Contacts of the helix formed by residues 646 - 674 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642G ASN* 3.6 12.2 - - + +
643G ALA* 2.9 32.6 + - + +
644G ARG 3.5 0.8 + - - -
645G ASP* 1.3 90.9 - - - +
647G VAL* 1.3 66.4 + - - +
648G PHE* 3.6 5.0 + - - -
649G TYR* 3.2 14.6 + - - +
650G ARG* 3.2 28.5 + - - +
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Residues in contact with VAL 647 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A LYS 3.9 17.0 - - - +
595A GLU* 3.9 22.7 - - - +
597A PRO* 4.5 11.1 - - + +
646G THR* 1.3 72.2 - - - +
648G PHE* 1.3 81.1 + - + +
650G ARG* 3.6 20.3 + - - +
651G ALA* 3.0 28.6 + - - +
654G ARG* 5.2 0.3 + - - -
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Residues in contact with PHE 648 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A LYS* 4.5 10.1 - - + -
586G ILE* 3.8 43.7 - - + -
587G PHE* 4.3 0.2 - - - -
638G CYS* 3.5 15.6 - - - -
642G ASN* 3.8 32.8 - - - +
646G THR* 3.2 4.9 + - - +
647G VAL* 1.3 92.0 - - + +
649G TYR* 1.3 66.2 + - - +
651G ALA* 3.0 6.0 + - - +
652G ALA 3.0 18.2 + - - -
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Residues in contact with TYR 649 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638G CYS* 4.6 3.1 - - - -
639G MET* 3.3 47.2 - - + +
642G ASN* 3.4 24.9 - - - +
643G ALA 3.3 18.4 - - - +
644G ARG* 3.6 38.8 - - + +
646G THR* 3.2 8.2 + - - +
648G PHE* 1.3 75.0 - - - +
650G ARG* 1.3 69.8 + - + +
652G ALA* 3.0 9.5 + - - +
653G VAL* 3.0 37.9 + - + +
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Residues in contact with ARG 650 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644G ARG 4.4 13.5 + - - +
645G ASP* 3.6 33.7 + - - +
646G THR* 3.2 21.3 + - - +
647G VAL* 3.8 19.8 - - - +
649G TYR* 1.3 83.7 - - + +
651G ALA* 1.3 61.5 + - - +
653G VAL* 3.6 7.8 + - - +
654G ARG* 3.1 49.7 + - - +
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Residues in contact with ALA 651 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 4.1 22.7 - - + -
586G ILE* 4.3 8.1 - - + -
587G PHE* 4.0 18.1 - - + -
647G VAL 3.0 19.0 + - - +
648G PHE* 3.0 6.0 + - - +
650G ARG* 1.3 74.2 - - - +
652G ALA* 1.3 61.5 + - - +
654G ARG* 3.3 12.7 + - - +
655G LEU* 2.8 30.0 + - - +
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Residues in contact with ALA 652 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587G PHE* 3.8 10.7 - - + -
635G ILE* 3.6 19.9 - - + +
638G CYS* 3.8 26.7 - - + -
639G MET* 3.9 15.0 - - + -
648G PHE 3.0 11.2 + - - +
649G TYR 3.0 10.1 + - - +
651G ALA* 1.3 74.0 - - - +
653G VAL* 1.3 56.3 + - - +
655G LEU* 3.1 0.9 + - - -
656G ARG* 2.8 35.9 + - - +
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Residues in contact with VAL 653 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639G MET* 3.7 18.8 - - + -
649G TYR* 3.0 42.6 + - + +
650G ARG* 3.7 10.5 - - - +
652G ALA* 1.3 75.0 - - - +
654G ARG* 1.3 65.3 + - + +
656G ARG* 3.4 23.4 + - - +
657G ASP* 3.1 39.3 + - - +
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Residues in contact with ARG 654 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 4.4 14.1 - - - +
598A ASP* 3.5 53.0 + - - +
601A ASP* 4.4 2.2 - - - -
641A TYR* 5.5 0.4 + - - -
650G ARG* 3.1 54.6 + - - +
651G ALA* 3.6 13.3 - - - +
652G ALA 3.2 0.4 - - - -
653G VAL* 1.3 79.6 - - + +
655G LEU* 1.3 55.9 + - - +
657G ASP* 3.4 8.4 + - - +
658G GLN* 3.0 54.7 + - - +
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Residues in contact with LEU 655 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578G LEU* 3.7 24.5 - - - +
581G LYS* 3.9 24.2 - - + +
582G ASP* 4.5 2.2 - - + -
587G PHE* 3.5 36.6 - - + -
609G PHE* 4.0 20.6 - - + -
631G PHE* 3.5 12.8 - - + -
634G ILE* 4.4 3.1 - - + -
635G ILE* 3.8 18.2 - - + -
