 + - - -
445B ARG* 3.6 31.4 + - - +
518B ASP* 3.0 37.7 + - - +
519B ALA 3.4 3.1 - - - -
521B ALA* 1.3 80.2 - - - +
523B ALA* 1.4 56.0 + - - +
524B GLU 3.4 2.9 + - - -
525B ALA* 3.4 17.1 + - + +
526B ASP* 2.9 30.7 + - - +
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Residues in contact with ALA 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ALA 2.9 11.0 + - - +
520B GLU* 3.4 18.6 + - - +
521B ALA 3.5 0.8 + - - -
522B ASN* 1.4 76.3 - - - +
524B GLU* 1.3 58.1 + - - +
526B ASP* 3.4 5.4 + - - +
527B ARG* 3.1 27.4 + - - +
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ALA 5.3 1.7 + - - +
522B ASN 3.4 0.6 - - - -
523B ALA* 1.3 75.2 - - - +
525B ALA* 1.3 64.0 + - - +
527B ARG* 2.7 47.7 + - - +
528B LYS* 3.0 44.6 + - - +
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Residues in contact with ALA 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A GLY* 6.4 0.2 - - - -
579A GLU 6.4 0.2 - - - +
445B ARG* 5.7 1.3 - - - +
447B ARG* 5.2 6.8 + - - +
522B ASN* 3.4 25.3 + - + +
524B GLU* 1.3 76.9 - - - +
526B ASP* 1.4 58.4 + - - +
528B LYS* 3.3 13.1 + - - +
529B PHE* 2.9 27.0 + - - +
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Residues in contact with ASP 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLU 4.5 1.6 - - - +
445B ARG* 2.8 45.6 + - - -
446B LYS* 3.0 38.8 + - + +
447B ARG* 4.1 14.0 + - - +
519B ALA* 5.0 2.1 - - - +
522B ASN 2.9 20.8 + - - +
523B ALA* 3.8 5.4 - - - +
525B ALA* 1.4 74.2 - - - +
527B ARG* 1.3 59.7 + - - +
529B PHE* 3.3 6.5 + - - +
530B GLU* 3.0 35.7 + - - +
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Residues in contact with ARG 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ALA 3.1 14.1 + - - +
524B GLU* 2.7 38.3 + - - +
526B ASP* 1.3 75.3 - - - +
528B LYS* 1.4 73.3 + - - +
530B GLU* 3.6 13.5 + - - +
531B GLU* 2.8 61.9 + - - +
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Residues in contact with LYS 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B GLU* 3.0 42.5 + - + +
525B ALA* 3.6 11.9 - - - +
527B ARG* 1.4 89.3 - - - +
529B PHE* 1.4 58.5 + - - +
531B GLU* 3.3 16.5 + - - +
532B LEU* 3.1 26.7 + - - +
579B GLU* 5.9 0.4 - - - -
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Residues in contact with PHE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLY 3.5 12.1 - - - -
406B GLY 3.6 13.7 - - - -
407B VAL* 3.7 22.4 - - + -
446B LYS* 3.8 13.7 - - + -
447B ARG* 3.5 63.3 - - + +
525B ALA 2.9 13.4 + - - +
526B ASP* 3.3 14.1 + - - +
528B LYS* 1.4 73.2 - - - +
530B GLU* 1.3 61.9 + - - +
532B LEU* 3.1 9.5 + - + +
533B VAL* 3.0 49.2 + - + +
536B ARG* 4.5 4.9 - - - -
579B GLU* 4.7 6.1 - - - -
703B SO4 4.3 8.5 - - - -
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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
----------------------------------------------------------
407B VAL* 5.0 16.6 - - + +
408B MET 5.4 0.5 - - - +
446B LYS* 3.4 48.1 - - + +
526B ASP 3.0 17.0 + - - +
527B ARG* 3.8 13.0 - - - +
528B LYS 3.4 0.2 - - - -
529B PHE* 1.3 79.8 - - + +
