Contacts of the helix formed by residues 603 - 628 (chain G) 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 LYS 603 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599G LEU* 4.8 0.9 - - - +
600G LYS* 3.0 41.5 + - + +
601G SER 3.2 1.9 - - - -
602G ASP* 1.3 108.8 + - - +
604G PRO* 1.3 61.9 - - - +
605G GLN* 3.0 10.1 - - + +
606G THR* 2.6 39.3 + - + +
577H GLU* 3.4 29.2 - - - +
3Y T 4.4 8.5 + - - -
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Residues in contact with PRO 604 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601G SER 5.0 3.1 - - - +
602G ASP 3.8 2.2 - - - +
603G LYS* 1.3 84.5 - - - +
605G GLN* 1.3 61.0 + - - +
606G THR 3.2 0.4 - - - -
607G LYS* 3.1 34.5 + - + +
608G LEU* 3.5 4.3 + - - +
577H GLU* 3.7 24.7 - - + +
578H ARG 3.4 22.0 - - - +
579H LEU* 3.7 35.4 - - + +
580H ARG* 5.0 1.6 - - - +
584H ILE* 3.8 9.4 - - + +
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Residues in contact with GLN 605 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579E LEU* 3.6 26.7 - - + +
583E ASP* 4.3 6.2 + - - -
608F LEU* 5.9 4.2 - - - +
603G LYS* 3.0 7.4 - - + -
604G PRO* 1.3 80.5 - - - +
606G THR* 1.3 61.8 + - + +
608G LEU* 3.3 8.5 + - + +
609G LEU* 3.1 30.0 + - + +
577H GLU* 5.4 8.2 + - - +
578H ARG 4.6 2.8 + - - +
580H ARG* 4.0 27.9 - - + +
4Y A 5.4 3.6 + - - -
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Residues in contact with THR 606 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576E ARG* 5.2 11.4 - - - +
597G LEU* 5.0 1.6 - - + -
598G HIS 4.0 12.8 - - - +
599G LEU* 3.4 6.1 - - - +
600G LYS* 3.1 51.8 + - + -
603G LYS* 2.6 26.2 + - + +
605G GLN* 1.3 76.7 - - + +
607G LYS* 1.3 60.1 + - - +
609G LEU* 3.3 11.6 + - + +
610G ILE* 2.9 36.3 + - - +
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Residues in contact with LYS 607 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584G ILE* 5.4 5.5 - - - +
585G ASN* 3.1 26.7 + - - -
588G PHE* 3.6 46.2 - - + -
599G LEU* 3.6 23.6 - - + -
600G LYS 5.9 0.7 - - - -
601G SER* 5.9 3.6 - - - +
604G PRO* 3.1 24.5 + - + +
606G THR* 1.3 78.4 + - - +
608G LEU* 1.3 61.3 + - - +
610G ILE* 3.3 1.1 + - - -
611G LEU* 3.1 29.2 + - - +
584H ILE* 4.0 13.7 - - + -
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Residues in contact with LEU 608 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579E LEU* 3.9 22.4 - - + -
604G PRO 3.5 3.3 + - - +
605G GLN* 3.3 12.6 + - + +
607G LYS* 1.3 78.4 - - - +
609G LEU* 1.3 62.3 + - - +
611G LEU* 3.3 4.8 + - - +
612G HIS* 3.0 55.2 + - + +
580H ARG* 3.8 34.8 - - + +
583H ASP* 3.4 40.4 - - + +
584H ILE* 3.9 14.9 - - + +
587H ALA* 3.9 6.3 - - + -
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Residues in contact with LEU 609 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575E ALA* 3.4 38.0 - - + +
576E ARG* 3.8 36.6 - - + +
579E LEU* 3.7 26.0 - - + -
597G LEU* 3.6 17.2 - - + +
605G GLN* 3.1 27.8 + - + +
606G THR* 3.3 11.9 + - + +
608G LEU* 1.3 72.1 - - - +
610G ILE* 1.3 60.8 + - - +
612G HIS* 3.3 9.0 + - - +
613G GLN* 2.8 31.7 + - - +
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Residues in contact with ILE 610 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588G PHE* 3.5 34.3 - - + +
591G LEU* 3.8 31.6 - - + -
592G GLY* 3.8 10.8 - - - +
595G VAL* 4.6 3.0 - - + +
597G LEU* 3.2 33.4 - - + +
599G LEU* 3.8 24.5 - - + -
606G THR 2.9 21.1 + - - +
607G LYS 3.7 4.7 - - - +
608G LEU 3.3 0.2 - - - -
609G LEU* 1.3 75.3 - - - +
611G LEU* 1.3 58.2 + - - +
613G GLN* 3.8 5.2 - - - +
614G ALA* 2.8 29.5 + - - +
