Contacts of the helix formed by residues 646 - 674 (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 ILE 646 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A LEU* 3.6 27.8 - - + +
598A GLU* 4.7 2.0 - - - +
600A TYR* 3.8 22.2 - - + -
601A THR* 3.1 28.0 - - - +
606A GLU* 5.8 3.6 - - + -
609A LEU* 3.2 32.3 - - + -
639A LEU* 4.5 9.0 - - + +
644A PHE* 2.9 12.7 + - + -
645A THR* 1.3 83.8 - - - +
647A PHE* 1.3 66.5 + - - +
648A ASN 3.2 1.3 - - - -
649A ARG* 3.0 19.2 + - + +
650A VAL* 3.3 18.4 + - + +
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Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A LEU 4.6 7.8 + - - -
640A CYS* 3.7 22.1 - - + +
641A ASN 3.5 14.6 + - - +
642A GLU* 3.3 58.8 - - + -
644A PHE 3.1 10.2 + - - +
645A THR 3.3 0.2 - - - -
646A ILE* 1.3 76.7 - - - +
648A ASN* 1.3 74.1 + - - +
650A VAL* 3.0 4.0 + - - +
651A ASP* 2.7 66.4 + - + +
654A ARG* 4.1 13.7 - - - -
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Residues in contact with ASN 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A GLU* 5.6 2.0 + - - +
644A PHE 4.9 0.5 - - - +
645A THR* 3.6 16.4 - - - +
646A ILE 3.1 0.6 + - - -
647A PHE* 1.3 93.9 - - - +
649A ARG* 1.3 61.6 + - - +
651A ASP* 4.0 3.4 - - - +
652A ILE* 3.2 31.5 + - + +
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Residues in contact with ARG 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A GLU* 3.5 35.5 + - - +
609A LEU* 3.7 25.7 - - + +
610A ASP* 2.6 49.8 + - - +
613A LEU* 4.7 3.1 - - + +
645A THR 5.0 1.2 + - - +
646A ILE* 3.0 13.5 + - + +
648A ASN* 1.3 80.6 - - - +
650A VAL* 1.3 62.4 + - + +
652A ILE* 3.5 18.7 + - - +
653A SER* 3.4 8.7 + - - -
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Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A LEU* 4.6 3.6 - - + -
613A LEU* 3.7 33.0 - - + -
636A TYR* 3.8 11.9 - - + -
639A LEU* 3.7 25.8 - - + +
640A CYS* 3.5 22.4 - - - -
646A ILE* 3.5 32.1 - - + +
647A PHE 3.0 4.4 + - - +
649A ARG* 1.3 74.2 - - - +
651A ASP* 1.3 61.9 + - - +
653A SER* 2.5 20.5 + - - -
654A ARG* 2.8 15.9 + - - +
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Residues in contact with ASP 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A CYS* 4.2 4.7 - - - -
647A PHE* 2.7 50.2 + - + +
648A ASN* 4.0 5.6 - - - +
649A ARG 3.4 0.2 - - - -
650A VAL* 1.3 72.1 - - - +
652A ILE* 1.3 57.9 + - + +
654A ARG* 3.3 29.4 + - - +
655A SER* 2.8 33.9 + - - -
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Residues in contact with ILE 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ASN* 3.2 19.9 + - + +
649A ARG* 3.6 10.8 - - - +
650A VAL 3.1 0.6 - - - -
651A ASP* 1.3 78.3 - - + +
653A SER* 1.3 57.6 + - - +
655A SER* 3.3 6.5 + - - -
656A GLN* 2.9 61.7 + - + +
----------------------------------------------------------
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Residues in contact with SER 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 3.7 18.1 - - - +
617A ARG* 3.3 29.0 + - - +
636A TYR* 3.7 15.2 - - - -
649A ARG 3.4 4.0 + - - -
650A VAL* 2.5 33.4 + - - +
652A ILE* 1.3 74.5 - - - +
654A ARG* 1.3 59.0 + - - +
656A GLN* 3.7 1.8 - - - +
657A LEU* 2.8 32.1 + - - +
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Residues in contact with ARG 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A TYR* 3.9 20.5 - - + -
637A HIS* 5.3 3.8 - - - +
640A CYS* 3.5 31.6 + - - +
647A PHE* 4.1 15.4 - - - -
650A VAL 2.8 15.0 + - - +
651A ASP* 3.3 28.6 + - - +
653A SER* 1.3 76.2 + - - +
655A SER* 1.3 63.8 + - - +
656A GLN 3.0 1.4 + - - -
657A LEU* 3.9 3.6 - - - +
658A ILE* 3.3 40.2 + - + +
697A PHE* 5.8 2.5 - - + -
701A HIS* 3.2 45.7 + - + +
702A ASP 5.7 1.3 - - - +
703A LEU* 5.6 1.6 - - + -
706A TRP* 6.2 0.7 - - + -
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Residues in contact with SER 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A ASP* 2.8 28.3 + - - -
652A ILE* 3.6 7.2 - - - -
654A ARG* 1.3 74.2 - - - +
