Contacts of the helix formed by residues 599 - 626 (chain A) in PDB entry 3KUT
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 SER 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A HIS* 3.0 27.9 + - - -
596A MET 3.2 9.2 + - - +
598A GLU* 1.3 80.6 - - - +
600A PRO* 1.3 67.2 - - - +
601A GLU* 3.3 3.7 + - - +
602A SER* 2.8 31.2 + - - -
603A LEU 3.0 17.0 + - - -
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Residues in contact with PRO 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A MET 4.4 0.6 - - - +
597A LEU 5.7 0.4 - - - +
598A GLU 3.6 7.9 - - - +
599A SER* 1.3 85.7 - - - +
601A GLU* 1.3 58.0 + - + +
603A LEU* 3.3 8.9 + - + +
604A ARG* 2.8 30.8 + - - +
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Residues in contact with GLU 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A SER* 3.3 4.8 + - - +
600A PRO* 1.3 79.0 - - + +
602A SER* 1.3 58.5 + - - +
604A ARG* 3.3 12.6 + - - +
605A SER* 2.9 29.5 + - - -
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Residues in contact with SER 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A HIS* 2.8 29.3 - - - -
596A MET* 4.2 9.7 - - - +
599A SER* 2.8 27.6 + - - -
601A GLU* 1.3 76.2 - - - +
603A LEU* 1.3 66.5 + - - +
605A SER* 3.3 6.5 + - - -
606A LYS* 3.0 24.8 + - - +
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Residues in contact with LEU 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A LEU* 3.9 23.6 - - + -
569A LEU* 3.9 38.8 - - + -
570A ILE* 4.4 5.2 - - + -
573A MET* 4.3 11.0 - - - -
585A LEU* 3.8 26.9 - - + -
596A MET* 3.8 30.6 - - + +
599A SER 3.0 6.6 + - - +
600A PRO* 3.7 10.3 - - + +
602A SER* 1.3 76.0 - - - +
604A ARG* 1.3 57.8 + - - +
606A LYS* 3.2 1.7 + - - -
607A VAL* 2.8 44.0 + - + +
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Residues in contact with ARG 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A MET* 3.7 23.5 - - + +
600A PRO 2.8 18.7 + - - +
601A GLU* 3.6 14.6 - - - +
603A LEU* 1.3 77.6 - - - +
605A SER* 1.3 57.1 + - - +
607A VAL* 3.9 0.9 - - - +
608A ASP* 2.9 65.5 + - - +
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Residues in contact with SER 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A GLU 2.9 16.9 + - - -
602A SER* 3.7 6.7 - - - -
603A LEU 3.3 0.2 - - - -
604A ARG* 1.3 76.9 - - - +
606A LYS* 1.3 63.3 + - - +
608A ASP* 3.4 9.8 + - - +
609A GLU* 3.1 24.0 + - - +
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Residues in contact with LYS 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A LEU* 3.9 14.4 - - + -
588A ILE* 3.7 29.0 - - + +
592A GLU* 3.7 23.2 + - - -
596A MET* 3.9 13.7 - - - -
602A SER 3.0 16.7 + - - +
603A LEU 3.8 2.7 - - - +
605A SER* 1.3 73.5 - - - +
607A VAL* 1.3 62.2 + - - +
609A GLU* 3.3 27.1 + - - +
610A ALA* 2.9 27.5 + - - +
110C ASN 5.6 5.5 - - - +
111C LEU* 4.0 13.0 - - + +
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Residues in contact with VAL 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A ILE* 3.9 20.9 - - + -
573A MET* 3.7 25.8 - - + -
574A HIS* 3.5 33.2 - - + +
581A ILE* 4.2 10.8 - - + -
585A LEU* 3.9 19.3 - - + -
603A LEU* 2.8 22.9 + - + +
604A ARG 4.8 0.2 - - - +
606A LYS* 1.3 73.9 - - - +
608A ASP* 1.3 65.8 + - - +
610A ALA* 3.2 6.8 + - - +
611A VAL* 2.9 25.7 + - + +
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Residues in contact with ASP 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A HIS* 4.6 10.9 + - - -
604A ARG* 2.9 58.8 + - - +
605A SER* 3.6 8.0 - - - +
607A VAL* 1.3 77.0 - - - +
609A GLU* 1.3 61.9 + - - +
611A VAL* 3.5 6.1 + - - +
612A ALA* 3.1 23.2 + - - +
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Residues in contact with GLU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A SER* 3.1 15.4 + - - +
606A LYS* 3.4 32.4 + - - +
608A ASP* 1.3 77.2 - - - +
610A ALA* 1.3 62.3 + - - +
612A ALA* 3.2 6.1 + - - +
613A VAL* 2.9 36.8 + - + +
110C ASN* 5.2 5.9 + - - -
111C LEU* 3.7 23.8 + - + +
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Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A ILE* 3.8 18.2 - - + -
584A MET* 3.6 14.7 - - + +
585A LEU* 3.7 23.6 - - + -
606A LYS 2.9 16.7 + - - +
607A VAL 3.7 4.5 - - - +
609A GLU* 1.3 76.0 - - - +
611A VAL* 1.3 56.4 + - - +
613A VAL* 4.5 0.4 - - - -
614A LEU* 2.8 32.7 + - - +
111C LEU* 3.5 14.1 - - + +
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Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A HIS* 3.8 41.1 - - + +
577A LEU* 4.1 18.8 - - + +
581A ILE* 3.8 19.5 - - + -
607A VAL* 2.9 22.8 + - + +
608A ASP* 3.9 5.8 - - - +
610A ALA* 1.3 76.0 - - - +
612A ALA* 1.3 60.0 + - - +
614A LEU* 3.9 2.1 - - - +