651G ALA 2.8 17.0 + - - +
652G ALA 3.8 2.7 - - - +
654G ARG* 1.3 72.8 - - - +
656G ARG* 1.3 58.0 + - - +
658G GLN* 4.5 2.2 - - - +
659G GLY* 2.7 36.3 + - - +
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Residues in contact with ARG 656 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631G PHE* 4.5 7.1 - - + -
632G ASP* 6.0 1.6 - - - +
635G ILE* 3.8 29.8 - - + +
639G MET* 4.1 23.6 - - - +
652G ALA 2.8 16.7 + - - +
653G VAL* 3.4 25.7 - - - +
655G LEU* 1.3 71.9 - - - +
657G ASP* 1.3 75.5 + - - +
660G GLY* 2.7 32.7 + - - -
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Residues in contact with ASP 657 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653G VAL* 3.1 26.6 + - - +
654G ARG* 3.8 9.6 - - - +
655G LEU 3.4 0.2 - - - -
656G ARG* 1.3 103.5 + - - +
658G GLN* 1.3 67.0 + - + +
660G GLY* 3.6 3.8 + - - -
661G VAL* 3.5 19.1 + - - +
664G ARG* 4.9 2.1 + - - -
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Residues in contact with GLN 658 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ASP* 3.3 30.3 + - - +
668B ARG* 5.6 9.2 - - - +
581G LYS* 3.5 41.9 - - + +
654G ARG* 3.0 36.6 + - - +
655G LEU* 4.4 1.8 - - - +
657G ASP* 1.3 80.1 - - + +
659G GLY* 1.3 65.6 - - - +
661G VAL* 3.3 22.5 + - - +
662G VAL* 3.6 11.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 659 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578G LEU* 3.6 23.6 - - - -
581G LYS* 4.8 2.9 - - - +
631G PHE* 3.8 7.9 - - - -
655G LEU* 2.7 25.1 + - - +
658G GLN* 1.3 70.5 - - - +
660G GLY* 1.3 63.4 + - - -
662G VAL* 3.2 5.8 + - - +
663G LEU* 3.1 27.5 + - - +
----------------------------------------------------------
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Residues in contact with GLY 660 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631G PHE* 4.6 2.7 - - - -
656G ARG 2.7 23.4 + - - -
657G ASP 3.6 2.2 + - - -
659G GLY* 1.3 71.5 - - - +
661G VAL* 1.3 55.3 + - - +
663G LEU* 3.4 7.8 + - - +
664G ARG* 2.8 52.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 661 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ARG* 3.5 52.0 - - + +
671B ASP* 6.0 2.2 - - + +
657G ASP 3.5 17.6 + - - +
658G GLN* 3.5 10.5 - - - +
659G GLY 3.2 0.6 - - - -
660G GLY* 1.3 75.0 - - - +
662G VAL* 1.3 60.5 + - + +
664G ARG* 3.3 22.1 + - - +
665G GLN* 2.9 29.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 662 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B ASP* 4.7 8.5 - - + +
675B LEU* 3.7 4.7 - - + +
574G VAL* 4.0 26.0 - - + -
577G GLN* 3.8 36.6 - - + +
578G LEU* 4.1 13.2 - - + -
581G LYS* 4.4 20.2 - - + -
658G GLN 3.6 14.8 - - - +
659G GLY* 3.2 7.5 + - - +
661G VAL* 1.3 78.7 - - + +
663G LEU* 1.3 58.9 + - - +
665G GLN* 3.2 7.8 + - - +
666G ALA* 2.8 26.2 + - - +
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Residues in contact with LEU 663 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574G VAL* 3.7 27.4 - - + -
578G LEU* 4.6 5.4 - - + -
624G LEU* 4.1 11.8 - - + +
627G PHE* 4.1 19.1 - - + -
628G GLU* 4.0 32.7 - - + +
631G PHE* 3.7 35.4 - - + -
632G ASP* 5.3 2.0 - - - +
659G GLY 3.1 17.6 + - - +
660G GLY* 3.8 6.5 - - - +
662G VAL* 1.3 76.3 - - - +
664G ARG* 1.3 65.8 + - + +
665G GLN 3.1 0.9 - - - -
666G ALA* 3.7 3.1 - - + +
667G ARG* 2.9 23.9 + - - +
----------------------------------------------------------
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Residues in contact with ARG 664 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657G ASP 4.9 1.6 + - - -
660G GLY* 2.8 36.3 + - - +
661G VAL* 3.8 31.8 - - - +
663G LEU* 1.3 71.5 - - - +
665G GLN* 1.3 59.3 + - - +
667G ARG* 3.4 8.6 + - - +
668G ARG* 2.9 40.3 + - - +
----------------------------------------------------------
