Contacts of the helix formed by residues 657 - 682 (chain K) in PDB entry 6D6R
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 ARG 657 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590K TYR* 3.8 17.2 - - + +
591K ALA* 3.1 41.7 - - - +
594K GLN* 4.1 28.8 - - + +
655K GLU* 4.0 28.6 + - - +
656K LEU* 1.3 80.6 + - - +
658K GLU* 1.3 81.0 + - + +
659K THR* 3.4 8.1 - - - +
660K ASN* 3.3 20.6 + - + +
661K SER* 3.6 5.7 + - - -
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Residues in contact with GLU 658 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594K GLN* 5.1 11.9 - - + +
597K ILE* 5.4 10.4 - - + +
598K ASP* 5.2 4.9 - - - +
614K ASN* 5.0 15.0 - - - +
618K LYS* 2.9 38.9 + - - -
657K ARG* 1.3 79.9 - - + +
659K THR* 1.3 66.8 + - - +
661K SER* 2.7 29.4 + - - +
662K MET* 2.9 7.7 + - - +
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Residues in contact with THR 659 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478K VAL* 3.6 20.6 - - + -
590K TYR* 3.3 34.9 + - + -
593K ALA* 3.7 24.1 - - + +
594K GLN* 4.2 7.8 + - - +
597K ILE* 4.2 10.1 - - + +
614K ASN* 4.6 2.5 - - - +
657K ARG* 3.4 5.0 - - - +
658K GLU* 1.3 78.0 - - - +
660K ASN* 1.3 63.0 + - - +
662K MET* 3.3 22.8 + - + +
663K VAL* 3.0 23.7 + - + +
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Residues in contact with ASN 660 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590K TYR* 4.0 19.4 + - + -
655K GLU 5.6 2.2 + - - +
656K LEU* 4.7 17.8 - - + +
657K ARG* 3.3 16.4 + - + +
658K GLU 2.9 0.8 + - - -
659K THR* 1.3 78.3 - - - +
661K SER* 1.3 62.9 + - - +
663K VAL* 3.1 12.2 - - - +
664K GLU* 2.9 28.6 + - - +
60O A 3.5 37.7 + - - +
61O A 5.7 0.2 - - - -
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Residues in contact with SER 661 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617K ALA* 5.1 2.6 - - - +
618K LYS* 5.8 4.5 - - - +
621K LYS* 4.3 28.4 - - - +
657K ARG 3.6 5.4 + - - -
658K GLU* 2.7 25.0 + - - -
660K ASN* 1.3 77.9 - - - +
662K MET* 1.3 62.0 + - - +
664K GLU* 3.6 11.2 - - - +
665K GLU* 2.9 31.3 + - - +
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Residues in contact with MET 662 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478K VAL* 4.5 11.9 - - + -
490K LEU* 3.7 14.8 - - + -
597K ILE* 6.1 1.1 - - + -
610K LEU* 5.3 9.0 - - + -
613K LEU* 3.2 36.6 - - + -
614K ASN* 3.4 27.4 - - - +
617K ALA* 3.5 22.4 - - + -
658K GLU 2.9 4.6 + - - +
659K THR* 3.4 32.3 - - + +
660K ASN 3.2 0.2 - - - -
661K SER* 1.3 83.2 + - - +
663K VAL* 1.3 85.7 + - + +
665K GLU* 3.1 1.2 + - - +
666K PHE* 3.0 27.4 + - + -
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Residues in contact with VAL 663 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478K VAL* 5.5 8.1 - - + -
490K LEU* 4.5 9.6 - - + -
590K TYR* 4.5 15.3 - - + +
659K THR* 3.0 13.3 + - + +
660K ASN* 3.1 21.8 - - - +
662K MET* 1.3 94.2 - - + +
664K GLU* 1.3 67.4 + - - +
666K PHE* 3.4 3.3 + - - +
667K MET* 2.9 57.0 + - + +
2001K MG 4.5 13.2 - - - -
60O A 4.5 8.1 - - - +
61O A 4.8 5.4 - - - +
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Residues in contact with GLU 664 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621K LYS* 5.8 3.1 + - - -
624K ARG* 5.2 4.7 + - - -
660K ASN* 2.9 27.0 + - - +
661K SER* 3.6 9.8 - - - +
663K VAL* 1.3 78.9 - - - +
665K GLU* 1.3 65.0 + - + +
667K MET* 3.3 1.9 + - - +
668K LEU* 2.9 46.6 + - + +
59O A 3.2 29.2 + - - +
60O A 3.3 38.8 - - - +
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Residues in contact with GLU 665 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617K ALA* 4.2 11.7 - - - +
620K LEU* 4.2 20.0 - - + +
621K LYS* 2.8 45.0 - - + +
624K ARG* 2.2 48.9 + - - +
661K SER* 2.9 21.4 + - - +
662K MET* 3.7 4.0 - - - +
664K GLU* 1.3 78.0 - - + +
666K PHE* 1.3 66.6 + - + +
668K LEU* 3.3 5.1 + - - +
669K LEU* 2.9 25.0 + - - +
