Contacts of the helix formed by residues 646 - 675 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B ASN* 3.5 13.0 - - + +
643B ALA* 3.1 33.5 + - + +
644B ARG 3.3 0.4 - - - +
645B ASP* 1.3 85.0 - - + +
647B VAL* 1.3 60.0 + - - +
648B PHE* 3.7 5.6 + - - -
649B TYR* 3.2 14.7 + - - +
650B ARG* 3.3 34.6 + - - +
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Residues in contact with VAL 647 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ILE* 5.1 2.2 - - + -
646B THR* 1.3 73.0 - - - +
648B PHE* 1.3 68.6 + - + +
650B ARG* 3.5 27.9 + - - +
651B ALA* 3.1 21.7 + - - +
654B ARG* 4.6 1.4 + - - -
595H GLU 6.0 0.7 - - - +
596H VAL* 5.7 1.3 - - + -
597H PRO* 4.2 18.2 - - + -
598H ASP* 3.2 40.8 - - + +
641H TYR* 4.0 16.4 - - - +
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Residues in contact with PHE 648 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ILE* 3.8 42.6 - - + -
638B CYS* 3.2 21.1 - - - -
642B ASN* 3.5 37.0 - - + +
646B THR* 3.4 3.7 + - - +
647B VAL* 1.3 77.9 - - + +
649B TYR* 1.3 65.1 + - - +
651B ALA* 3.3 4.3 + - - +
652B ALA 3.2 12.6 + - - -
597H PRO* 4.0 28.7 - - + -
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Residues in contact with TYR 649 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B CYS 4.6 6.1 - - - -
639B MET* 3.2 59.6 - - + +
642B ASN* 3.8 8.8 - - + +
643B ALA 3.0 27.4 - - - +
644B ARG* 3.7 43.1 - - + +
646B THR* 3.2 8.5 + - - +
648B PHE* 1.3 79.3 - - - +
650B ARG* 1.3 69.1 + - + +
652B ALA* 3.3 5.5 + - - +
653B VAL* 3.1 34.3 + - + +
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Residues in contact with ARG 650 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B ARG 4.6 9.2 - - - +
645B ASP 3.9 18.8 + - - -
646B THR* 3.3 17.9 + - - +
647B VAL* 3.6 34.2 - - - +
648B PHE 3.3 0.2 - - - -
649B TYR* 1.3 80.9 - - + +
651B ALA* 1.3 55.2 + - - +
653B VAL* 3.3 9.1 + - - +
654B ARG* 2.9 44.4 + - + +
598H ASP* 4.3 10.5 + - - -
602H HIS* 5.7 2.4 - - - -
641H TYR* 5.2 2.2 + - - -
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Residues in contact with ALA 651 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ILE* 3.8 27.1 - - + -
587B PHE* 3.8 14.8 - - + -
647B VAL 3.1 17.3 + - - +
648B PHE* 3.7 5.8 - - - +
649B TYR 3.3 0.2 - - - -
650B ARG* 1.3 72.9 - - - +
652B ALA* 1.3 60.2 + - - +
654B ARG* 3.5 22.1 + - - +
655B LEU* 3.0 30.5 + - - +
598H ASP* 5.1 0.2 - - + -
601H ASP* 4.3 5.4 - - - +
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Residues in contact with ALA 652 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B PHE* 3.6 10.7 - - + -
635B ILE* 3.6 17.3 - - - +
638B CYS* 3.8 26.2 - - + -
639B MET* 3.9 16.2 - - + -
648B PHE 3.2 10.4 + - - +
649B TYR 3.5 9.0 - - - +
651B ALA* 1.3 79.8 - - - +
653B VAL* 1.3 57.0 + - - +
655B LEU* 3.1 2.8 + - - -
656B ARG* 2.8 30.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B MET* 3.9 27.8 - - + -
649B TYR* 3.1 30.2 + - + +
650B ARG* 3.3 11.4 + - - +
652B ALA* 1.3 73.0 - - - +
654B ARG* 1.3 62.8 + - + +
656B ARG* 3.3 14.9 + - - +
657B ASP* 2.9 42.6 + - - +
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Residues in contact with ARG 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LYS 5.7 1.8 + - - -
647B VAL 4.6 0.8 + - - -
650B ARG* 2.9 29.8 + - + +
651B ALA* 3.7 27.3 + - - +
653B VAL* 1.3 77.0 - - + +
655B LEU* 1.3 58.2 + - - +
657B ASP* 4.4 6.5 - - - +
658B GLN* 2.9 49.5 + - - +
598H ASP* 3.6 18.0 + - - +
601H ASP* 3.2 30.1 + - - +
602H HIS* 3.5 33.4 + - - -
----------------------------------------------------------
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Residues in contact with LEU 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B LEU* 3.8 23.8 - - + +
581B LYS* 4.1 22.7 - - + +
582B ASP* 4.8 2.7 - - + -
587B PHE* 3.5 33.4 - - + -
609B PHE* 3.8 21.3 - - + -
631B PHE* 3.6 15.1 - - + -
634B ILE* 4.7 2.0 - - + -
