Contacts of the helix formed by residues 646 - 674 (chain C) in PDB entry 3RCW
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 THR 646 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C ASN* 3.5 13.6 - - + +
643C ALA* 3.1 30.2 + - + +
644C ARG 3.3 0.2 - - - -
645C ASP* 1.3 90.5 - - - +
647C VAL* 1.3 63.9 + - - +
648C PHE* 3.6 6.7 + - - -
649C TYR* 3.4 13.9 + - - +
650C ARG* 3.3 25.2 + - - -
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Residues in contact with VAL 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C ILE* 5.1 8.3 - - + -
646C THR* 1.3 71.2 - - - +
648C PHE* 1.3 78.3 + - + +
650C ARG* 3.5 23.4 + - - +
651C ALA* 3.0 22.4 + - + +
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Residues in contact with PHE 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MB3 3.5 33.2 - + - -
586C ILE* 3.8 43.5 - - + -
595C GLU* 5.8 4.0 - - - -
596C VAL* 5.6 2.9 - - + -
638C CYS* 3.7 13.1 - - - -
642C ASN* 3.7 28.5 - - - +
646C THR* 3.3 5.3 + - - +
647C VAL* 1.3 84.6 - - + +
649C TYR* 1.3 63.3 + - - +
651C ALA* 2.9 7.4 + - - +
652C ALA 2.9 19.8 + - - -
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Residues in contact with TYR 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C CYS* 4.2 8.9 - - - -
639C MET* 3.4 51.7 - - + +
642C ASN* 3.5 21.7 - - + +
643C ALA 3.3 20.9 - - - +
644C ARG* 3.5 30.8 - - + +
646C THR* 3.4 9.9 + - - +
648C PHE* 1.3 76.8 - - - +
650C ARG* 1.3 60.8 + - + +
652C ALA* 3.2 6.7 + - - +
653C VAL* 3.0 46.4 + - + +
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Residues in contact with ARG 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644C ARG 4.4 11.4 - - - +
645C ASP* 2.7 31.4 + - - +
646C THR 3.3 17.4 + - - +
647C VAL* 3.8 22.6 - - - +
648C PHE 3.2 0.6 - - - -
649C TYR* 1.3 78.6 - - + +
651C ALA* 1.3 64.2 + - - +
653C VAL* 3.2 9.6 + - + +
654C ARG* 3.1 24.3 + - - +
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Residues in contact with ALA 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C ILE* 4.1 24.9 - - + -
587C PHE* 4.2 12.7 - - + -
647C VAL* 3.0 14.4 + - + +
648C PHE* 2.9 10.9 + - - +
650C ARG* 1.3 75.6 - - - +
652C ALA* 1.3 64.4 + - - +
654C ARG* 3.3 5.9 + - - +
655C LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C PHE* 3.9 11.6 - - + -
635C ILE* 3.5 29.6 - - + +
638C CYS* 3.8 32.5 - - + -
639C MET* 4.0 8.3 - - + -
648C PHE 2.9 6.1 + - - -
649C TYR 3.5 8.7 - - - +
651C ALA* 1.3 75.4 - - - +
653C VAL* 1.3 64.2 + - - +
655C LEU* 3.3 0.4 + - - -
656C ARG* 3.0 22.2 + - - +
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Residues in contact with VAL 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639C MET* 4.3 17.9 - - + -
649C TYR* 3.0 43.4 + - + +
650C ARG* 3.2 10.7 + - + +
652C ALA* 1.3 77.9 - - - +
654C ARG* 1.3 61.7 + - - +
656C ARG* 3.5 9.6 + - - +
657C ASP* 3.3 30.0 + - - +
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Residues in contact with ARG 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650C ARG 3.1 15.1 + - - +
651C ALA* 4.0 4.9 - - - +
653C VAL* 1.3 76.6 - - - +
655C LEU* 1.3 60.8 + - - +
657C ASP* 3.3 9.2 + - - +
658C GLN* 2.9 46.3 + - - +
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Residues in contact with LEU 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578C LEU* 3.8 12.1 - - - +
581C LYS* 3.6 40.2 - - + +
582C ASP* 4.4 2.5 - - + -
587C PHE* 3.4 35.0 - - + -
609C PHE* 4.0 19.5 - - + -
631C PHE* 3.5 17.6 - - + -
634C ILE* 5.1 0.7 - - + -
635C ILE* 4.1 11.0 - - + -
651C ALA 3.0 17.3 + - - +