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Residues in contact with PHE 666 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490K LEU* 4.6 9.4 - - + -
502K VAL* 3.8 34.1 - - + -
504K VAL* 4.5 17.1 - - + +
564K TRP* 4.6 3.8 - + - -
566K MET* 5.4 4.7 - - + -
613K LEU* 3.2 52.0 - - + -
616K LEU* 4.1 11.0 - - + -
617K ALA* 3.7 22.2 - - + -
620K LEU* 4.6 13.9 - - + -
662K MET* 3.0 29.8 + - + +
663K VAL 3.9 3.8 - - - +
665K GLU* 1.3 76.7 - - + +
667K MET* 1.3 59.9 + - + +
669K LEU* 3.3 12.7 + - + +
670K ALA* 3.0 27.4 + - - +
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Residues in contact with MET 667 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488K ASP* 3.3 41.3 - - + +
489K ALA 4.7 1.8 - - - +
490K LEU* 3.7 26.7 - - + -
504K VAL* 4.6 19.3 - - + -
506K ILE* 4.8 2.2 - - + -
663K VAL* 2.9 32.4 + - + +
664K GLU* 3.8 3.8 - - - +
666K PHE* 1.3 76.2 - - + +
668K LEU* 1.3 58.7 + - - +
670K ALA* 3.3 5.6 + - - +
671K ASN* 2.9 35.8 + - - +
776K THR* 3.5 28.5 - - + +
60O A 4.2 14.6 - - - +
61O A 4.2 3.6 - - - +
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Residues in contact with LEU 668 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624K ARG* 3.2 36.1 - - - +
664K GLU* 2.9 46.1 + - + +
665K GLU* 3.7 4.0 - - - +
667K MET* 1.3 73.9 - - - +
669K LEU* 1.3 65.9 + - - +
671K ASN* 3.3 3.9 + - - +
672K ILE* 2.9 33.0 + - + +
767K LEU* 3.9 16.6 - - + -
772K TYR* 3.0 38.8 - - + +
59O A 4.1 6.5 - - - +
60O A 3.8 14.8 - - - -
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Residues in contact with LEU 669 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564K TRP* 4.1 18.4 - - + -
566K MET* 3.7 31.0 - - + -
572K ILE* 4.3 17.5 - - + -
620K LEU* 4.2 25.1 - - + -
665K GLU 2.9 13.5 + - - +
666K PHE* 3.3 13.7 + - + +
668K LEU* 1.3 77.0 - - - +
670K ALA* 1.3 62.6 + - - +
672K ILE* 3.3 12.4 + - + +
673K SER* 3.0 30.7 + - - +
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Residues in contact with ALA 670 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504K VAL* 3.8 18.4 - - + -
562K CYS* 5.1 3.6 - - + -
564K TRP* 3.4 25.3 - - + -
577K PHE* 5.0 0.2 - - - -
666K PHE 3.0 12.4 + - - +
667K MET* 3.5 11.4 - - - +
668K LEU 3.2 0.2 - - - -
669K LEU* 1.3 76.3 - - - +
671K ASN* 1.3 62.6 + - - +
673K SER* 3.3 1.6 + - - -
674K VAL* 2.9 30.6 + - + +
775K PHE* 5.3 9.4 - - + -
776K THR* 5.3 5.2 - - + -
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Residues in contact with ASN 671 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667K MET* 2.9 27.5 + - - +
668K LEU* 3.3 2.4 + - - +
670K ALA* 1.3 76.3 - - - +
672K ILE* 1.3 57.5 + - - +
674K VAL* 3.4 0.5 + - - +
675K ALA* 2.9 30.7 + - - +
772K TYR* 3.1 36.8 + - + -
773K THR* 2.9 21.7 - - - +
774K HIS* 4.1 2.3 - - - +
775K PHE* 2.6 41.3 + - - +
776K THR* 3.8 13.4 + - - +
781K ARG* 6.0 0.8 - - - +
60O A 4.6 4.4 + - - -
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Residues in contact with ILE 672 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624K ARG* 5.7 4.5 - - - +
627K LYS* 6.1 2.2 - - - +
668K LEU* 2.9 27.1 + - + +
669K LEU* 3.8 12.1 - - + +
671K ASN* 1.3 75.3 - - - +
673K SER* 1.3 64.4 + - - +
675K ALA* 3.2 6.7 + - - +
676K LYS* 2.9 50.3 + - + +
767K LEU* 4.8 9.9 - - + -
769K SER* 4.5 18.2 - - - -
770K PRO* 6.3 1.1 - - + -
771K ILE* 4.0 16.8 - - + +
772K TYR* 3.9 19.3 - - + -
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Residues in contact with SER 673 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564K TRP* 3.5 26.3 + - - -
572K ILE* 4.4 8.8 - - - +
575K THR* 5.8 1.5 - - - +
577K PHE* 3.8 19.3 - - - -
669K LEU* 3.0 18.8 + - - +
670K ALA 3.8 3.1 - - - -
672K ILE* 1.3 78.8 - - - +
674K VAL* 1.3 63.3 + - - +
676K LYS* 3.3 10.2 + - - +
677K LYS* 3.0 23.7 + - - +
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Residues in contact with VAL 674 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562K CYS* 5.3 1.3 - - - -
