Contacts of the helix formed by residues 636 - 659 (chain A) in PDB entry 1OMW
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 636 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ASN* 3.3 15.7 + - - -
183A ASN* 3.4 28.7 - - - -
634A CYS* 3.3 4.2 + - - +
635A ASP* 1.3 77.8 - - - +
637A ASP* 1.3 66.5 + - - +
638A PRO* 3.1 14.7 - - - +
639A GLU* 2.3 38.9 + - - +
640A LEU* 3.1 10.2 + - - +
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Residues in contact with ASP 637 (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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182A LEU 4.4 7.6 - - - +
183A ASN* 3.2 4.5 + - - +
185A HIS* 3.0 38.9 + - - -
618A LYS* 4.9 22.3 + - - +
636A SER* 1.3 68.9 - - - +
638A PRO* 1.3 74.2 - - + +
640A LEU* 2.8 20.5 + - - +
641A VAL* 3.2 19.6 + - + +
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Residues in contact with PRO 638 (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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42A VAL* 4.8 2.2 - - - -
43A MET* 3.9 24.0 - - - -
46A TYR* 3.6 36.0 - - + +
179A ASN* 4.3 7.9 - - - +
182A LEU* 3.7 39.0 - - + +
183A ASN* 4.4 0.4 - - + -
636A SER* 3.1 17.0 - - - +
637A ASP* 1.3 93.9 - - + +
639A GLU* 1.3 60.9 + - - +
641A VAL* 3.5 0.9 + - + +
642A GLN* 3.2 19.2 + - - +
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Residues in contact with GLU 639 (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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39A ILE* 3.6 29.3 - - + +
42A VAL* 3.8 22.2 - - + -
179A ASN* 3.8 7.0 + - - +
564A TYR* 4.1 10.9 + - - +
634A CYS* 3.8 11.7 - - + -
635A ASP* 3.7 25.5 + - - +
636A SER* 2.3 54.4 + - - +
638A PRO* 1.3 73.4 - - - +
640A LEU* 1.3 69.4 + - - +
642A GLN* 3.4 1.0 + - - +
643A TRP* 3.0 28.7 + - + -
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Residues in contact with LEU 640 (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 GLU* 5.3 7.4 - - + -
618A LYS* 3.4 54.5 - - + +
619A CYS* 4.3 10.3 - - - +
620A LEU* 4.4 20.7 - - + +
633A GLN* 5.0 0.4 - - - -
634A CYS* 3.7 32.0 - - + +
636A SER 3.1 9.0 + - - +
637A ASP* 2.8 20.1 + - - +
639A GLU* 1.3 70.4 - - - +
641A VAL* 1.3 59.6 + - + +
643A TRP* 2.8 25.6 + - - +
644A LYS* 3.0 15.3 + - + +
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Residues in contact with VAL 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 4.2 12.8 - - + +
50A ARG* 4.0 25.4 - - - +
637A ASP* 3.4 19.7 - - + +
638A PRO 3.7 6.7 - - - +
640A LEU* 1.3 78.9 - - + +
642A GLN* 1.3 58.7 + - - +
644A LYS* 3.8 19.4 + - - +
645A LYS* 3.1 27.2 + - + +
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Residues in contact with GLN 642 (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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42A VAL* 3.8 26.7 - - + +
45A LYS* 3.8 7.1 - - + +
46A TYR* 3.4 26.9 - - + +
49A ASP* 2.6 30.4 + - - +
50A ARG* 4.4 4.5 + - - -
561A MET* 3.5 20.8 - - - +
638A PRO 3.2 13.7 + - - +
640A LEU 3.0 0.8 + - - -
641A VAL* 1.3 79.9 - - - +
643A TRP* 1.3 59.6 + - - +
645A LYS* 4.1 7.2 - - - +
646A GLU* 2.9 58.9 + - - +
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Residues in contact with TRP 643 (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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42A VAL* 4.1 14.1 - - + +
561A MET* 3.5 27.8 - - + -
562A HIS* 3.9 5.2 - - - -
563A GLY 3.7 31.5 + - - -
564A TYR 4.8 2.2 + - - -
565A MET* 3.4 44.2 - - + +
581A PHE* 3.9 15.5 - - + -
583A LEU* 3.6 35.4 - - + -
588A LEU* 4.1 11.9 - - + -
620A LEU* 4.1 6.3 - - + -
634A CYS* 4.0 9.0 - - + -
639A GLU* 3.0 30.6 + - + +
640A LEU 2.8 10.5 + - - +
