Contacts of the helix formed by residues 554 - 586 (chain B) in PDB entry 4N3Z
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 ARG 554 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B THR* 1.3 68.2 - - - +
555B ASP* 1.3 59.6 + - - +
556B GLN 3.3 0.2 - - - -
557B VAL* 3.6 26.3 - - - +
558B LYS* 2.9 42.2 + - + +
553C THR* 2.7 48.0 + - - +
556C GLN* 2.9 31.8 - - - +
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Residues in contact with ASP 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B THR* 2.7 18.6 + - - +
554B ARG* 1.3 75.1 - - - +
556B GLN* 1.3 63.3 + - + +
558B LYS* 3.2 19.9 + - - +
559B LYS* 3.2 21.8 + - - +
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Residues in contact with GLN 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B THR* 2.7 30.2 + - + +
555B ASP* 1.3 74.3 - - + +
557B VAL* 1.3 54.3 + - - +
559B LYS* 2.9 8.0 + - - +
560B LEU* 2.7 54.9 + - + +
557C VAL* 4.1 25.2 - - + +
561C GLN* 4.4 4.9 + - - +
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Residues in contact with VAL 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B THR 4.2 1.6 - - - +
554B ARG* 3.4 47.8 + - - +
555B ASP 3.4 0.6 - - - -
556B GLN* 1.3 78.1 - - - +
558B LYS* 1.3 59.0 + - + +
560B LEU* 3.7 6.7 - - - +
561B GLN* 3.2 54.7 + - - +
553C THR 4.5 2.5 - - - +
556C GLN* 4.1 20.2 - - + +
557C VAL* 3.4 28.0 - - + +
560C LEU* 3.7 7.7 - - + +
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Residues in contact with LYS 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B ARG* 2.9 25.8 + - + +
555B ASP* 3.2 26.0 + - - +
557B VAL* 1.3 78.7 - - + +
559B LYS* 1.3 61.3 + - + +
561B GLN* 3.8 15.2 + - - +
562B LEU* 3.4 19.2 + - - +
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Residues in contact with LYS 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ASP* 3.2 18.1 + - - +
556B GLN* 2.9 6.5 + - - +
558B LYS* 1.3 78.7 - - + +
560B LEU* 1.3 59.7 + - + +
561B GLN 3.2 0.2 - - - -
562B LEU* 3.2 13.0 + - + +
563B MET* 2.8 50.1 + - + +
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Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B GLN* 2.7 45.3 + - - +
557B VAL* 3.7 5.8 - - - +
559B LYS* 1.3 72.7 - - - +
561B GLN* 1.3 56.4 + - - +
563B MET* 3.5 9.0 + - - +
564B LEU* 2.9 30.7 + - - +
557C VAL* 4.3 24.0 - - + +
560C LEU* 4.0 31.9 - - + +
561C GLN* 4.3 16.4 - - + -
564C LEU* 3.7 31.6 - - + +
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Residues in contact with GLN 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B VAL* 3.2 40.8 + - - +
558B LYS* 3.8 14.4 - - - +
560B LEU* 1.3 72.5 - - - +
562B LEU* 1.3 60.5 + - - +
564B LEU* 3.4 7.5 + - - +
565B ARG* 2.9 30.5 + - - +
556C GLN* 5.0 4.0 + - - -
560C LEU* 3.7 21.1 - - + +
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B LYS 3.4 12.3 + - - +
559B LYS* 3.2 17.4 + - + +
561B GLN* 1.3 79.1 - - - +
563B MET* 1.3 59.7 + - + +
565B ARG* 3.4 17.4 + - + +
566B GLN* 3.0 60.3 + - + +
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Residues in contact with MET 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LYS* 2.8 42.8 + - + +
560B LEU* 3.8 7.9 - - - +
562B LEU* 1.3 74.9 - - + +
564B LEU* 1.3 59.8 + - - +
566B GLN* 3.8 11.5 - - - +
567B ALA* 2.9 30.3 + - - +
564C LEU* 3.7 27.7 - - + +
568C ASN* 6.3 0.9 - - - +
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Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B LEU 2.9 19.0 + - - +
561B GLN* 3.6 5.8 - - - +
562B LEU 3.3 0.2 - - - -
563B MET* 1.3 74.3 - - - +
565B ARG* 1.3 64.8 + - - +
567B ALA* 3.3 4.1 + - - +
568B ASN* 3.0 40.1 + - - +
560C LEU* 3.9 25.8 - - + -
563C MET* 3.5 51.8 - - + +
564C LEU* 3.6 14.7 - - + +
567C ALA* 3.9 11.2 - - + -
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Residues in contact with ARG 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B GLN 2.9 17.8 + - - +
562B LEU* 3.7 17.8 - - - +