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Residues in contact with LEU 611 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588G PHE* 3.9 17.7 - - + -
591G LEU* 4.9 1.8 - - + -
607G LYS 3.1 16.4 + - - +
608G LEU* 3.6 3.6 - - - +
609G LEU 3.3 0.2 - - - -
610G ILE* 1.3 77.1 - - - +
612G HIS* 1.3 62.7 + - - +
614G ALA* 3.5 4.8 + - - +
615G VAL* 3.2 29.3 + - - +
584H ILE* 3.8 13.2 - - + +
587H ALA* 3.6 32.8 - - + +
588H PHE* 3.6 37.9 - - + +
591H LEU* 3.7 25.8 - - + +
611H LEU* 3.9 11.9 - - + -
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Residues in contact with HIS 612 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575E ALA* 4.9 11.9 + - + -
579E LEU* 4.9 11.1 - - + +
582E ARG* 6.5 0.7 - - - -
608G LEU* 3.0 52.0 + - + +
609G LEU* 3.7 13.9 - - - +
611G LEU* 1.3 77.0 - - - +
613G GLN* 1.3 61.3 + - - +
615G VAL* 3.4 7.5 + - + +
616G ALA* 3.2 21.4 + - - +
583H ASP* 5.0 0.8 + - + -
587H ALA* 3.9 18.4 - - + +
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Residues in contact with GLN 613 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568E MET* 3.2 27.5 + - - +
571E MET* 3.0 35.6 - - - +
572E ALA* 3.3 11.9 + - - +
575E ALA* 3.8 6.6 - - + +
595G VAL* 3.5 36.4 + - + +
597G LEU* 3.8 12.6 - - + -
609G LEU 2.8 21.4 + - - +
610G ILE 3.8 2.9 - - - +
612G HIS* 1.3 73.8 - - - +
614G ALA* 1.3 56.9 + - - +
616G ALA* 3.2 7.2 + - - +
617G VAL* 2.8 45.1 + - - +
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Residues in contact with ALA 614 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591G LEU* 4.0 31.2 - - + -
595G VAL* 4.2 11.8 - - + +
610G ILE 2.8 21.7 + - - +
611G LEU 3.8 4.5 - - - +
612G HIS 3.3 0.4 - - - -
613G GLN* 1.3 75.5 - - - +
615G VAL* 1.3 56.5 + - - +
617G VAL* 3.8 1.1 - - - +
618G ILE* 3.0 36.4 + - - +
591H LEU* 4.1 16.8 - - + -
614H ALA* 5.0 0.9 - - + -
618H ILE* 4.7 3.6 - - + -
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Residues in contact with VAL 615 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611G LEU 3.2 15.9 + - - +
612G HIS* 3.8 9.4 - - + +
614G ALA* 1.3 74.7 - - - +
616G ALA* 1.3 57.6 + - - +
618G ILE* 3.5 4.1 + - - +
619G LEU* 3.0 43.1 + - + +
587H ALA 4.8 1.6 - - - +
590H GLU* 4.3 19.3 - - + +
591H LEU* 3.8 38.1 - - + +
594H MET* 4.1 19.0 - - + +
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Residues in contact with ALA 616 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E MET* 3.3 26.9 - - + +
612G HIS 3.2 14.7 + - - +
613G GLN* 3.2 11.9 + - - +
615G VAL* 1.3 78.2 - - - +
617G VAL* 1.3 56.7 + - - +
619G LEU* 3.9 8.3 - - - +
620G SER* 3.0 22.9 + - - -
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Residues in contact with VAL 617 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E HIS* 5.7 2.5 - - + -
568E MET* 4.2 23.1 - - + -
571E MET* 4.1 7.4 - - + -
595G VAL* 3.9 19.5 - - + -
613G GLN* 2.8 44.8 + - - +
614G ALA 3.8 3.4 - - - +
615G VAL 3.3 0.2 - - - -
616G ALA* 1.3 71.9 - - - +
618G ILE* 1.3 59.6 + - - +
620G SER* 3.2 3.1 + - - -
621G LEU* 2.8 51.0 + - + +
618H ILE* 4.1 19.1 - - + -
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Residues in contact with ILE 618 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614G ALA 3.0 22.3 + - - +
615G VAL* 3.9 2.9 - - - +
617G VAL* 1.3 76.1 - - - +
619G LEU* 1.3 58.1 + - - +
621G LEU* 3.3 2.3 + - - +
622G GLU* 2.9 54.8 + - - +
591H LEU* 3.9 23.3 - - + -
594H MET* 3.7 19.1 - - + +
595H VAL* 4.5 11.9 - - + -
598H HIS* 4.5 1.6 - - + +
614H ALA* 4.6 4.9 - - + +
617H VAL* 4.2 20.9 - - + -
618H ILE* 3.7 24.2 - - + -
621H LEU* 4.0 15.7 - - + -