635B ILE* 3.9 17.3 - - + -
651B ALA 3.0 19.1 + - - +
652B ALA 3.6 4.3 - - - +
654B ARG* 1.3 74.0 - - - +
656B ARG* 1.3 62.2 + - - +
658B GLN* 4.7 3.8 - - - -
659B GLY* 3.0 25.3 + - - +
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Residues in contact with ARG 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A LYS* 4.5 28.3 + - - +
631B PHE* 4.6 6.4 - - + -
635B ILE* 3.8 27.2 - - + +
636B ASP* 4.7 3.6 + - - -
639B MET* 4.1 27.4 - - - +
652B ALA 2.8 17.1 + - - +
653B VAL* 3.5 12.7 - - - +
655B LEU* 1.3 74.3 - - - +
657B ASP* 1.3 80.0 + - - +
659B GLY* 3.2 0.9 + - - -
660B GLY* 3.2 20.8 + - - -
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Residues in contact with ASP 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B VAL* 2.9 35.2 + - - +
654B ARG* 3.8 7.5 - - - +
656B ARG* 1.3 91.1 + - - +
658B GLN* 1.3 66.9 - - + +
659B GLY 3.4 0.2 + - - -
660B GLY* 3.6 6.6 + - - -
661B VAL* 4.1 11.1 + - - +
664B ARG* 5.1 2.6 + - - -
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Residues in contact with GLN 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LYS* 4.3 47.9 - - + +
654B ARG* 2.9 36.7 + - - +
655B LEU* 4.5 2.0 - - - +
657B ASP* 1.3 80.2 - - + +
659B GLY* 1.3 60.5 + - - +
660B GLY 3.6 0.2 + - - -
661B VAL* 3.8 19.0 - - - +
662B VAL* 4.0 9.4 - - - +
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Residues in contact with GLY 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B LEU* 4.1 20.3 - - - +
581B LYS* 5.7 1.3 - - - -
631B PHE* 4.5 5.8 - - - -
655B LEU* 3.0 21.6 + - - -
656B ARG 3.2 1.1 + - - -
658B GLN* 1.3 75.1 - - - +
660B GLY* 1.3 65.4 + - - +
661B VAL 3.2 2.5 - - - -
662B VAL* 3.3 4.2 + - - +
663B LEU* 3.0 31.5 + - - +
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Residues in contact with GLY 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B PHE* 6.1 0.2 - - - -
656B ARG 3.2 13.6 + - - -
657B ASP 3.6 3.3 + - - -
658B GLN 3.4 0.6 - - - -
659B GLY* 1.3 78.2 - - - +
661B VAL* 1.3 53.0 + - - +
663B LEU* 3.2 6.9 + - - +
664B ARG* 2.8 59.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B ASP 4.1 9.2 - - - +
658B GLN* 3.8 15.0 - - - +
660B GLY* 1.3 76.7 - - - +
662B VAL* 1.3 64.6 + - + +
664B ARG* 3.6 20.5 - - - +
665B GLN* 3.1 23.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B VAL* 3.8 37.4 - - + +
577B GLN* 3.9 41.5 - - + +
578B LEU* 4.0 11.2 - - + -
581B LYS* 4.7 13.2 - - + +
658B GLN 4.0 14.1 - - - +
659B GLY 3.3 7.0 + - - +
661B VAL* 1.3 79.4 - - + +
663B LEU* 1.3 57.6 + - - +
665B GLN* 3.4 7.6 + - + +
666B ALA* 2.9 24.9 + - - +
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Residues in contact with LEU 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A LYS* 6.0 1.1 - - - +
574B VAL* 3.7 26.2 - - + -
578B LEU* 5.0 3.8 - - + -
624B LEU* 4.5 9.8 - - + +
627B PHE* 3.9 18.8 - - + -
628B GLU* 3.9 34.4 - - + +
631B PHE* 3.8 35.2 - - + -
632B ASP* 5.6 1.8 - - - +
659B GLY 3.0 20.2 + - - +
660B GLY* 3.9 5.4 - - - +
662B VAL* 1.3 76.6 - - - +
664B ARG* 1.3 59.2 + - + +
666B ALA* 3.1 4.9 + - + +
667B ARG* 2.8 28.1 + - - +
----------------------------------------------------------
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Residues in contact with ARG 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B ASP 5.1 2.6 + - - -
660B GLY* 2.8 35.7 + - - +
661B VAL* 3.6 31.1 - - - +
663B LEU* 1.3 69.4 - - + +
665B GLN* 1.3 65.9 + - - +
667B ARG* 3.2 10.9 + - + +
668B ARG* 3.0 48.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B VAL* 3.1 16.5 + - + +
662B VAL* 3.4 11.7 - - + +
664B ARG* 1.3 76.8 - - - +
666B ALA* 1.3 61.1 + - - +
668B ARG* 3.4 20.4 + - - +
669B GLU* 3.1 31.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B LEU* 4.6 8.3 - - + +
571B LEU* 5.9 0.4 - - + -
574B VAL* 3.5 26.7 - - + -
624B LEU* 4.1 17.0 - - + -
662B VAL 2.9 15.2 + - - +
663B LEU* 3.1 13.7 + - + +
