Contacts of the helix formed by residues 568 - 600 (chain E) in PDB entry 6OD3
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 MET 568 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E HIS* 1.3 98.0 + - + +
569E ARG* 1.3 58.3 + - - +
570E ARG 3.4 0.2 - - - -
571E MET* 3.8 2.9 - - - -
572E ALA* 2.9 27.7 + - - +
594G MET 3.3 27.1 - - - +
595G VAL* 3.9 17.7 - - - +
596G GLN* 3.9 29.8 + - + +
613G GLN* 3.2 10.1 + - - +
617G VAL* 4.2 24.0 - - + -
618H ILE* 6.3 0.9 - - - -
573I ASN* 4.5 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 569 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E HIS* 3.2 2.5 - - - +
568E MET* 1.3 78.4 - - - +
570E ARG* 1.3 92.8 + - + +
572E ALA* 3.3 6.0 + - - +
573E ASN* 3.0 59.4 + - - +
596G GLN* 3.6 16.6 + - - +
573I ASN* 5.9 0.9 - - + +
574I ASN* 6.0 7.2 - - - +
577I GLU* 5.6 9.1 - - - +
10Z G 4.9 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 570 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E HIS* 3.4 11.6 + - - +
569E ARG* 1.3 108.3 - - - +
571E MET* 1.3 59.6 + - + +
573E ASN* 3.4 8.9 + - - +
574E ASN* 2.9 30.0 + - - +
581I VAL* 5.7 7.3 - - - +
9Z T 3.2 60.3 + - + +
10Z G 3.6 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 571 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E HIS* 3.2 45.0 + - + +
568E MET* 4.3 2.9 - - - -
570E ARG* 1.3 77.8 - - + +
572E ALA* 1.3 58.4 + - - +
574E ASN* 3.4 6.5 + - - +
575E ALA* 2.9 23.9 + - - +
613G GLN* 3.0 20.0 - - - +
616G ALA* 3.3 45.8 - - + +
617G VAL* 3.9 12.3 - - + +
620G SER* 4.2 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 572 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568E MET 2.9 18.7 + - - +
569E ARG* 3.3 5.6 + - - +
571E MET* 1.3 74.5 - - - +
573E ASN* 1.3 67.9 + - - +
575E ALA* 3.3 2.9 + - - +
576E ARG* 3.1 32.4 + - - +
596G GLN 3.6 22.7 - - - +
597G LEU* 4.2 14.9 - - + +
613G GLN* 3.3 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 573 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569E ARG* 3.0 52.5 + - - +
570E ARG* 3.4 7.7 + - - +
572E ALA* 1.3 76.9 - - - +
574E ASN* 1.3 62.9 + - - +
576E ARG* 3.4 16.7 + - - +
577E GLU* 3.1 22.3 + - - +
3Y T 5.7 5.2 - - - +
9Z T 3.8 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 574 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570E ARG 2.9 17.8 + - - +
571E MET* 3.7 8.0 - - - +
573E ASN* 1.3 73.7 - - - +
575E ALA* 1.3 60.7 + - - +
577E GLU* 3.1 1.0 + - - -
578E ARG* 2.7 71.9 + - - +
8Z G 2.8 46.4 + - - +
9Z T 3.7 14.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 575 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E MET 2.9 17.8 + - - +
572E ALA* 3.6 6.3 - - - +
574E ASN* 1.3 77.4 - - - +
576E ARG* 1.3 60.5 + - - +
578E ARG* 3.5 6.2 + - - +
579E LEU* 3.2 17.7 + - - +
597G LEU* 4.5 6.5 - - + -
609G LEU* 3.4 25.3 - - + +
612G HIS* 4.9 9.6 + - + -
613G GLN* 3.8 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 576 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572E ALA* 3.1 20.2 + - - +
573E ASN* 3.7 15.6 + - - +
574E ASN 3.2 0.2 - - - -
575E ALA* 1.3 75.3 - - - +
577E GLU* 1.3 63.8 + - - +
