Contacts of the helix formed by residues 598 - 632 (chain C) in PDB entry 4D0G
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 GLN 598 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C LEU 3.2 2.9 + - - -
597C ILE* 1.3 79.1 - - + +
599C LEU* 1.3 56.2 + - - +
600C VAL 3.0 6.3 - - - -
601C LEU* 3.0 30.8 + - + +
602C LYS* 3.2 15.7 + - - +
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Residues in contact with LEU 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C LEU 4.1 13.3 + - - +
597C ILE* 3.2 5.2 - - - +
598C GLN* 1.3 75.8 - - - +
600C VAL* 1.3 73.5 + - + +
602C LYS* 3.6 22.4 - - + -
603C GLN* 2.5 62.1 + - + +
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Residues in contact with VAL 600 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C ILE* 3.4 23.1 - - + +
598C GLN 3.0 0.4 - - - -
599C LEU* 1.3 90.0 - - + +
601C LEU* 1.3 53.2 + - - +
603C GLN* 3.3 10.2 + - - +
604C LYS* 2.8 34.8 + - + +
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Residues in contact with LEU 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C GLN* 3.0 22.2 + - + +
600C VAL* 1.3 78.3 - - - +
602C LYS* 1.3 55.7 + - - +
604C LYS* 3.4 8.6 - - - +
605C GLU* 3.0 26.2 + - - +
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Residues in contact with LYS 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C GLN* 3.2 10.7 + - - +
599C LEU* 3.5 26.5 - - + +
600C VAL 3.2 0.2 - - - -
601C LEU* 1.3 78.0 - - - +
603C GLN* 1.3 61.9 + - + +
604C LYS 3.2 0.4 - - - -
605C GLU* 3.4 8.8 - - + +
606C THR* 2.9 37.8 + - - -
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Residues in contact with GLN 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599C LEU* 2.5 53.8 + - + +
600C VAL* 3.7 10.4 - - - +
602C LYS* 1.3 74.2 - - + +
604C LYS* 1.3 61.1 + - - +
606C THR* 3.3 9.0 + - - -
607C ILE* 2.9 41.4 + - + +
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Residues in contact with LYS 604 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C VAL* 2.8 18.5 + - + +
601C LEU* 3.4 9.6 - - - +
602C LYS 3.2 0.2 - - - -
603C GLN* 1.3 72.2 - - - +
605C GLU* 1.3 67.4 + - - +
607C ILE* 3.0 22.6 + - - +
608C SER* 3.0 17.4 + - - +
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Residues in contact with GLU 605 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C LEU 3.0 15.5 + - - +
602C LYS* 3.4 12.8 - - + +
604C LYS* 1.3 74.8 - - - +
606C THR* 1.3 64.0 + - - +
608C SER* 3.3 8.1 + - - -
609C LYS* 3.1 24.4 + - - +
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Residues in contact with THR 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C LYS* 2.9 31.0 + - - +
603C GLN* 3.4 13.0 - - - -
604C LYS 3.1 0.4 - - - -
605C GLU* 1.3 75.3 - - - +
607C ILE* 1.3 67.5 + - + +
609C LYS* 3.1 19.9 + - + +
610C LYS* 3.1 33.0 + - + +
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Residues in contact with ILE 607 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603C GLN* 2.9 32.0 + - + +
604C LYS* 3.0 10.7 + - - +
606C THR* 1.3 79.1 - - + +
608C SER* 1.3 63.6 + - - +
610C LYS* 3.0 18.2 + - + +
611C GLU* 3.0 33.0 + - + +
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Residues in contact with SER 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C LYS 3.0 12.6 + - - -
605C GLU* 3.6 10.5 - - - -
607C ILE* 1.3 77.6 - - - +
609C LYS* 1.3 62.5 + - - +
611C GLU* 3.4 17.5 + - - +
612C PHE* 3.1 22.3 + - - +
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Residues in contact with LYS 609 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605C GLU* 3.1 13.4 + - - +
606C THR* 3.1 15.2 + - + +
607C ILE 3.1 0.2 - - - -
608C SER* 1.3 78.0 - - - +
610C LYS* 1.3 62.2 + - + +
612C PHE* 3.3 13.1 + - + +