665B GLN* 1.3 72.6 - - - +
667B ARG* 1.3 66.4 + - - +
669B GLU* 3.1 6.4 + - - +
670B VAL* 3.0 27.2 + - - +
----------------------------------------------------------
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Residues in contact with ARG 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B LEU* 3.8 20.6 - - + +
628B GLU* 5.2 7.2 - - - +
663B LEU 2.8 13.4 + - - +
664B ARG* 3.2 11.9 + - - +
666B ALA* 1.3 77.3 - - - +
668B ARG* 1.4 70.6 + - - +
669B GLU 3.3 0.3 + - - -
670B VAL* 3.5 7.4 + - - +
671B ASP* 3.2 33.4 + - - +
581G LYS* 5.0 11.2 - - - +
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Residues in contact with ARG 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B ARG* 3.0 49.8 + - - +
665B GLN* 3.4 29.6 - - - +
667B ARG* 1.4 83.1 - - - +
669B GLU* 1.3 60.0 + - - +
671B ASP* 3.3 11.7 + - - +
672B SER* 2.8 28.0 + - - -
658G GLN* 5.6 9.5 - - - +
661G VAL* 3.5 44.2 - - + +
665G GLN* 5.6 0.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B LEU* 3.5 32.1 - - + -
665B GLN* 3.1 22.6 + - + +
666B ALA* 3.1 7.3 + - - +
668B ARG* 1.3 76.1 - - - +
670B VAL* 1.3 66.1 + - - +
672B SER* 3.9 16.7 + - - -
673B ILE* 3.0 39.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B LEU* 4.7 12.8 - - + -
570B LEU* 4.0 17.8 - - + +
624B LEU* 4.4 25.1 - - + -
666B ALA* 3.0 15.5 + - + +
667B ARG* 3.7 12.6 - - - +
669B GLU* 1.3 72.7 - - - +
671B ASP* 1.3 71.0 + - - +
673B ILE* 3.3 6.3 + - - +
674B GLY* 3.1 18.5 + - - -
----------------------------------------------------------
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Residues in contact with ASP 671 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B ARG* 3.2 20.9 + - - +
668B ARG* 3.3 13.6 + - - +
670B VAL* 1.3 82.8 - - - +
672B SER* 1.3 62.8 + - - +
674B GLY 3.1 6.2 + - - -
675B LEU* 3.1 7.4 + - + +
577G GLN* 2.8 46.5 + - - +
581G LYS* 2.9 34.8 + - - -
661G VAL* 6.0 1.9 - - + +
662G VAL* 4.7 8.7 - - + +
665G GLN* 6.3 1.1 - - + -
----------------------------------------------------------
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Residues in contact with SER 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ARG 2.8 19.5 + - - -
669B GLU* 3.7 23.2 + - - -
670B VAL 3.2 0.4 - - - -
671B ASP* 1.3 72.8 - - - +
673B ILE* 1.3 62.8 + - - +
675B LEU* 3.1 13.9 + - - +
676B GLU* 3.5 11.6 + - - +
665G GLN* 3.1 43.4 + - - +
669G GLU* 4.9 3.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 673 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B PRO* 4.7 26.7 - - + +
570B LEU* 4.2 19.5 - - + -
669B GLU* 3.0 36.5 + - + +
670B VAL* 4.0 4.5 - - - +
672B SER* 1.3 75.5 - - - +
674B GLY* 1.3 62.7 + - - +
676B GLU* 3.1 32.1 + - + +
677B GLU 4.5 1.2 + - - -
----------------------------------------------------------
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Residues in contact with GLY 674 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B VAL 3.1 9.1 + - - -
671B ASP 3.1 9.9 + - - -
673B ILE* 1.3 79.4 - - - +
675B LEU* 1.3 58.1 + - - +
676B GLU 3.6 0.5 + - - -
677B GLU* 4.3 7.1 + - - +
573G SER* 3.7 17.2 + - - -
577G GLN* 3.8 13.0 - - - -
----------------------------------------------------------
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Residues in contact with LEU 675 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B ASP 3.1 10.3 + - - +
672B SER 3.1 10.9 + - - +
674B GLY* 1.3 74.3 - - - +
676B GLU* 1.3 61.9 + - - +
677B GLU* 3.3 4.1 + - - -
678B ALA* 4.0 3.1 + - - +
570G LEU* 3.5 23.0 - - + +
573G SER* 3.7 24.0 - - - -
574G VAL* 3.8 17.7 - - + +
577G GLN* 3.4 29.6 - - - +
662G VAL* 3.7 24.2 - - + +
665G GLN* 4.0 14.8 - - + -
666G ALA* 3.8 23.8 - - + +
669G GLU* 3.9 14.3 - - + +
----------------------------------------------------------
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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