531B GLU* 1.3 61.0 + - + +
533B VAL* 3.5 12.0 + - - +
534B GLN* 3.6 12.5 + - - +
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Residues in contact with GLU 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ARG* 2.8 49.6 + - - +
528B LYS* 3.3 17.8 + - - +
529B PHE 3.2 0.2 - - - -
530B GLU* 1.3 78.1 - - + +
532B LEU* 1.3 61.0 + - - +
533B VAL 3.6 0.3 + - - -
534B GLN* 3.8 12.0 + - - +
535B THR* 3.9 12.6 + - - -
581B LYS* 5.0 9.7 - - + +
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B LYS 3.1 13.3 + - - +
529B PHE* 3.1 13.2 + - + +
531B GLU* 1.3 76.0 - - - +
533B VAL* 1.4 51.6 + - - +
535B THR* 3.3 7.4 + - - -
536B ARG* 2.8 63.4 + - + +
579B GLU* 3.4 60.8 - - + +
581B LYS* 3.9 16.8 - - + +
584B ILE* 3.7 24.2 - - + -
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B MET 3.5 14.6 - - - +
405B GLY* 3.2 24.7 - - - +
407B VAL* 3.8 15.9 - - + -
529B PHE* 3.0 38.1 + - + +
530B GLU 3.5 4.2 + - - +
531B GLU 3.4 0.6 - - - -
532B LEU* 1.4 74.2 - - - +
534B GLN* 1.3 55.3 + - - +
536B ARG* 3.8 14.8 - - + -
537B ASN* 2.6 56.1 + - - +
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Residues in contact with GLN 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B GLU 3.6 10.3 + - - +
531B GLU* 4.0 9.9 - - - +
532B LEU 3.4 0.6 - - - -
533B VAL* 1.3 76.3 - - - +
535B THR* 1.4 58.3 + - - +
537B ASN* 3.5 6.7 + - - +
538B GLN* 3.1 48.7 + - + +
581B LYS* 6.4 0.4 - - - +
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Residues in contact with THR 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B GLU 3.9 5.0 + - - -
532B LEU 3.3 9.5 + - - -
533B VAL 3.3 0.2 - - - -
534B GLN* 1.4 74.2 + - - +
536B ARG* 1.3 60.5 + - - +
538B GLN* 3.2 15.0 + - - +
539B GLY* 2.9 25.8 + - - -
581B LYS* 3.3 59.6 - - + +
584B ILE* 3.8 20.3 - - + +
585B GLU* 3.9 15.8 + - + +
588B MET* 4.1 2.6 - - + +
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Residues in contact with ARG 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLY* 5.3 5.1 + - - -
529B PHE* 4.5 8.9 - - - -
532B LEU* 2.8 38.3 + - + +
533B VAL* 3.5 18.3 - - + +
535B THR* 1.3 72.2 - - - +
537B ASN* 1.4 63.6 + - - +
539B GLY 3.2 2.3 + - - -
540B ASP* 3.2 24.7 + - - +
576B LEU* 2.8 37.8 + - + +
577B LYS* 2.9 21.4 + - - +
578B GLY 2.8 25.4 + - - -
584B ILE* 3.8 15.3 - - + -
703B SO4 2.8 39.6 + - - -
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Residues in contact with ASN 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B MET* 3.2 59.3 + - + +
405B GLY* 3.6 15.6 + - - -
533B VAL* 2.6 31.1 + - - +
534B GLN* 3.8 6.9 - - - +
536B ARG* 1.4 71.2 - - - +
538B GLN* 1.3 63.2 + - + +
540B ASP* 3.2 7.1 + - - +
541B HIS* 3.0 33.3 + - + -
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Residues in contact with GLN 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B GLN* 3.1 35.5 + - + +
535B THR* 3.5 23.6 + - - +
537B ASN* 1.3 74.2 - - - +
539B GLY* 1.3 62.2 + - - +
541B HIS* 3.2 12.0 + - - +
542B LEU* 3.1 25.6 + - - +
585B GLU* 4.9 6.2 - - - +
588B MET* 4.2 13.8 - - - +