613C GLN* 3.0 26.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 610 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C THR* 3.3 30.6 - - + +
607C ILE* 3.0 7.7 + - + +
609C LYS* 1.3 78.8 - - + +
611C GLU* 1.3 61.9 + - - +
612C PHE 3.2 0.2 - - - -
613C GLN* 3.2 27.4 + - - +
614C VAL* 2.8 35.7 + - + +
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Residues in contact with GLU 611 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607C ILE* 3.0 26.0 + - + +
608C SER* 3.4 25.9 + - - +
610C LYS* 1.3 74.3 - - + +
612C PHE* 1.3 66.0 + - - +
614C VAL* 3.8 7.7 - - - +
615C ARG* 3.1 24.6 + - - +
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Residues in contact with PHE 612 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C SER 3.1 13.4 + - - +
609C LYS* 3.3 16.4 - - + +
610C LYS 3.2 0.2 - - - -
611C GLU* 1.3 75.9 - - - +
613C GLN* 1.3 66.4 + - + +
615C ARG* 3.3 5.6 + - + +
616C GLU* 3.0 57.1 + - + +
----------------------------------------------------------
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Residues in contact with GLN 613 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C LYS* 3.0 14.9 + - - +
610C LYS* 3.4 34.0 - - + +
612C PHE* 1.3 78.5 - - + +
614C VAL* 1.3 61.8 + - + +
616C GLU* 3.3 19.1 - - - +
617C LEU* 3.2 41.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 614 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610C LYS* 2.8 25.8 + - + +
611C GLU* 3.8 8.5 - - - +
612C PHE 3.2 0.2 - - - -
613C GLN* 1.3 75.4 - - + +
615C ARG* 1.3 62.6 + - - +
617C LEU* 3.3 12.3 + - + +
618C GLU* 3.0 44.0 + - + +
----------------------------------------------------------
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Residues in contact with ARG 615 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611C GLU 3.1 17.4 + - - +
612C PHE* 3.9 4.9 - - + +
614C VAL* 1.3 74.4 - - + +
616C GLU* 1.3 54.9 - - - +
618C GLU* 3.2 15.4 + - - +
619C ASP* 2.8 47.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 616 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C PHE* 3.0 45.4 + - + +
613C GLN* 3.3 26.3 - - - +
615C ARG* 1.3 75.2 - - - +
617C LEU* 1.3 59.0 + - + +
619C ASP* 3.2 10.6 + - - +
620C TYR* 3.0 26.6 + - - +
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Residues in contact with LEU 617 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C GLN* 3.2 33.3 + - + +
614C VAL* 3.3 11.6 + - + +
616C GLU* 1.3 79.2 - - + +
618C GLU* 1.3 60.8 + - + +
620C TYR* 3.4 11.4 + - + +
621C ILE* 3.1 38.7 + - + +
----------------------------------------------------------
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Residues in contact with GLU 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.8 26.1 + - - +
74A ARG* 5.1 7.2 - - - +
614C VAL* 3.0 32.6 + - + +
615C ARG* 3.6 20.4 - - - +
617C LEU* 1.3 74.3 - - + +
619C ASP* 1.3 66.6 + - - +
621C ILE* 3.9 10.0 - - + +
622C ASP* 3.1 31.9 + - - +
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Residues in contact with ASP 619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 4.9 11.8 + - - -
615C ARG* 2.8 27.2 + - - +
616C GLU* 3.5 8.2 + - - +
617C LEU 3.2 0.2 - - - -
618C GLU* 1.3 78.9 - - - +
620C TYR* 1.3 64.2 + - - +
622C ASP* 3.4 3.3 + - - +
623C ASN* 2.6 37.6 + - - +
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Residues in contact with TYR 620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616C GLU 3.0 12.5 + - - +
617C LEU* 3.6 15.3 - - + +
618C GLU 3.4 0.2 - - - -
619C ASP* 1.3 73.9 - - - +
621C ILE* 1.3 76.6 + - + +
623C ASN* 3.0 7.2 + - - +
624C LEU* 2.9 54.2 + - + +
627C ARG* 4.7 6.9 + - - -
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Residues in contact with ILE 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 4.0 22.4 - - + -
45A GLY* 4.3 11.9 - - - +