564B LEU* 1.3 75.7 - - - +
566B GLN* 1.3 66.6 + - + +
568B ASN* 3.0 19.5 + - + +
569B ASP* 2.8 35.2 + - - +
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Residues in contact with GLN 566 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B LEU* 3.0 45.7 + - + +
563B MET* 3.8 10.8 - - - +
565B ARG* 1.3 80.5 - - + +
567B ALA* 1.3 62.5 + - - +
569B ASP* 2.9 21.5 - - - +
570B GLN* 3.2 18.1 - - - +
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Residues in contact with ALA 567 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B MET 2.9 19.1 + - - +
564B LEU* 3.6 6.5 - - - +
566B GLN* 1.3 76.9 - - - +
568B ASN* 1.3 57.5 + - - +
570B GLN* 4.0 6.8 - - - +
571B LEU* 3.0 30.0 + - - +
564C LEU* 4.8 1.8 - - + -
567C ALA* 4.2 23.3 - - + -
568C ASN* 4.2 15.3 - - - +
571C LEU* 4.6 11.3 - - + +
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Residues in contact with ASN 568 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B LEU* 3.0 38.3 + - - +
565B ARG* 3.0 12.7 + - + +
567B ALA* 1.3 75.6 - - - +
569B ASP* 1.3 61.0 + - - +
571B LEU* 3.2 13.2 + - - +
572B GLU* 3.0 28.1 + - - +
567C ALA* 4.1 15.6 - - - +
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Residues in contact with ASP 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B ARG* 2.8 39.8 + - - +
566B GLN* 2.9 28.1 - - - +
568B ASN* 1.3 76.4 - - - +
570B GLN* 1.3 58.7 + - - +
572B GLU* 3.4 8.3 + - - +
573B LYS* 3.1 27.5 + - - +
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Residues in contact with GLN 570 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B GLN 3.2 20.1 + - - +
567B ALA* 4.0 2.2 - - - +
569B ASP* 1.3 78.0 + - - +
571B LEU* 1.3 60.2 + - - +
573B LYS* 3.2 22.1 + - - +
574B THR* 2.9 32.2 + - - -
571C LEU* 4.1 25.8 - - + +
575C MET* 5.5 6.3 - - - -
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Residues in contact with LEU 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B ALA 3.0 21.4 + - - +
568B ASN* 3.2 14.8 + - - +
570B GLN* 1.3 74.7 - - - +
572B GLU* 1.3 60.0 + - - +
574B THR* 2.9 5.5 + - - -
575B MET* 2.9 42.3 + - + +
567C ALA* 4.4 8.3 - - - +
570C GLN* 3.7 23.1 - - + -
571C LEU* 3.6 31.2 - - + +
574C THR* 3.3 31.4 - - - +
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Residues in contact with GLU 572 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ASN 3.0 12.9 + - - +
569B ASP* 3.7 11.2 - - - +
571B LEU* 1.3 76.6 - - - +
573B LYS* 1.3 58.2 + - - +
575B MET* 3.1 22.3 + - - +
576B LYS* 3.0 38.1 + - - +
579B GLN* 5.6 1.9 + - - -
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Residues in contact with LYS 573 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B ASP 3.1 14.1 + - - +
570B GLN* 3.3 24.5 - - - +
571B LEU 3.1 0.2 - - - -
572B GLU* 1.3 76.9 - - - +
574B THR* 1.3 59.3 + - - +
576B LYS* 3.1 39.8 - - - +
577B ASP* 2.8 30.0 - - - +
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Residues in contact with THR 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B GLN* 2.9 21.4 + - - -
571B LEU 2.9 9.5 + - - -
573B LYS* 1.3 75.5 - - - +
575B MET* 1.3 57.8 + - - +
577B ASP* 3.5 9.5 - - - +
578B LYS* 3.0 24.8 + - - +
571C LEU* 3.5 16.1 - - - +
574C THR* 3.8 21.1 - - + +
575C MET* 3.9 30.7 - - + +
578C LYS* 4.4 15.2 - - + +
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Residues in contact with MET 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B LEU* 2.9 35.2 + - + +
572B GLU* 3.1 29.1 + - - +
574B THR* 1.3 75.7 - - - +
576B LYS* 1.3 59.8 + - - +
577B ASP 3.1 1.3 - - - -
578B LYS* 3.2 6.9 + - + +
579B GLN* 2.8 52.9 + - - +
570C GLN* 4.5 11.4 - - + +
574C THR* 3.9 20.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B GLU* 3.0 17.8 + - - +
573B LYS* 3.1 52.4 - - - +
575B MET* 1.3 75.0 - - - +
577B ASP* 1.3 75.7 + - - +
579B GLN* 3.6 7.5 - - - +
580B GLU* 3.2 38.0 + - - +
----------------------------------------------------------
