Contacts of the helix formed by residues 646 - 676 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642F ASN* 3.4 25.3 - - + +
643F ALA* 3.0 31.9 + - + +
645F ASP* 1.3 83.7 - - + +
647F VAL* 1.3 66.9 + - - +
648F PHE* 3.9 5.2 + - - -
649F TYR* 3.4 6.2 + - - +
650F ARG* 3.3 20.1 + - - +
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Residues in contact with VAL 647 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586F ILE* 4.5 16.8 - - + -
646F THR* 1.3 72.9 - - - +
648F PHE* 1.3 72.6 + - + +
650F ARG* 3.3 6.3 + - - +
651F ALA* 3.0 22.2 + - + +
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Residues in contact with PHE 648 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586F ILE* 3.3 38.1 - - + -
587F PHE* 4.4 0.3 - - - -
638F CYS* 3.5 17.0 - - - -
642F ASN* 3.4 37.0 - - - +
646F THR* 3.3 3.8 + - - +
647F VAL* 1.3 83.2 - - + +
649F TYR* 1.3 62.1 + - - +
651F ALA* 3.2 7.7 + - - +
652F ALA 2.9 19.1 + - - -
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Residues in contact with TYR 649 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638F CYS* 4.6 7.0 - - - -
639F MET* 3.7 38.7 - - + +
642F ASN* 3.6 21.4 - - + +
643F ALA 3.4 20.4 - - - +
644F ARG* 3.4 32.9 - - + +
646F THR* 3.4 11.3 + - - +
647F VAL 3.3 0.2 - - - -
648F PHE* 1.3 77.8 - - - +
650F ARG* 1.3 61.4 + - + +
652F ALA* 3.1 6.5 + - - +
653F VAL* 3.0 45.6 + - + +
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Residues in contact with ARG 650 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644F ARG 5.7 1.1 - - - +
645F ASP 5.2 2.5 - - - +
646F THR 3.3 9.7 + - - +
647F VAL* 3.7 8.7 - - - +
648F PHE 3.3 0.6 - - - -
649F TYR* 1.3 81.5 - - + +
651F ALA* 1.3 68.3 + - - +
653F VAL* 2.9 9.5 + - - +
654F ARG* 2.8 31.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 651 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581F LYS 5.7 0.2 - - - +
582F ASP* 5.7 0.9 - - - +
586F ILE* 3.8 28.0 - - + -
587F PHE* 4.4 11.1 - - + -
647F VAL* 3.0 14.9 + - + +
648F PHE* 3.4 8.7 - - - +
650F ARG* 1.3 75.8 - - - +
652F ALA* 1.3 56.7 + - - +
654F ARG* 3.4 8.7 + - - +
655F LEU* 2.9 29.8 + - - +
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Residues in contact with ALA 652 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587F PHE* 3.8 12.9 - - + -
635F ILE* 3.0 23.6 - - + +
638F CYS* 3.7 25.6 - - + -
639F MET* 4.1 13.5 - - + -
648F PHE 2.9 13.5 + - - +
649F TYR 3.4 9.0 - - - +
651F ALA* 1.3 76.2 - - - +
653F VAL* 1.3 56.9 + - - +
656F ARG* 2.9 26.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 653 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639F MET* 3.9 20.0 - - - -
649F TYR* 3.0 34.0 + - + +
650F ARG* 2.9 11.3 + - - +
652F ALA* 1.3 74.4 - - - +
654F ARG* 1.3 69.0 + - + +
656F ARG* 3.2 23.4 + - - +
657F ASP* 3.1 36.1 + - - +
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Residues in contact with ARG 654 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581F LYS 6.0 1.1 - - - +
650F ARG* 2.8 26.3 + - - +
651F ALA* 3.9 7.2 - - - +
653F VAL* 1.3 74.8 - - + +
655F LEU* 1.3 58.9 + - - +
657F ASP* 3.3 6.0 + - - +
658F GLN* 2.9 51.5 + - + +
572H ARG* 5.6 10.8 - - - +
576H ASP* 4.8 13.2 - - - +
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Residues in contact with LEU 655 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578F LEU* 3.6 26.5 - - + +
581F LYS* 3.8 27.7 + - + +
582F ASP* 4.5 1.3 - - + +
587F PHE* 3.3 37.7 - - + -
609F PHE* 4.0 18.2 - - + -
631F PHE* 3.8 13.3 - - + -
634F ILE* 4.8 2.5 - - + -
635F ILE* 3.7 19.5 - - + -
651F ALA 2.9 17.8 + - - +
652F ALA 4.2 0.2 - - - -
654F ARG* 1.3 75.3 - - - +
656F ARG* 1.3 54.0 + - - +
658F GLN* 4.9 2.2 - - - -
659F GLY* 2.6 35.2 + - - +
----------------------------------------------------------