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Residues in contact with GLY 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B THR 2.9 13.7 + - - -
536B ARG 3.4 6.3 - - - -
537B ASN 3.2 0.6 - - - -
538B GLN* 1.3 76.5 - - - +
540B ASP* 1.3 56.9 + - - +
542B LEU* 3.7 0.5 + - - +
543B LEU* 3.3 23.0 + - - +
572B LEU* 3.4 10.3 - - - +
576B LEU* 3.8 17.9 - - - -
588B MET* 3.9 21.0 - - - -
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Residues in contact with ASP 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B MET* 4.0 17.2 - - + +
430B GLU* 4.2 6.1 - - - +
536B ARG* 3.2 21.0 + - - +
537B ASN* 3.2 9.4 + - - +
539B GLY* 1.3 74.1 - - - +
541B HIS* 1.3 59.2 + - - +
543B LEU* 3.3 17.7 + - - +
544B HIS* 2.9 46.4 + - + -
576B LEU* 4.3 13.1 - - - +
----------------------------------------------------------
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Residues in contact with HIS 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B MET* 3.5 28.7 - - + +
429B ALA 2.7 29.3 + - - -
430B GLU* 3.5 10.4 - - - +
467B ARG* 3.2 41.6 + - - +
537B ASN* 3.0 22.1 + - + +
538B GLN* 3.2 12.6 + - - +
540B ASP* 1.3 75.9 - - - +
542B LEU* 1.4 54.3 + - - +
544B HIS* 3.6 1.6 + - - +
545B SER* 3.0 30.9 + - - -
9C ARG* 3.4 24.2 + - - -
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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 GLN 3.1 15.5 + - - +
539B GLY 4.0 2.2 - - - +
541B HIS* 1.4 72.4 - - - +
543B LEU* 1.3 57.3 + - - +
545B SER* 3.0 7.6 + - - +
546B THR* 2.9 48.8 + - - +
572B LEU* 3.9 11.7 - - + -
588B MET* 3.8 44.9 - - + +
591B LEU* 3.8 25.1 - - + -
592B ALA* 5.7 5.6 - - + -
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Residues in contact with LEU 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B GLY 3.3 13.1 + - - +
540B ASP* 3.3 16.8 - - - +
542B LEU* 1.3 77.6 - - - +
544B HIS* 1.4 65.6 + - + +
547B ARG* 3.3 44.8 + - - +
569B LEU* 3.3 48.2 - - + +
572B LEU* 4.0 17.9 - - + -
573B GLU* 3.7 27.8 - - + +
576B LEU* 4.2 18.2 - - + -
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Residues in contact with HIS 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B GLU* 3.4 48.0 + - + +
540B ASP* 2.9 38.8 + - - +
541B HIS 3.9 1.8 - - - +
543B LEU* 1.4 82.4 - - + +
545B SER* 1.4 63.2 + - - +
547B ARG* 3.6 11.3 + - - +
548B LYS* 3.3 26.9 + - - +
12C ARG* 5.9 4.9 - - - -
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Residues in contact with SER 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ASP* 5.4 9.2 - - - -
467B ARG* 5.6 7.2 - - - -
541B HIS 3.0 16.8 + - - -
542B LEU* 3.0 20.3 + - - +
544B HIS* 1.4 76.1 - - - +
546B THR* 1.3 62.2 + - - +
548B LYS* 3.7 4.3 + - - +
549B GLN* 3.2 36.3 + - - +
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Residues in contact with THR 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 2.9 25.9 + - - +
545B SER* 1.3 74.8 + - - +
547B ARG* 1.4 57.7 + - - +
549B GLN* 3.2 13.6 + - - +
550B VAL* 2.9 24.1 + - - +
565B ILE* 4.1 22.0 - - + -
569B LEU* 4.4 11.0 - - + -