579E LEU* 3.4 4.0 + - - +
580E ARG* 3.1 21.8 + - - +
596G GLN 5.3 1.0 + - - -
597G LEU* 3.4 38.7 - - + +
598G HIS* 4.4 7.9 + - - +
600G LYS* 6.2 0.6 - - - +
606G THR* 5.2 7.7 - - - +
609G LEU* 3.8 31.3 - - + +
3Y T 4.1 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 577 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573E ASN 3.1 15.7 + - - +
574E ASN 3.8 2.7 - - - +
576E ARG* 1.3 76.1 - - - +
578E ARG* 1.3 86.1 + - - +
580E ARG* 2.7 45.1 + - - -
581E VAL* 3.0 31.0 + - - +
5Y C 3.3 16.5 + - - +
6Y A 3.1 20.3 + - - +
7Z C 6.0 0.2 - - - -
8Z G 4.4 2.3 - - - +
9Z T 3.3 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 578 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574E ASN* 2.7 59.1 + - - +
575E ALA* 4.0 6.3 - - - +
577E GLU* 1.3 97.9 - - - +
579E LEU* 1.3 57.2 + - - +
581E VAL* 3.7 16.7 - - - +
582E ARG* 3.0 30.5 + - - +
6Z A 4.3 0.2 - - - +
7Z C 2.5 72.5 + - - +
8Z G 3.1 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 579 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575E ALA 3.2 17.0 + - - +
576E ARG 3.8 4.3 - - - +
578E ARG* 1.3 75.9 - - - +
580E ARG* 1.3 60.2 + - - +
582E ARG* 4.5 11.9 - - + +
583E ASP* 2.9 56.6 + - - +
605G GLN* 3.6 36.1 - - + +
608G LEU* 3.9 21.5 - - + -
609G LEU* 3.7 22.0 - - + -
612G HIS* 4.9 10.3 - - + +
580H ARG* 3.8 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 580 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576E ARG 3.1 17.5 + - - +
577E GLU* 2.7 44.2 + - - +
579E LEU* 1.3 76.6 - - - +
581E VAL* 1.3 70.5 + - - +
583E ASP* 3.8 5.6 - - - +
584E ILE* 3.0 52.1 + - + +
607F LYS* 4.8 4.2 - - - +
608F LEU* 6.4 0.9 - - + -
4Y A 3.9 16.6 - - - -
5Y C 3.0 64.5 + - - +
6Y A 4.3 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 581 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577E GLU* 3.0 41.7 + - - +
578E ARG* 3.7 15.9 - - - +
580E ARG* 1.3 84.5 - - - +
582E ARG* 1.3 58.5 + - - +
584E ILE* 3.3 8.3 + - + +
585E ASN* 2.9 27.6 + - + +
607E LYS* 5.4 2.9 + - - +
6Z A 3.7 46.6 + - + +
7Z C 4.4 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 582 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578E ARG 3.0 20.5 + - - +
579E LEU* 3.9 12.0 - - + +
581E VAL* 1.3 79.7 - - - +
583E ASP* 1.3 59.6 + - - +
585E ASN* 3.3 7.8 + - + +
586E GLU* 2.9 63.0 + - + +
612G HIS* 6.5 0.4 - - - -
580H ARG* 5.5 2.2 - - - +
582H ARG* 5.9 2.8 - - - +
583H ASP* 3.9 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 583 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ARG* 5.9 0.5 + - - -
579E LEU* 2.9 33.0 + - - +
580E ARG* 3.8 6.3 - - - +
582E ARG* 1.3 78.5 + - - +
584E ILE* 1.3 62.1 + - - +
586E GLU* 3.4 15.1 + - - +
587E ALA* 3.1 18.7 + - - +
608F LEU* 3.5 33.7 - - + +
605G GLN* 4.3 7.4 + - - -
578H ARG* 4.9 6.4 + - - +
580H ARG* 3.2 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 584 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580E ARG* 3.0 55.3 + - + +
581E VAL* 3.7 6.7 - - - +
583E ASP* 1.3 76.2 - - + +
585E ASN* 1.3 58.6 + - - +
587E ALA* 3.3 2.6 + - - +
588E PHE* 2.9 53.7 + - + -
607E LYS* 4.2 6.5 - - - +
701E CL 4.1 10.8 - - + -