656A GLN* 1.3 57.6 + - - +
658A ILE 4.3 0.9 - - - -
659A ASP* 3.0 31.5 + - - +
705A LYS* 4.3 14.0 + - - -
706A TRP* 3.7 22.5 - - - -
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Residues in contact with GLN 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ARG* 3.2 29.2 - - - +
652A ILE* 2.9 43.3 + - + +
653A SER* 3.7 3.6 - - - +
655A SER* 1.3 80.0 - - - +
657A LEU* 1.3 65.6 + - - +
658A ILE 3.2 1.9 + - - -
659A ASP* 3.4 18.1 + - - +
660A GLU* 3.4 20.6 + - - +
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ARG* 3.9 31.5 - - + +
620A VAL* 4.3 20.0 - - + -
621A GLU* 4.4 21.3 - - + +
636A TYR* 4.2 15.9 - - + -
653A SER 2.8 17.9 + - - +
654A ARG* 3.3 5.1 + - - +
656A GLN* 1.3 76.4 - - - +
658A ILE* 1.3 61.7 + - + +
660A GLU* 3.3 10.9 - - - +
661A LEU* 3.2 29.7 + - + +
697A PHE* 3.7 39.5 - - + -
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Residues in contact with ILE 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ARG* 3.3 30.6 + - + +
656A GLN 3.2 0.6 - - - -
657A LEU* 1.3 82.3 - - + +
659A ASP* 1.3 61.0 + - - +
660A GLU 3.1 1.6 - - - -
661A LEU* 4.2 13.5 - - + +
662A ALA* 2.9 31.5 + - + +
694A ILE* 6.1 3.1 - - + -
697A PHE* 4.5 20.2 - - + -
701A HIS* 5.0 0.2 - - + -
703A LEU* 3.2 49.6 - - + -
706A TRP* 3.6 32.5 - - + +
708A LEU* 6.0 1.6 - - + -
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Residues in contact with ASP 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A SER* 3.0 21.6 + - - +
656A GLN* 3.4 15.2 + - - +
658A ILE* 1.3 77.5 - - - +
660A GLU* 1.3 63.0 + - + +
662A ALA* 4.1 0.2 - - - +
663A ASP* 2.8 35.0 + - - +
706A TRP* 3.0 28.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ARG* 4.3 15.4 + - - -
621A GLU* 3.0 29.4 - - - +
656A GLN* 3.4 16.5 - - - +
657A LEU* 3.3 15.4 - - - +
658A ILE 3.1 0.4 - - - -
659A ASP* 1.3 78.8 - - + +
661A LEU* 1.3 56.8 + - + +
663A ASP* 3.9 3.6 - - - +
664A LYS* 3.0 30.7 + - - +
667A ARG* 5.3 0.5 + - - -
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Residues in contact with LEU 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A VAL* 4.4 13.0 - - + -
621A GLU* 5.3 8.7 - - + +
657A LEU* 3.2 25.2 + - + +
658A ILE* 3.2 15.5 + - + +
660A GLU* 1.3 80.1 - - + +
662A ALA* 1.3 56.6 + - - +
664A LYS* 3.4 7.5 + - + +
665A PHE* 2.9 30.5 + - - +
690A THR* 4.0 16.4 - - + +
693A ARG* 3.9 54.7 - - + +
694A ILE* 3.6 16.8 - - + +
697A PHE* 4.7 6.7 - - + -
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Residues in contact with ALA 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ILE* 2.9 11.2 + - + +
659A ASP 4.1 1.8 - - - +
661A LEU* 1.3 76.8 - - - +
663A ASP* 1.3 62.4 + - - +
665A PHE* 3.1 2.6 + - - +
666A ASN* 2.9 42.5 + - - +
694A ILE* 4.0 13.6 - - + +
706A TRP* 3.4 37.7 - - + +
708A LEU* 5.3 4.7 - - + -
----------------------------------------------------------
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Residues in contact with ASP 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A ASP* 2.8 27.9 + - - +
660A GLU* 3.9 4.3 - - - +
662A ALA* 1.3 77.8 - - - +
664A LYS* 1.3 66.2 + - - +
666A ASN* 3.4 11.2 + - - +
667A ARG* 3.2 42.1 + - - +
706A TRP* 5.5 1.0 - - - -
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Residues in contact with LYS 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A GLU 3.0 18.8 + - - +
661A LEU* 3.7 7.2 - - + +
663A ASP* 1.3 76.5 - - - +
665A PHE* 1.3 62.5 - - - +
667A ARG* 3.5 28.8 + - - +
668A LEU* 3.1 42.3 + - + +
686A GLN* 3.9 18.3 + - - -
690A THR* 3.4 31.6 - - + +
693A ARG* 5.4 4.9 - - - +
----------------------------------------------------------
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Residues in contact with PHE 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A LEU 2.9 18.2 + - - +
662A ALA* 3.4 6.1 - - - +
664A LYS* 1.3 75.7 - - - +
666A ASN* 1.3 62.2 + - - +
668A LEU* 3.4 5.0 + - + +
669A LEU* 3.0 42.2 + - + +
687A VAL* 4.1 17.9 - - + -
690A THR* 3.9 19.3 - - + -