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Residues in contact with ARG 656 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631F PHE* 4.7 6.1 - - + -
632F ASP* 5.5 5.8 - - - +
635F ILE* 3.5 28.7 - - + +
636F ASP* 6.0 0.2 - - - -
639F MET* 4.4 22.1 - - - +
652F ALA 2.9 18.5 + - - +
653F VAL* 3.2 21.9 + - - +
655F LEU* 1.3 76.8 - - - +
657F ASP* 1.3 83.7 + - - +
660F GLY* 2.8 26.2 + - - -
----------------------------------------------------------
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Residues in contact with ASP 657 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653F VAL* 3.1 25.0 + - - +
654F ARG* 3.9 4.3 - - - +
656F ARG* 1.3 105.8 + - - +
658F GLN* 1.3 66.6 + - + +
660F GLY* 3.3 9.2 + - - -
661F VAL* 3.4 16.7 + - - +
664F ARG* 5.2 1.7 + - - -
617H GLU* 5.4 5.8 - - - +
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Residues in contact with GLN 658 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581F LYS* 3.1 53.3 + - + +
654F ARG* 2.9 35.6 + - + +
655F LEU 4.3 0.9 - - - +
657F ASP* 1.3 74.6 - - + +
659F GLY* 1.3 67.4 + - - +
661F VAL* 3.2 23.7 + - - +
662F VAL* 3.4 10.9 + - - +
572H ARG* 4.8 21.8 + - - +
----------------------------------------------------------
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Residues in contact with GLY 659 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578F LEU* 4.3 12.5 - - - +
581F LYS* 5.4 2.2 - - - +
631F PHE* 4.0 19.5 - - - -
655F LEU* 2.6 28.0 + - - +
656F ARG 3.9 0.2 - - - -
658F GLN* 1.3 73.2 - - - +
660F GLY* 1.3 63.6 + - - +
662F VAL* 2.9 6.6 + - - +
663F LEU* 2.9 24.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 660 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631F PHE* 4.8 1.0 - - - -
656F ARG 2.8 18.2 + - - -
657F ASP 3.3 2.9 + - - -
658F GLN 3.2 0.4 - - - -
659F GLY* 1.3 76.9 - - - +
661F VAL* 1.3 60.9 + - - +
663F LEU* 3.2 7.4 + - - +
664F ARG* 2.9 42.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 661 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657F ASP 3.4 16.5 + - - +
658F GLN* 3.2 12.5 + - - +
660F GLY* 1.3 73.7 - - - +
662F VAL* 1.3 64.3 + - + +
664F ARG* 3.8 27.1 + - - +
665F GLN* 3.3 20.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 662 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F EDO 5.8 1.1 + - - -
574F VAL* 3.9 19.0 - - + +
577F GLN* 3.8 35.9 - - + +
578F LEU* 3.7 26.7 - - + -
581F LYS* 4.3 19.5 - - + +
658F GLN 3.8 11.2 - - - +
659F GLY* 2.9 7.7 + - - +
661F VAL* 1.3 79.7 - - + +
663F LEU* 1.3 60.1 + - - +
665F GLN* 3.3 7.0 + - + +
666F ALA* 3.0 24.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 663 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574F VAL* 4.1 20.9 - - + -
578F LEU* 4.9 4.3 - - + -
624F LEU* 3.7 31.7 - - + +
627F PHE* 4.3 5.8 - - + -
628F GLU* 3.7 31.4 - - + +
631F PHE* 3.2 44.9 - - + -
632F ASP* 5.4 1.6 - - - +
659F GLY 2.9 12.6 + - - +
660F GLY* 3.9 6.3 - - - +
662F VAL* 1.3 74.1 - - - +
664F ARG* 1.3 61.4 + - - +
666F ALA* 3.1 7.3 + - + +
667F ARG* 2.9 26.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 664 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657F ASP 5.2 1.2 + - - -
660F GLY* 2.9 30.3 + - - +
661F VAL* 3.9 27.6 + - - +
663F LEU* 1.3 76.7 - - - +
665F GLN* 1.3 63.3 + - - +
667F ARG* 3.1 9.3 + - + +
668F ARG* 3.0 31.1 + - - +
----------------------------------------------------------
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Residues in contact with GLN 665 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F EDO 5.5 5.8 - - - +
661F VAL* 3.3 13.0 + - + +
662F VAL* 3.7 9.9 - - - +
663F LEU 3.3 0.2 - - - -
664F ARG* 1.3 76.3 - - - +
666F ALA* 1.3 58.1 + - - +
668F ARG* 3.4 15.5 + - - +