642A GLN* 1.3 70.9 - - - +
644A LYS* 1.3 58.1 + - - +
647A LEU* 2.9 53.5 + - + +
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Residues in contact with LYS 644 (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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609A VAL* 4.8 5.2 - - + +
611A GLU* 3.9 26.6 + - + +
620A LEU* 3.7 31.6 - - + +
640A LEU* 3.0 14.6 + - + +
641A VAL* 3.9 17.6 - - - +
643A TRP* 1.3 74.9 - - - +
645A LYS* 1.3 66.4 + - - +
647A LEU* 4.2 2.6 - - - +
648A ARG* 3.2 54.7 + - - +
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Residues in contact with LYS 645 (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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49A ASP* 2.8 41.1 + - - +
641A VAL* 3.1 20.9 + - + +
642A GLN* 3.9 8.7 - - - +
643A TRP 3.3 0.4 - - - -
644A LYS* 1.3 80.4 - - - +
646A GLU* 1.3 74.3 + - - +
648A ARG* 3.2 6.1 + - - +
649A ASP* 3.0 50.9 + - - +
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Residues in contact with GLU 646 (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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45A LYS* 3.6 21.5 + - + +
49A ASP* 4.0 1.6 - - - +
560A ILE* 4.0 16.3 - - + +
561A MET* 3.8 25.1 - - + -
583A LEU* 3.7 12.9 - - + +
642A GLN* 2.9 47.9 + - - +
645A LYS* 1.3 93.8 + - - +
647A LEU* 1.4 57.0 + - - +
648A ARG 3.4 0.2 - - - -
649A ASP* 3.9 9.3 - - - +
650A ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 647 (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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583A LEU* 3.6 32.5 - - + -
588A LEU* 4.1 21.5 - - + -
603A MET* 4.1 11.6 - - + +
606A ILE* 5.0 3.9 - - + +
609A VAL* 4.3 14.5 - - + +
620A LEU* 4.4 18.4 - - + -
622A LEU* 4.2 24.2 - - + -
632A LEU* 4.5 5.4 - - + -
643A TRP* 2.9 33.6 + - + +
644A LYS* 4.2 2.9 - - - +
646A GLU* 1.4 76.6 - - - +
648A ARG* 1.3 62.7 + - - +
650A ALA* 4.0 1.6 - - - +
651A TYR* 3.2 28.1 + - - +
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Residues in contact with ARG 648 (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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609A VAL* 3.2 34.0 + - + +
610A GLU* 4.0 11.7 + - - -
611A GLU* 3.7 10.9 + - - -
644A LYS* 3.2 51.1 + - - +
645A LYS* 3.2 6.0 + - - +
647A LEU* 1.3 74.6 - - - +
649A ASP* 1.3 69.8 + - - +
651A TYR* 3.7 17.7 - - + +
652A ARG* 3.2 63.9 + - - +
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Residues in contact with ASP 649 (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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645A LYS* 3.0 42.9 + - - +
646A GLU* 4.1 11.8 - - - +
648A ARG* 1.3 78.6 - - - +
650A ALA* 1.3 65.6 + - - +
652A ARG* 5.0 2.7 - - - +
653A GLU* 3.1 28.9 + - + +
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Residues in contact with ALA 650 (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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560A ILE* 4.6 11.0 - - + -
583A LEU* 4.3 16.2 - - + -
584A PHE 4.6 1.8 - - - +
585A PRO* 3.8 12.1 - - - +
603A MET* 3.8 18.8 - - - -
646A GLU 2.9 21.2 + - - +
647A LEU 3.5 2.2 + - - +
648A ARG 3.1 0.6 - - - -
649A ASP* 1.3 79.4 - - - +
651A TYR* 1.3 52.9 + - - +
653A GLU* 3.7 2.4 - - - +
654A ALA* 2.9 32.2 + - - +
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Residues in contact with TYR 651 (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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603A MET* 3.6 33.0 - - - +
606A ILE* 3.9 17.9 - - + -
607A GLN 4.2 7.2 + - - -
608A SER* 3.9 17.0 - - - -
609A VAL* 3.7 29.9 + - + -
647A LEU 3.2 23.2 + - - +
648A ARG* 3.7 18.2 - - + +