607F LYS* 4.0 23.8 - - + -
608F LEU* 4.2 25.4 - - + +
611F LEU* 3.9 5.1 - - + +
5Y C 4.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 585 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581E VAL* 2.9 17.4 + - + +
582E ARG* 3.6 9.0 - - + +
583E ASP 3.2 0.4 - - - -
584E ILE* 1.3 77.7 - - - +
586E GLU* 1.3 67.3 + - - +
588E PHE* 3.3 8.5 + - - +
589E LYS* 3.1 55.1 + - - +
607E LYS* 5.2 5.1 - - - +
5Z C 5.1 0.2 + - - -
6Z A 3.3 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 586 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B HIS* 4.8 9.7 - - - -
570B ARG* 6.1 3.6 - - - +
571B MET* 4.7 1.0 - - - +
582E ARG* 2.9 48.4 + - + +
583E ASP* 3.7 23.0 - - - +
584E ILE 3.4 0.2 - - - -
585E ASN* 1.3 81.3 - - - +
587E ALA* 1.3 61.5 + - - +
589E LYS* 3.4 9.3 + - + +
590E GLU* 3.3 21.7 + - - +
578H ARG* 5.9 1.7 + - - -
580H ARG* 4.8 4.2 + - - -
582H ARG* 4.7 13.3 + - - -
583H ASP* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 587 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ARG* 5.5 1.3 - - - +
571B MET* 3.7 32.3 - - + +
583E ASP 3.1 17.7 + - - +
584E ILE 3.8 0.2 - - - +
585E ASN 3.2 0.2 - - - -
586E GLU* 1.3 75.8 - - - +
588E PHE* 1.3 63.4 + - - +
590E GLU 3.5 0.5 + - - -
591E LEU* 3.0 26.0 + - - +
608F LEU* 4.0 11.7 - - + -
611F LEU* 3.6 25.5 - - + +
612F HIS* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 588 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584E ILE* 2.9 44.9 + - + +
585E ASN* 3.6 7.9 - - - +
587E ALA* 1.3 76.9 - - - +
589E LYS* 1.3 54.1 + - + +
591E LEU* 4.0 2.6 - - - +
592E GLY* 2.7 33.4 + - - -
607E LYS* 3.5 57.0 - - + -
610E ILE* 3.7 35.7 - - + +
611E LEU* 3.8 17.3 - - + -
701E CL 4.0 2.0 - - + -
588F PHE* 3.6 34.3 - + - -
611F LEU* 3.8 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 589 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585E ASN* 3.1 46.4 + - - +
586E GLU* 3.8 8.3 - - + +
587E ALA 3.3 0.2 - - - -
588E PHE* 1.3 78.2 - - + +
590E GLU* 1.3 60.8 + - - +
592E GLY* 4.0 0.6 - - - -
593E ARG* 3.1 37.6 + - - +
610E ILE* 5.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 590 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B HIS 4.6 1.0 - - - +
568B MET 3.3 23.3 - - - +
569B ARG* 3.1 23.6 + - - +
570B ARG* 3.3 8.0 + - - +
571B MET* 3.1 44.8 + - + +
572B ALA* 2.7 30.1 + - - +
586E GLU 3.3 9.9 + - - +
589E LYS* 1.3 77.4 - - - +
591E LEU* 1.3 65.9 + - - +
593E ARG* 3.4 13.1 + - - +
594E MET* 3.1 26.6 + - + +
615F VAL* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 591 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587E ALA 3.0 17.7 + - - +
588E PHE* 4.0 2.2 - - - +
590E GLU* 1.3 76.7 - - - +
592E GLY* 1.3 58.0 + - - +
594E MET* 3.2 5.8 + - - +
595E VAL* 3.0 44.2 + - + +
610E ILE* 4.1 14.8 - - + -
611E LEU* 5.3 0.9 - - + -
614E ALA* 4.2 17.5 - - + -
591F LEU* 4.5 3.4 - - + -
611F LEU* 3.7 30.1 - - + +
614F ALA* 4.2 16.6 - - + -
615F VAL* 3.8 27.0 - - + +
618F ILE* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 592 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588E PHE 2.7 23.1 + - - -
589E LYS* 4.0 1.3 - - - -