577K PHE* 3.4 27.1 - - + -
670K ALA* 2.9 21.5 + - + +
671K ASN 3.7 3.8 - - - +
673K SER* 1.3 75.6 - - - +
675K ALA* 1.3 58.8 + - - +
677K LYS* 3.3 2.6 + - - +
678K ILE* 2.9 33.8 + - + +
773K THR* 4.4 3.1 - - + -
775K PHE* 3.6 37.0 - - + -
787K VAL* 3.7 29.8 - - + -
791K LEU* 4.0 13.2 - - + -
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Residues in contact with ALA 675 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671K ASN 2.9 13.1 + - - +
672K ILE* 3.5 5.4 - - - +
673K SER 3.1 0.2 - - - -
674K VAL* 1.3 74.1 - - - +
676K LYS* 1.3 65.2 + - - +
678K ILE* 3.4 6.4 - - - +
679K HIS* 2.9 27.0 + - - +
688K LEU* 5.2 2.9 - - + +
771K ILE* 3.3 28.0 - - + +
772K TYR 4.3 0.4 - - - -
773K THR* 3.3 33.7 - - + +
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Residues in contact with LYS 676 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672K ILE* 2.9 39.9 + - + +
673K SER* 3.7 8.3 - - - +
675K ALA* 1.3 75.2 - - - +
677K LYS* 1.3 56.9 + - - +
679K HIS* 3.6 5.3 - - - +
680K GLU* 2.9 45.0 + - + +
770K PRO* 5.9 6.5 - - - -
771K ILE* 4.5 19.3 - - + +
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Residues in contact with LYS 677 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577K PHE* 3.4 33.3 - - + -
673K SER 3.0 16.3 + - - +
674K VAL* 3.6 5.6 - - - +
675K ALA 3.2 0.2 - - - -
676K LYS* 1.3 78.1 - - - +
678K ILE* 1.3 56.7 + - - +
679K HIS 3.0 0.3 + - - -
680K GLU* 3.3 8.0 + - - +
681K GLU* 3.0 47.8 + - + +
791K LEU* 3.7 16.6 - - + -
794K ALA* 5.1 8.8 + - + -
795K ILE* 3.5 31.8 - - - +
----------------------------------------------------------
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Residues in contact with ILE 678 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674K VAL* 2.9 20.9 + - + +
675K ALA* 3.4 15.3 - - - +
677K LYS* 1.3 75.2 - - - +
679K HIS* 1.3 57.6 + - + +
681K GLU* 4.6 1.8 - - - -
682K PHE* 3.0 41.8 + - + +
686K ALA* 4.8 11.5 - - + +
687K LEU 4.5 11.4 - - - +
688K LEU* 5.2 3.1 - - + -
773K THR* 4.5 6.3 - - + -
787K VAL* 4.2 22.9 - - + +
790K LEU* 4.5 17.7 - - + -
791K LEU* 3.7 44.2 - - + +
794K ALA* 5.3 1.8 - - + -
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Residues in contact with HIS 679 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675K ALA 2.9 18.9 + - - +
676K LYS* 3.6 6.9 + - - +
678K ILE* 1.3 75.6 - - + +
680K GLU* 1.3 73.3 + - - +
681K GLU 3.1 1.1 - - - -
682K PHE 2.6 29.3 - - - +
683K SER* 3.6 16.9 + - - -
686K ALA* 5.8 1.3 - - - -
688K LEU* 4.6 17.9 - - + -
756K SER* 4.6 7.4 - - - -
762K PHE* 3.4 38.7 - + - -
771K ILE* 5.4 11.3 - - + +
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Residues in contact with GLU 680 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676K LYS* 2.9 27.7 + - + +
677K LYS* 3.8 7.0 - - - +
679K HIS* 1.3 81.4 + - - +
681K GLU* 1.3 67.6 + - + +
682K PHE 5.0 0.2 - - - -
683K SER* 5.3 1.9 + - - -
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Residues in contact with GLU 681 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677K LYS* 3.0 35.9 + - + +
678K ILE* 4.6 0.2 - - - -
680K GLU* 1.3 85.3 - - + +
682K PHE* 1.3 77.3 + - + +
683K SER 4.2 0.7 + - - -
794K ALA* 4.4 24.3 - - + +
----------------------------------------------------------
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Residues in contact with PHE 682 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678K ILE* 3.0 30.4 + - + +
679K HIS* 2.6 24.4 - - - +
681K GLU* 1.3 88.3 - - + +
683K SER* 1.3 58.3 + - - +
684K GLU* 3.6 2.5 - - - +
685K HIS* 3.1 57.3 - + + +
686K ALA* 4.8 3.1 - - + +
756K SER* 4.5 2.8 + - - -
790K LEU* 3.6 28.3 - - + -
793K VAL* 3.7 24.7 - - + -
794K ALA* 3.8 17.3 - - + -
804K LEU* 6.3 0.4 - - + -
----------------------------------------------------------
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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