691A LEU* 3.8 43.1 - - + -
694A ILE* 3.7 24.9 - - + -
708A LEU* 5.6 5.2 - - + -
711A CYS* 4.1 27.4 - - + -
712A ASN* 4.4 15.0 - - - -
715A LEU* 4.4 7.4 - - + -
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Residues in contact with ASN 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ALA* 2.9 29.5 + - - +
663A ASP* 3.8 11.5 + - - +
665A PHE* 1.3 79.0 - - - +
667A ARG* 1.3 63.5 + - + +
669A LEU* 3.4 8.3 + - - +
670A GLU* 3.2 31.5 + - - +
711A CYS* 3.5 27.7 - - - -
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Residues in contact with ARG 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A GLU 5.3 0.4 + - - -
663A ASP* 3.2 20.9 + - - +
664A LYS* 3.9 43.7 - - - +
666A ASN* 1.3 75.2 - - + +
668A LEU* 1.3 66.7 + - - +
670A GLU* 3.2 32.0 + - - +
671A ASP* 3.7 7.1 + - - +
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A LYS* 3.1 41.0 + - + +
665A PHE* 3.8 6.3 - - + +
667A ARG* 1.3 78.2 - - + +
669A LEU* 1.3 58.6 + - + +
670A GLU 3.2 0.2 + - - -
671A ASP* 3.6 4.1 + - - +
672A PHE* 3.1 30.1 + - - +
683A ASP 5.4 0.4 - - - +
686A GLN* 3.9 40.6 - - + +
687A VAL* 4.5 14.3 - - + +
690A THR* 3.4 31.0 - - + +
----------------------------------------------------------
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Residues in contact with LEU 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A PHE* 3.0 34.9 + - + +
666A ASN* 3.7 7.6 - - - +
667A ARG 3.2 0.2 - - - -
668A LEU* 1.3 74.5 - - + +
670A GLU* 1.3 60.7 + - - +
672A PHE* 3.9 17.5 - - + -
673A LEU* 3.1 43.4 + - + +
687A VAL* 4.0 27.4 - - + -
711A CYS* 3.5 46.0 - - + +
714A LYS* 5.8 0.9 - - + -
715A LEU* 4.3 13.2 - - + -
----------------------------------------------------------
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Residues in contact with GLU 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ASN* 3.2 20.8 + - - +
667A ARG* 3.5 25.1 - - - +
668A LEU 3.1 1.0 - - - -
669A LEU* 1.3 77.4 - - - +
671A ASP* 1.3 66.0 + - - +
672A PHE 3.1 1.8 + - - -
673A LEU* 3.7 7.2 + - - +
674A GLN* 3.8 16.1 + - - +
----------------------------------------------------------
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Residues in contact with ASP 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A ARG 3.7 5.4 + - - +
668A LEU* 3.6 7.2 + - - +
670A GLU* 1.3 78.6 - - - +
672A PHE* 1.3 60.9 + - - +
674A GLN* 3.6 35.3 + - - +
676A GLY* 4.4 10.6 - - - -
677A GLU* 4.9 14.6 + - - +
679A PRO* 5.7 2.1 - - - +
683A ASP* 5.0 7.1 - - - +
----------------------------------------------------------
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Residues in contact with PHE 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LEU 3.1 19.9 + - - +
669A LEU* 4.0 17.7 - - + -
670A GLU 3.1 1.0 - - - -
671A ASP* 1.3 79.1 - - - +
673A LEU* 1.3 68.1 + - + +
674A GLN 3.6 2.0 - - - +
679A PRO* 3.6 48.2 - - + +
683A ASP* 4.0 15.5 - - + -
684A ALA* 4.1 11.0 - - + -
687A VAL* 3.7 28.7 - - + -
715A LEU* 4.1 20.6 - - + -
725A MSE 4.2 17.7 - - + -
726A PRO* 5.5 2.7 - - + -
729A ILE* 4.2 16.2 - - + -
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Residues in contact with LEU 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A LEU* 3.1 33.7 + - + +
670A GLU 3.7 2.4 + - - +
671A ASP 3.5 0.2 - - - -
672A PHE* 1.3 89.0 - - + +
674A GLN* 1.3 68.5 + - - +
714A LYS* 3.7 52.9 - - + +
715A LEU* 4.9 2.9 - - + -
718A THR* 4.2 21.4 + - + +
----------------------------------------------------------
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Residues in contact with GLN 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A GLU 3.8 14.1 + - - +
671A ASP* 3.6 35.7 + - - +
672A PHE 3.8 7.8 - - - +
673A LEU* 1.3 84.7 - - - +
675A GLU* 1.3 70.3 + - - +
676A GLY* 3.7 14.5 - - - +
679A PRO* 4.5 4.0 - - - +
----------------------------------------------------------
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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