591B LEU* 3.3 32.4 - - + +
595B SER* 4.1 1.7 - - - +
598B LEU* 3.9 22.1 - - + +
599B MET* 5.9 1.6 - - - -
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Residues in contact with ARG 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LEU* 3.3 36.2 + - - +
544B HIS* 3.6 11.6 + - - +
545B SER 3.6 0.2 - - - -
546B THR* 1.4 75.0 - - - +
548B LYS* 1.4 59.9 + - - +
550B VAL* 3.3 29.0 - - + +
551B GLU* 3.6 11.3 + - - +
566B GLU* 4.6 4.8 + - - +
569B LEU* 3.9 32.7 - - + +
573B GLU* 3.6 36.5 + - - -
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Residues in contact with LYS 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ASP* 4.6 10.8 + - + +
432B ASN* 3.2 33.3 + - - +
544B HIS 3.3 17.4 + - - +
545B SER* 4.1 5.6 - - - +
546B THR 3.3 0.6 - - - -
547B ARG* 1.4 75.9 - - - +
549B GLN* 1.4 62.1 + - + +
550B VAL 3.3 0.2 - - - -
551B GLU* 3.4 7.3 + - - +
552B GLU* 3.3 35.6 + - + +
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Residues in contact with GLN 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B SER* 3.2 25.9 + - - +
546B THR* 3.2 13.0 + - - +
548B LYS* 1.4 76.4 - - + +
550B VAL* 1.4 61.3 + - - +
551B GLU 3.3 0.2 - - - -
552B GLU* 3.8 17.6 - - - +
553B ALA* 3.3 25.3 + - - +
598B LEU* 4.2 26.6 + - + +
599B MET* 3.9 32.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B THR 2.9 12.7 + - - +
547B ARG* 3.3 24.7 - - + +
548B LYS 3.3 0.2 - - - -
549B GLN* 1.4 77.4 - - - +
551B GLU* 1.4 69.2 + - - +
553B ALA* 4.3 1.4 - - - +
554B GLY* 3.5 17.2 + - - -
557B LEU* 3.8 23.5 - - + +
562B LYS* 4.7 16.4 - - + -
565B ILE* 4.1 18.6 - - + -
566B GLU* 3.9 18.2 - - - +
598B LEU* 3.7 21.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ARG 3.6 9.9 + - - +
548B LYS* 3.4 10.6 + - - +
549B GLN 3.3 0.2 - - - -
550B VAL* 1.4 88.7 - - - +
552B GLU* 1.4 63.1 + - + +
553B ALA 3.5 0.7 + - - -
554B GLY* 3.5 12.6 + - - -
562B LYS* 5.9 2.8 + - - -
----------------------------------------------------------
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Residues in contact with GLU 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B LYS* 3.3 24.7 + - + +
549B GLN* 3.8 20.8 - - - +
550B VAL 3.6 0.2 - - - -
551B GLU* 1.4 77.8 - - + +
553B ALA* 1.4 59.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B GLN 3.3 15.2 + - - +
550B VAL* 4.4 3.1 - - - +
552B GLU* 1.4 79.6 - - - +
554B GLY* 1.3 59.9 + - - +
555B ASP* 3.0 2.1 + - - +
556B LYS* 3.0 35.1 + - + +
557B LEU* 3.8 26.5 - - + +
597B LYS 6.1 0.2 - - - +
598B LEU* 5.2 9.9 - - + +
----------------------------------------------------------
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Residues in contact with GLY 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B VAL 3.5 11.0 + - - -
551B GLU 3.5 13.6 + - - -
553B ALA* 1.3 73.6 - - - +
555B ASP* 1.3 61.9 + - - -
557B LEU* 3.5 22.1 + - - +
562B LYS* 6.2 0.5 - - - +
----------------------------------------------------------
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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