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Residues in contact with LEU 619 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615G VAL* 3.0 34.0 + - + +
616G ALA* 3.9 7.6 - - - +
618G ILE* 1.3 76.4 - - - +
620G SER* 1.3 61.6 + - - +
622G GLU* 3.5 14.3 + - - +
623G GLN* 3.3 21.3 + - - +
594H MET* 3.6 25.8 - - + -
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Residues in contact with SER 620 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E HIS* 3.8 13.2 + - - -
571E MET* 4.2 14.6 - - - -
616G ALA 3.0 18.3 + - - -
617G VAL* 3.2 5.4 + - - -
619G LEU* 1.3 76.3 - - - +
621G LEU* 1.3 63.5 + - - +
623G GLN* 3.2 8.2 + - - +
624G GLN* 3.1 40.2 + - - +
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Residues in contact with LEU 621 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E HIS* 5.0 6.5 - - + +
617G VAL* 2.8 33.9 + - + +
618G ILE* 4.9 0.2 - - - -
620G SER* 1.3 72.1 - - - +
622G GLU* 1.3 63.1 + - - +
624G GLN* 3.3 26.8 + - - +
625G VAL* 3.2 28.6 + - - +
618H ILE* 3.8 35.7 - - + +
621H LEU* 3.7 33.4 - - + -
622H GLU* 4.2 11.4 - - + +
625H VAL* 4.2 10.7 - - + +
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Residues in contact with GLU 622 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618G ILE* 2.9 31.6 + - - +
619G LEU* 3.8 22.5 - - - +
621G LEU* 1.3 77.1 - - - +
623G GLN* 1.3 62.6 + - - +
625G VAL* 3.6 6.4 + - - +
626G ARG* 3.3 28.4 + - + +
594H MET* 4.1 7.6 - - - +
597H LEU* 4.3 14.1 - - - +
598H HIS* 2.6 33.1 + - + +
621H LEU* 3.9 15.5 - - + -
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Residues in contact with GLN 623 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619G LEU 3.3 10.9 + - - +
620G SER* 3.2 10.8 + - - +
622G GLU* 1.3 77.5 - - - +
624G GLN* 1.3 58.9 + - + +
626G ARG* 3.2 6.4 + - - +
627G GLU* 2.8 30.9 + - - +
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Residues in contact with GLN 624 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E HIS* 3.0 34.1 + - - -
620G SER* 3.1 26.9 + - - +
621G LEU* 3.3 20.7 + - - +
623G GLN* 1.3 79.5 - - + +
625G VAL* 1.3 61.5 + - - +
627G GLU* 3.5 16.2 + - - +
628G ARG 3.8 8.1 + - - +
625H VAL* 3.3 34.2 - - + +
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Residues in contact with VAL 625 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621G LEU 3.2 17.8 + - - +
622G GLU* 3.9 5.4 - - - +
624G GLN* 1.3 76.1 - - - +
626G ARG* 1.3 64.9 + - + +
628G ARG 3.3 18.7 - - - +
621H LEU* 4.4 15.7 - - + +
624H GLN* 4.2 24.5 - - + +
625H VAL* 3.7 20.4 - - + +
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Residues in contact with ARG 626 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622G GLU* 3.3 17.2 + - + +
623G GLN* 3.2 7.2 + - - +
625G VAL* 1.3 81.4 - - + +
627G GLU* 1.3 65.4 + - - +
628G ARG* 4.8 0.9 + - - -
597H LEU* 6.3 1.0 - - - +
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Residues in contact with GLU 627 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623G GLN 2.8 16.6 + - - +
624G GLN* 3.8 10.1 - - - +
625G VAL 3.3 0.8 - - - -
626G ARG* 1.3 81.3 - - - +
628G ARG* 1.3 92.5 + - + +
604J PRO* 4.8 9.3 - - + +
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Residues in contact with ARG 628 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624G GLN 3.8 8.0 + - - +
625G VAL* 3.3 18.2 - - - +
626G ARG 5.2 0.8 + - - -
627G GLU* 1.3 104.7 + - + +
628H ARG* 5.0 13.1 - - - +
602J ASP* 3.0 32.6 + - - +
603J LYS* 4.2 9.4 - - + +
604J PRO* 3.7 32.2 - - + +
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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