650A ALA* 1.3 74.1 - - - +
652A ARG* 1.3 108.8 + - + +
653A GLU 3.1 1.6 - - - -
654A ALA* 3.9 0.2 - - - +
655A GLN* 3.1 44.2 + - - +
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Residues in contact with ARG 652 (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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648A ARG* 3.2 62.4 + - - +
649A ASP* 4.4 2.7 - - - +
651A TYR* 1.3 112.8 + - + +
653A GLU* 1.3 63.5 + - - +
655A GLN* 3.3 5.2 + - - +
656A GLN* 3.1 22.2 + - - +
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Residues in contact with GLU 653 (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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649A ASP* 3.1 20.3 + - - +
650A ALA* 4.0 2.5 - - - +
652A ARG* 1.3 77.7 - - - +
654A ALA* 1.3 64.7 + - - +
656A GLN* 3.7 10.6 + - + +
657A LEU* 3.4 24.3 + - + +
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Residues in contact with ALA 654 (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 PRO 3.9 4.7 - - - +
586A ASN* 4.8 0.4 - - - -
603A MET* 3.7 27.1 - - + -
604A GLU* 5.2 4.0 - - + +
650A ALA 2.9 18.5 + - - +
651A TYR 3.3 2.4 + - - +
652A ARG 3.3 0.2 - - - -
653A GLU* 1.3 78.4 - - - +
655A GLN* 1.3 59.4 + - + +
657A LEU* 2.9 20.1 + - - +
658A VAL* 3.1 16.6 + - + +
99B TRP* 3.9 25.7 - - + -
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Residues in contact with GLN 655 (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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603A MET 3.2 20.4 + - - +
604A GLU* 3.7 19.5 + - + +
606A ILE 3.2 25.1 + - - -
651A TYR* 3.1 31.0 + - - +
652A ARG* 3.9 4.8 - - - +
654A ALA* 1.3 76.1 - - + +
656A GLN* 1.3 61.6 + - - +
658A VAL* 4.4 6.8 - - + +
659A GLN* 3.3 24.8 + - - +
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Residues in contact with GLN 656 (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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652A ARG 3.1 15.3 + - - +
653A GLU* 3.8 13.5 - - + +
654A ALA 3.2 0.2 - - - -
655A GLN* 1.3 78.0 - - - +
657A LEU* 1.3 62.9 + - + +
659A GLN* 3.4 26.5 + - - +
660A ARG* 2.8 57.4 - - - +
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Residues in contact with LEU 657 (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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653A GLU* 3.4 12.7 + - + +
654A ALA 2.9 10.7 + - - +
656A GLN* 1.3 79.4 - - + +
658A VAL* 1.3 65.2 + - - +
660A ARG* 3.3 33.3 + - + +
661A VAL* 3.3 17.9 - - + +
99B TRP* 3.9 37.9 - - + +
117B LEU* 4.1 20.2 - - + -
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Residues in contact with VAL 658 (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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604A GLU* 4.0 27.4 - - + +
654A ALA* 3.1 11.4 + - + +
655A GLN* 4.4 7.0 - - + +
656A GLN 3.4 0.2 - - - -
657A LEU* 1.3 74.2 - - + +
659A GLN* 1.3 68.1 + - - +
660A ARG 2.7 6.5 + - - -
661A VAL* 2.8 24.6 + - - +
664A MET* 4.0 26.0 - - + +
665A LYS* 3.5 23.6 - - + +
666A ASN* 6.0 0.9 - - - +
99B TRP* 3.9 26.9 - - + -
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Residues in contact with GLN 659 (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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655A GLN 3.3 15.5 + - - +
656A GLN* 3.4 28.1 + - - +
657A LEU 3.4 0.2 - - - -
658A VAL* 1.3 80.2 - - - +
660A ARG* 1.3 63.9 + - - +
665A LYS* 3.4 37.8 + - + +
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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
------------------------------------------------------------
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