652C ALA* 3.3 4.2 + - - +
654C ARG* 1.3 73.8 - - - +
656C ARG* 1.3 57.7 + - - +
658C GLN* 4.4 2.9 - - - +
659C GLY* 2.7 34.9 + - - +
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Residues in contact with ARG 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631C PHE* 4.4 7.8 - - + -
632C ASP* 4.7 13.8 + - - +
635C ILE* 3.4 35.2 - - + +
636C ASP* 2.7 35.6 + - - -
639C MET* 4.2 18.7 - - - +
652C ALA 3.0 13.1 + - - +
653C VAL* 3.6 12.3 - - - +
654C ARG 3.3 0.2 - - - -
655C LEU* 1.3 76.7 - - - +
657C ASP* 1.3 62.2 + - - +
660C GLY* 3.0 25.8 + - - -
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Residues in contact with ASP 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C VAL* 3.3 21.6 + - - +
654C ARG* 3.3 11.7 + - - +
655C LEU 3.2 0.4 - - - -
656C ARG* 1.3 82.6 - - - +
658C GLN* 1.3 66.2 + - + +
659C GLY 3.4 0.5 + - - -
660C GLY* 3.4 8.0 + - - -
661C VAL* 3.5 16.7 + - - +
664C ARG* 4.5 3.3 + - - -
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Residues in contact with GLN 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C LYS* 3.7 47.1 + - + +
654C ARG* 2.9 37.2 + - - +
655C LEU* 4.4 1.7 - - - +
657C ASP* 1.3 74.2 - - + +
659C GLY* 1.3 62.0 + - - +
661C VAL* 3.5 21.4 + - + +
662C VAL* 3.7 12.0 + - - +
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Residues in contact with GLY 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578C LEU* 3.8 21.0 - - - +
581C LYS* 5.2 1.1 - - - -
631C PHE* 4.2 7.2 - - - -
655C LEU* 2.7 22.4 + - - +
658C GLN* 1.3 77.2 - - - +
660C GLY* 1.3 58.2 + - - +
662C VAL* 2.9 7.2 + - - +
663C LEU* 2.9 34.5 + - - +
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Residues in contact with GLY 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631C PHE* 4.8 1.6 - - - -
656C ARG 3.0 20.5 + - - -
657C ASP 3.8 2.2 - - - -
658C GLN 3.4 0.2 - - - -
659C GLY* 1.3 75.5 - - - +
661C VAL* 1.3 54.9 + - - +
663C LEU* 3.9 9.5 - - - +
664C ARG* 2.9 54.9 + - - +
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Residues in contact with VAL 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ASP 3.5 16.5 + - - +
658C GLN* 3.6 11.4 - - - +
659C GLY 3.2 0.8 - - - -
660C GLY* 1.3 75.8 - - - +
662C VAL* 1.3 60.8 + - + +
664C ARG* 3.5 19.7 + - - +
665C GLN* 3.0 28.8 + - + +
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Residues in contact with VAL 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C VAL* 4.0 18.6 - - + +
577C GLN* 3.5 33.4 - - + +
578C LEU* 4.0 21.3 - - + -
581C LYS* 4.4 23.1 - - + +
658C GLN 3.7 14.1 - - - +
659C GLY* 2.9 8.0 + - - +
661C VAL* 1.3 76.7 - - + +
663C LEU* 1.3 60.1 + - - +
665C GLN* 3.3 6.5 + - - +
666C ALA* 2.8 26.2 + - - +
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Residues in contact with LEU 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C VAL* 3.7 26.9 - - + -
578C LEU* 4.5 7.6 - - + -
624C LEU* 4.3 7.5 - - + +
627C PHE* 4.2 17.0 - - + -
628C GLU* 3.7 37.5 - - + +
631C PHE* 3.7 30.3 - - + -
632C ASP* 5.2 2.7 - - - +
659C GLY 2.9 19.5 + - - +
660C GLY* 3.9 7.0 - - - +
662C VAL* 1.3 71.6 - - - +
664C ARG* 1.3 67.0 + - - +
666C ALA* 2.9 6.8 + - - +
667C ARG* 2.9 21.5 + - - +
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Residues in contact with ARG 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ASP 4.5 3.0 + - - -
660C GLY* 2.9 31.0 + - - +
661C VAL* 3.5 33.0 - - - +
663C LEU* 1.3 74.6 - - - +
665C GLN* 1.3 63.8 + - - +
667C ARG* 3.1 22.5 + - - +
668C ARG* 3.2 25.0 + - - +