669F GLU* 2.9 29.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 666 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F EDO 4.9 5.5 + - - -
570F LEU* 5.3 4.2 - - + +
571F LEU* 6.0 0.7 - - + -
574F VAL* 3.6 26.9 - - + -
624F LEU* 3.9 18.4 - - + -
662F VAL 3.0 13.4 + - - +
663F LEU* 3.1 15.9 - - + +
665F GLN* 1.3 74.0 - - - +
667F ARG* 1.3 57.4 + - - -
669F GLU* 3.3 7.3 + - - +
670F VAL* 2.9 32.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG 667 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624F LEU* 3.6 24.3 - - + +
628F GLU* 5.2 9.6 - - - +
663F LEU 2.9 12.6 + - - +
664F ARG* 3.1 10.7 + - + +
666F ALA* 1.3 71.8 - - - +
668F ARG* 1.3 64.1 + - + +
670F VAL* 2.9 21.7 + - - +
671F ASP* 3.0 25.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 668 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664F ARG* 3.0 23.9 + - + +
665F GLN* 3.5 15.3 - - - +
667F ARG* 1.3 76.1 - - + +
669F GLU* 1.3 57.8 + - - +
671F ASP* 3.2 9.2 + - - +
672F SER* 2.8 28.0 + - - -
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Residues in contact with GLU 669 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F EDO 5.1 3.1 - - - +
570F LEU* 3.8 31.2 - - + -
665F GLN 2.9 16.2 + - - +
666F ALA* 3.6 8.1 - - - +
668F ARG* 1.3 75.9 - - - +
670F VAL* 1.3 65.1 + - - +
672F SER* 3.8 18.1 + - - -
673F ILE* 3.0 40.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 670 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567F LEU* 4.9 12.6 - - + -
570F LEU* 4.7 15.0 - - + -
624F LEU* 4.1 23.8 - - + +
666F ALA* 2.9 27.2 + - + +
667F ARG* 2.9 17.1 + - - +
669F GLU* 1.3 76.4 - - - +
671F ASP* 1.3 61.7 + - - +
673F ILE* 4.1 5.8 - - - +
674F GLY* 3.3 18.5 + - - -
----------------------------------------------------------
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Residues in contact with ASP 671 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667F ARG* 3.0 28.0 + - - +
668F ARG* 3.8 8.1 - - - +
670F VAL* 1.3 84.5 - - - +
672F SER* 1.3 65.6 + - - +
673F ILE 3.3 0.2 - - - -
674F GLY* 3.0 4.2 + - - +
675F LEU* 2.9 22.0 + - - +
----------------------------------------------------------
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Residues in contact with SER 672 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668F ARG 2.8 20.6 + - - -
669F GLU* 3.3 22.9 + - - -
671F ASP* 1.3 72.1 - - - +
673F ILE* 1.3 64.1 + - - +
675F LEU* 2.9 18.4 + - - +
676F GLU* 3.3 10.2 + - - +
----------------------------------------------------------
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Residues in contact with ILE 673 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566F PRO* 5.2 15.7 - - + -
570F LEU* 3.5 32.5 - - + -
669F GLU* 3.0 30.4 + - + +
670F VAL* 4.1 5.8 - - - +
672F SER* 1.3 74.6 + - - +
674F GLY* 1.3 64.2 + - - +
676F GLU* 3.1 24.5 + - + +
----------------------------------------------------------
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Residues in contact with GLY 674 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670F VAL 3.3 10.9 + - - -
671F ASP* 3.0 10.5 + - - -
673F ILE* 1.3 80.3 - - - +
675F LEU* 1.3 58.4 + - - +
676F GLU 4.5 2.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 675 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671F ASP 2.9 8.7 + - - +
672F SER* 2.9 13.0 + - - +
674F GLY* 1.3 73.3 - - - +
676F GLU* 1.3 66.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 676 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672F SER 3.3 8.2 + - - +
673F ILE* 3.1 19.7 + - + +
674F GLY 4.5 2.9 - - - +
675F LEU* 1.3 80.9 - - - +
----------------------------------------------------------
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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