591E LEU* 1.3 73.9 - - - +
593E ARG* 1.3 60.5 + - - +
595E VAL* 3.3 1.2 - - - +
596E GLN* 3.2 13.9 + - - +
605E GLN* 3.0 40.7 + - - +
610E ILE* 3.8 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 593 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B MET* 3.2 49.7 + - - +
569B ARG* 4.1 18.3 - - - +
589E LYS* 3.1 26.5 + - - +
590E GLU* 3.7 13.5 + - - +
591E LEU 3.3 0.2 - - - -
592E GLY* 1.3 75.3 - - - +
594E MET* 1.3 60.8 + - - +
596E GLN* 3.6 12.3 + - - +
597E LEU* 3.4 35.2 + - + +
605E GLN* 4.2 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 594 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B ARG* 4.0 28.9 - - - +
572B ALA* 4.2 6.7 - - + -
590E GLU* 3.1 13.3 + - + +
591E LEU* 3.2 9.6 + - + +
593E ARG* 1.3 75.8 - - - +
595E VAL* 1.3 65.4 + - - +
597E LEU* 3.3 9.0 + - - +
598E HIS* 3.3 37.1 + - + +
615F VAL* 3.6 41.1 - - + -
618F ILE* 4.0 31.6 - - + -
619F LEU* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 595 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591E LEU* 3.0 30.8 + - + +
592E GLY* 3.3 17.7 - - - +
594E MET* 1.3 74.2 - - - +
596E GLN* 1.3 63.8 + - - +
598E HIS* 4.0 1.5 - - - +
599E LEU* 3.1 30.5 + - - +
605E GLN* 3.5 2.9 - - - +
610E ILE* 4.5 4.9 - - + -
613E GLN* 3.3 36.6 - - + +
614E ALA* 3.8 27.6 - - + +
617E VAL* 4.2 11.9 - - + -
618F ILE* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 596 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592E GLY 3.2 10.5 + - - +
593E ARG* 3.8 12.3 - - - +
594E MET 3.2 0.2 - - - -
595E VAL* 1.3 77.7 - - - +
597E LEU* 1.3 61.2 + - + +
600E LYS* 2.7 26.3 + - - -
601E SER* 3.1 39.0 + - - +
602E ASP* 4.3 5.9 - - - +
603E LYS 3.2 26.3 + - - -
604E PRO* 5.2 0.4 - - - +
605E GLN* 3.3 36.9 + - + +
613E GLN* 4.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 597 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593E ARG* 3.4 26.2 + - + +
594E MET* 3.3 9.7 + - - +
596E GLN* 1.3 80.5 - - + +
598E HIS* 1.3 65.6 + - + +
600E LYS* 3.6 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 598 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E MET* 3.3 31.5 + - + +
595E VAL 4.0 0.4 - - - +
596E GLN 3.3 0.4 - - - -
597E LEU* 1.3 81.9 - - + +
599E LEU* 1.3 62.6 + - + +
600E LYS* 3.6 1.2 + - - +
617E VAL* 3.9 28.8 - - + +
621E LEU* 4.3 19.7 - - + +
618F ILE* 3.6 28.4 - - + +
619F LEU* 5.7 0.6 - - - +
622F GLU* 4.0 32.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 599 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595E VAL 3.1 15.8 + - - +
596E GLN 4.3 1.3 - - - +
598E HIS* 1.3 77.3 - - - +
600E LYS* 1.3 69.5 + - - +
601E SER* 3.3 12.1 + - - -
613E GLN* 3.7 44.2 - - + +
616E ALA* 5.0 10.5 - - + +
617E VAL* 3.7 25.8 - - + +
620E SER* 6.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 600 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596E GLN 2.7 11.3 + - - -
597E LEU* 3.6 7.7 + - - +
598E HIS 3.4 4.5 - - - +
599E LEU* 1.3 80.8 - - - +
601E SER* 1.3 57.2 + - - +
602E ASP* 4.3 0.9 + - - +
----------------------------------------------------------
Back to top of page
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