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Residues in contact with GLN 665 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ARG 5.6 0.4 - - - +
671B ASP* 5.5 0.9 - - + -
672B SER* 3.1 46.1 + - - +
675B LEU* 4.0 11.7 - - + -
661G VAL* 2.9 19.3 + - + +
662G VAL* 3.5 7.9 - - - +
663G LEU 3.1 0.4 - - - -
664G ARG* 1.3 75.4 - - - +
666G ALA* 1.3 64.3 + - - +
668G ARG* 3.0 52.3 + - - +
669G GLU* 3.3 31.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 666 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B LEU* 3.8 7.1 - - + +
570G LEU* 3.9 6.6 - - + +
574G VAL* 3.6 27.4 - - + -
624G LEU* 3.7 19.3 - - + -
662G VAL 2.8 17.1 + - - +
663G LEU* 3.2 7.6 + - - +
665G GLN* 1.3 75.7 - - - +
667G ARG* 1.3 64.2 + - - +
669G GLU* 3.1 9.7 + - - +
670G VAL* 3.0 24.6 + - - +
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Residues in contact with ARG 667 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G EDO 3.2 44.4 + - - -
624G LEU* 3.5 26.1 - - + +
625G HIS* 4.0 9.1 + - - +
628G GLU* 4.0 14.4 + - - +
663G LEU 2.9 13.6 + - - +
664G ARG* 3.5 14.1 - - - +
666G ALA* 1.3 77.4 - - - +
668G ARG* 1.3 57.9 + - + +
670G VAL* 3.4 14.2 + - - +
671G ASP* 2.9 48.8 + - - +
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Residues in contact with ARG 668 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664G ARG* 2.9 28.5 + - - +
665G GLN* 3.0 39.5 + - - +
667G ARG* 1.3 74.6 - - + +
669G GLU* 1.3 68.1 + - - +
671G ASP* 3.3 17.5 - - - +
672G SER* 3.1 23.2 + - - -
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Residues in contact with GLU 669 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B SER* 4.9 4.7 + - - +
675B LEU* 3.9 31.1 - - + +
676B GLU* 4.4 8.2 - - - +
679B SER* 4.2 21.8 + - - -
570G LEU* 4.1 18.2 - - + -
665G GLN* 3.3 31.2 + - - +
666G ALA* 3.1 10.5 + - - +
668G ARG* 1.3 79.7 - - - +
670G VAL* 1.3 51.8 + - - +
672G SER* 2.9 10.4 + - - -
673G ILE* 2.7 45.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 670 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G EDO 3.6 35.4 - - - +
567G LEU* 5.0 7.0 - - + -
570G LEU* 3.8 17.9 - - + +
624G LEU* 4.3 14.6 - - + -
666G ALA 3.0 14.1 + - - +
667G ARG* 3.7 19.5 - - - +
669G GLU* 1.3 72.1 - - - +
671G ASP* 1.3 68.1 + - - +
673G ILE* 4.6 6.1 - - + +
674G GLY* 2.8 24.5 + - - +
----------------------------------------------------------
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Residues in contact with ASP 671 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667G ARG* 2.9 42.4 + - - +
668G ARG* 3.3 21.9 - - - +
670G VAL* 1.3 76.6 - - - +
672G SER* 1.3 63.5 + - - +
674G GLY* 3.7 4.9 + - - -
675G LEU* 3.7 18.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 672 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B SER* 5.5 4.9 - - - -
668G ARG 3.1 10.3 + - - -
669G GLU* 2.9 15.2 + - - -
671G ASP* 1.3 76.9 - - - +
673G ILE* 1.3 68.3 + - - +
675G LEU* 3.2 26.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 673 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B ALA* 3.6 33.0 - - + +
679B SER* 3.9 25.8 - - - +
566G PRO* 4.4 24.0 - - + +
567G LEU* 6.3 0.4 - - - -
570G LEU* 5.0 5.4 - - + -
669G GLU* 2.7 34.7 + - + +
670G VAL* 4.4 5.4 - - - +
672G SER* 1.3 75.6 - - - +
674G GLY* 1.3 61.5 + - - +
675G LEU 3.2 9.2 + - - +
----------------------------------------------------------
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Residues in contact with GLY 674 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670G VAL* 2.8 20.7 + - - -
671G ASP 4.1 3.1 - - - -
672G SER 3.2 0.4 - - - -
673G ILE* 1.3 76.6 - - - +
675G LEU* 1.3 60.1 + - - +
----------------------------------------------------------
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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