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Residues in contact with ASP 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B LYS* 2.8 21.0 - - - +
574B THR* 3.5 9.8 - - - +
575B MET 3.1 0.4 - - - -
576B LYS* 1.3 95.3 + - - +
578B LYS* 1.3 65.7 + - - +
580B GLU* 3.4 7.4 + - - +
581B LEU* 3.1 26.6 + - + +
578C LYS* 3.7 31.2 + - + -
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Residues in contact with LYS 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B THR 3.0 17.8 + - - +
575B MET* 3.2 8.7 + - + +
577B ASP* 1.3 74.3 - - - +
579B GLN* 1.3 71.2 + - - +
581B LEU* 3.2 6.1 + - - +
582B GLU* 3.0 47.5 + - - +
573C LYS* 4.9 1.6 - - - +
574C THR* 4.2 17.1 - - + +
577C ASP* 3.2 40.1 + - + -
578C LYS* 4.4 12.0 - - + +
581C LEU* 3.5 18.6 - - + +
----------------------------------------------------------
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Residues in contact with GLN 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B GLU* 5.6 1.8 + - - -
575B MET* 2.8 50.1 + - - +
576B LYS* 3.6 9.8 - - - +
578B LYS* 1.3 85.6 - - - +
580B GLU* 1.3 53.0 + - + +
582B GLU* 3.0 20.9 + - - +
583B ASP* 2.8 44.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B LYS* 3.2 23.7 + - + +
577B ASP* 4.1 5.8 - - - +
578B LYS 3.4 0.2 - - - -
579B GLN* 1.3 78.6 - - + +
581B LEU* 1.3 60.5 + - - +
583B ASP* 3.7 13.5 - - + +
584B PHE* 2.8 30.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B ASP* 3.1 13.1 + - + +
578B LYS 3.4 9.2 - - - +
580B GLU* 1.3 77.7 - - - +
582B GLU* 1.3 56.0 + - - +
584B PHE* 3.7 3.6 - - + +
585B ILE* 3.0 37.5 + - - +
601B LEU* 5.1 10.1 - - + -
578C LYS* 3.5 44.2 - - + +
581C LEU* 3.7 15.9 - - + -
582C GLU* 3.5 21.1 - - + +
585C ILE* 3.7 27.8 - - + -
----------------------------------------------------------
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Residues in contact with GLU 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B LYS* 3.0 44.9 + - - +
579B GLN* 3.2 21.5 - - - +
581B LEU* 1.3 73.9 - - - +
583B ASP* 1.3 61.1 + - - +
585B ILE* 3.1 7.3 + - - -
586B LYS* 2.9 46.8 + - + +
581C LEU* 3.7 17.5 - - + +
----------------------------------------------------------
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Residues in contact with ASP 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B GLN* 2.8 32.7 + - - +
580B GLU* 3.5 13.8 + - + +
582B GLU* 1.3 74.1 - - - +
584B PHE* 1.3 57.6 + - - +
586B LYS* 3.1 34.5 + - - +
587B GLN* 4.3 6.4 + - - -
----------------------------------------------------------
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Residues in contact with PHE 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B GLU 2.8 19.7 + - - +
581B LEU* 3.7 5.4 - - + +
583B ASP* 1.3 75.7 - - - +
585B ILE* 1.3 65.2 + - - +
587B GLN* 3.2 34.1 - - - +
594B HIS* 3.4 48.9 - + - -
597B SER* 4.1 13.2 - - - -
598B ALA* 4.0 16.4 - - + -
601B LEU* 3.8 29.8 - - + -
585C ILE* 3.6 29.4 - - + -
----------------------------------------------------------
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Residues in contact with ILE 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LEU 3.0 22.8 + - - +
582B GLU* 3.7 4.5 - - - +
584B PHE* 1.3 77.0 - - + +
586B LYS* 1.3 62.6 + - + +
587B GLN 3.1 14.9 + - - +
589B SER* 5.6 1.6 - - - -
594B HIS* 4.9 3.4 - - - -
581C LEU* 3.7 48.2 - - + +
584C PHE* 3.7 33.4 - - + -
585C ILE* 3.8 21.3 - - + -
----------------------------------------------------------
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Residues in contact with LYS 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B GLU* 2.9 30.9 + - + +
583B ASP* 3.1 24.0 + - - +
585B ILE* 1.3 77.5 - - + +
587B GLN* 1.3 65.4 + - - +
----------------------------------------------------------
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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