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Residues in contact with GLN 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661C VAL* 3.0 20.5 + - + +
662C VAL* 3.6 7.0 - - - +
663C LEU 3.2 0.2 - - - -
664C ARG* 1.3 75.0 - - - +
666C ALA* 1.3 64.2 + - - +
668C ARG* 2.9 52.8 + - - +
669C GLU* 3.2 32.5 + - + +
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Residues in contact with ALA 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C LEU* 4.3 8.1 - - + +
571C LEU* 6.1 0.2 - - + -
574C VAL* 3.6 27.8 - - + -
624C LEU* 4.3 17.7 - - + -
662C VAL 2.8 14.8 + - - +
663C LEU* 2.9 13.0 + - - +
665C GLN* 1.3 74.6 - - - +
667C ARG* 1.3 63.9 + - - +
669C GLU* 2.9 13.3 + - - +
670C VAL* 2.9 24.2 + - - +
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Residues in contact with ARG 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C ASN* 6.4 0.2 - - - +
624C LEU* 3.7 38.4 - - + +
625C HIS* 4.4 13.3 - - - +
628C GLU* 4.0 10.8 + - - +
663C LEU 2.9 11.0 + - - +
664C ARG* 3.2 17.7 - - - +
666C ALA* 1.3 75.7 - - - +
668C ARG* 1.3 56.2 + - + +
670C VAL* 3.4 28.0 + - - +
671C ASP* 2.9 49.5 + - - +
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Residues in contact with ARG 668 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664C ARG* 3.5 22.9 + - - +
665C GLN* 2.9 47.4 + - - +
667C ARG* 1.3 76.9 - - + +
669C GLU* 1.3 66.2 + - - +
671C ASP* 3.4 14.0 - - - +
672C SER* 3.2 21.0 + - - -
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Residues in contact with GLU 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C LEU* 4.2 21.1 - - + -
665C GLN* 3.6 30.3 + - + +
666C ALA* 2.9 10.0 + - - +
668C ARG* 1.3 75.6 - - - +
670C VAL* 1.3 59.9 + - - +
672C SER* 2.9 15.9 + - - -
673C ILE* 2.8 39.8 + - + +
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Residues in contact with VAL 670 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C LEU* 5.2 9.2 - - + -
570C LEU* 3.7 19.9 - - + +
624C LEU* 4.7 19.1 - - + -
666C ALA 2.9 17.2 + - - +
667C ARG* 3.6 31.2 - - - +
669C GLU* 1.3 74.5 - - - +
671C ASP* 1.3 65.9 + - - +
673C ILE* 4.0 6.9 - - + +
674C GLY* 2.8 24.8 + - - -
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Residues in contact with ASP 671 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667C ARG* 2.9 42.7 + - - +
668C ARG* 3.4 17.5 - - - +
669C GLU 3.2 0.2 - - - -
670C VAL* 1.3 78.3 - - - +
672C SER* 1.3 62.5 + - - +
674C GLY* 3.7 2.0 + - - -
675C LEU* 3.6 21.1 + - - +
----------------------------------------------------------
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Residues in contact with SER 672 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C ARG 3.2 9.5 + - - -
669C GLU* 2.9 22.7 + - - -
671C ASP* 1.3 77.8 - - - +
673C ILE* 1.3 73.4 + - - +
675C LEU* 3.1 23.3 + - - +
----------------------------------------------------------
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Residues in contact with ILE 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C PRO* 4.7 30.3 - - + +
570C LEU* 4.3 20.2 - - + -
669C GLU* 2.8 31.4 + - + +
670C VAL* 4.0 5.4 - - + +
672C SER* 1.3 82.3 + - - +
674C GLY* 1.3 58.8 + - - +
675C LEU* 3.2 7.8 + - - -
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Residues in contact with GLY 674 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C VAL* 2.8 18.6 + - - -
671C ASP 4.1 2.9 - - - -
672C SER 3.2 0.2 - - - -
673C ILE* 1.3 76.4 - - - +
675C LEU* 1.3 62.9 + - - +
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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