615A GLN* 2.9 33.8 + - + +
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Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A ASP 3.1 17.4 + - - +
609A GLU* 3.2 6.5 + - - +
611A VAL* 1.3 76.6 - - - +
613A VAL* 1.3 64.2 + - + +
615A GLN* 3.9 5.3 - - - +
616A ALA* 3.1 26.5 + - - +
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Residues in contact with VAL 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A MET* 4.1 8.7 - - + -
609A GLU* 2.9 32.6 + - + +
610A ALA* 3.8 3.4 - - - +
612A ALA* 1.3 75.7 - - + +
614A LEU* 1.3 64.0 + - - +
616A ALA* 3.5 4.4 + - - +
617A HIS* 3.0 23.6 + - - +
111C LEU* 4.0 16.8 - - + +
113C PRO* 3.9 28.5 - - + -
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Residues in contact with LEU 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A LEU* 4.2 24.0 - - + -
580A LYS* 3.7 39.9 - - + -
581A ILE* 3.9 17.5 - - + -
584A MET* 4.1 8.0 - - - +
610A ALA 2.8 21.0 + - - +
611A VAL 3.9 2.9 - - - +
613A VAL* 1.3 74.6 - - - +
615A GLN* 1.3 57.1 + - - +
617A HIS* 3.2 3.6 + - - +
618A GLN* 2.9 60.4 + - + +
113C PRO* 3.8 27.8 - - + +
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Residues in contact with GLN 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A VAL* 2.9 22.9 + - + +
612A ALA* 3.9 5.7 - - - +
614A LEU* 1.3 75.9 - - - +
616A ALA* 1.3 68.9 + - - +
618A GLN* 3.4 9.6 + - - +
619A ALA* 2.9 43.4 + - - +
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Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A ALA 3.1 15.6 + - - +
613A VAL* 4.0 4.7 - - - +
615A GLN* 1.3 89.4 + - - +
617A HIS* 1.3 58.6 + - - +
619A ALA* 4.2 2.6 - - - +
620A LYS* 2.9 32.9 + - - +
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Residues in contact with HIS 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A VAL 3.0 17.7 + - - +
614A LEU* 3.2 4.2 + - - +
616A ALA* 1.3 78.0 - - - +
618A GLN* 1.3 70.5 + - - +
620A LYS* 3.9 3.6 - - + +
621A GLU* 3.0 66.9 + - + +
113C PRO* 3.6 34.0 + - + +
114C ASN* 3.1 37.7 + - - -
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Residues in contact with GLN 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A LEU* 5.1 7.4 - - - +
580A LYS* 5.7 3.8 - - - +
614A LEU* 2.9 50.7 + - + +
615A GLN* 3.9 6.9 - - - +
617A HIS* 1.3 81.9 - - - +
619A ALA* 1.3 57.6 + - - +
621A GLU* 3.9 5.1 - - - +
622A ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A GLN* 2.9 36.8 + - - +
616A ALA* 4.2 2.9 - - - +
618A GLN* 1.3 75.1 - - - +
620A LYS* 1.3 61.5 + - - +
622A ALA* 3.9 5.3 - - - +
623A ALA* 2.9 30.3 + - - +
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Residues in contact with LYS 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A ALA 2.9 20.5 + - - +
617A HIS* 3.9 4.7 - - - +
619A ALA* 1.3 77.4 - - - +
621A GLU* 1.3 58.4 + - + +
623A ALA* 3.3 9.3 + - + +
624A GLN* 2.9 64.9 + - + +
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Residues in contact with GLU 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A HIS* 3.0 53.0 + - + +
618A GLN* 3.9 4.8 - - - +
620A LYS* 1.3 77.0 - - + +
622A ALA* 1.3 61.8 + - - +
624A GLN* 3.4 16.9 + - - +
625A LYS* 3.3 30.8 + - + +
114C ASN* 4.9 1.2 + - - +
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Residues in contact with ALA 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A GLN 3.0 19.1 + - - +
619A ALA* 3.9 5.8 - - - +
621A GLU* 1.3 77.9 - - - +
623A ALA* 1.3 57.1 + - - +
625A LYS* 3.2 6.8 + - - +
626A ALA* 2.9 30.3 + - - +
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Residues in contact with ALA 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A ALA 2.9 18.5 + - - +
620A LYS* 3.3 12.3 + - + +
622A ALA* 1.3 75.8 - - - +
624A GLN* 1.3 62.0 + - - +
625A LYS 3.4 0.2 + - - -
626A ALA* 3.4 19.8 + - - +
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Residues in contact with GLN 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A LYS* 2.9 45.9 + - - +
621A GLU* 3.6 16.8 - - - +
622A ALA 3.3 0.4 - - - -
623A ALA* 1.3 76.2 - - - +
625A LYS* 1.3 62.5 + - + +
626A ALA 4.5 1.9 - - - +
110D ASN* 3.0 32.8 + - - +
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Residues in contact with LYS 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A GLU* 3.3 17.0 + - + +
622A ALA* 3.2 5.8 + - - +
624A GLN* 1.3 78.9 - - + +
626A ALA* 1.3 65.3 + - - +
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Residues in contact with ALA 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A ALA 2.9 16.5 + - - +
623A ALA* 3.4 17.4 + - - +
624A GLN 4.5 2.6 - - - +
625A LYS* 1.3 82.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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