617C LEU* 3.1 26.3 + - + +
618C GLU* 3.9 10.1 - - + +
620C TYR* 1.3 86.8 - - + +
622C ASP* 1.3 59.5 + - - +
624C LEU* 3.0 8.5 + - + +
625C LEU* 2.8 57.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 5.7 1.7 - - - -
72A ARG* 5.1 1.4 + - - -
74A ARG* 3.0 61.2 + - - +
75A ALA* 3.9 14.3 + - + +
76A VAL* 3.1 21.0 - - + +
618C GLU* 3.1 18.8 + - - +
619C ASP* 3.7 6.7 - - - +
621C ILE* 1.3 83.5 - - - +
623C ASN* 1.3 57.6 + - - +
625C LEU* 3.3 2.2 + - - +
626C VAL* 3.0 27.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 623 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 4.3 18.5 - - - +
619C ASP* 2.6 35.6 + - - +
620C TYR* 3.0 6.9 + - + +
622C ASP* 1.3 76.6 - - - +
624C LEU* 1.3 66.1 - - - +
626C VAL* 3.6 6.1 + - - +
627C ARG* 3.1 50.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 624 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C TYR* 2.9 42.7 + - + +
621C ILE* 3.3 10.8 - - + +
623C ASN* 1.3 77.7 - - - +
625C LEU* 1.3 66.3 + - + +
627C ARG* 3.0 34.2 + - + +
628C VAL* 3.0 31.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 625 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 3.5 22.4 - - - -
46A VAL* 3.5 31.2 - - + +
76A VAL* 3.6 15.0 - - + -
621C ILE* 2.8 34.7 + - + +
622C ASP* 4.9 2.0 - - - +
624C LEU* 1.3 75.4 - - + +
626C VAL* 1.3 66.1 + - - +
628C VAL* 3.8 7.4 - - + +
629C MET* 2.9 31.2 + - - +
636C LEU* 3.8 34.1 - - + -
----------------------------------------------------------
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Residues in contact with VAL 626 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.3 40.6 - - + +
76A VAL* 3.7 6.4 - - - +
79A SER* 4.9 8.0 + - - +
622C ASP 3.0 21.6 + - - +
623C ASN* 3.7 9.2 - - - +
624C LEU 3.3 0.2 - - - -
625C LEU* 1.3 77.6 - - - +
627C ARG* 1.3 67.5 + - + +
629C MET* 3.2 7.5 + - - +
630C GLU* 3.1 38.9 + - + +
----------------------------------------------------------
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Residues in contact with ARG 627 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C TYR* 4.7 8.1 + - - -
623C ASN* 3.1 48.9 + - - +
624C LEU* 3.0 25.9 + - + +
626C VAL* 1.3 84.6 - - + +
628C VAL* 1.3 58.8 + - + +
630C GLU* 3.2 4.7 + - - +
631C GLU* 3.0 53.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 628 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624C LEU* 3.2 35.7 - - + +
625C LEU* 3.8 11.0 - - + +
627C ARG* 1.3 78.9 - - + +
629C MET* 1.3 55.9 + - - +
631C GLU* 5.1 0.9 - - - -
632C THR* 2.9 54.2 + - - +
635C ILE* 3.9 22.9 - - + -
636C LEU* 4.0 21.3 - - + -
----------------------------------------------------------
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Residues in contact with MET 629 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 5.3 1.6 - - - +
46A VAL* 4.2 24.2 - - + -
65A TRP* 4.2 18.6 - - + -
76A VAL* 4.3 13.0 - - + +
79A SER* 3.4 46.9 - - - +
80A TYR* 3.9 11.9 - - + +
625C LEU* 2.9 27.2 + - - +
626C VAL 3.2 4.7 + - - +
628C VAL* 1.3 76.7 - - - +
630C GLU* 1.3 62.3 + - - +
633C PRO* 3.3 26.2 - - + +
636C LEU* 3.7 19.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 630 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 5.6 8.1 - - - -
626C VAL* 3.1 28.8 + - + +
627C ARG* 3.6 8.3 - - - +
629C MET* 1.3 80.3 - - + +
631C GLU* 1.3 70.1 + - + +
633C PRO* 4.4 2.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 631 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627C ARG* 3.0 39.9 + - - +
628C VAL* 5.1 0.7 - - - -
630C GLU* 1.3 88.4 - - + +
632C THR* 1.3 72.5 + - - +
633C PRO* 4.0 2.0 - - - -
----------------------------------------------------------
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Residues in contact with THR 632 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628C VAL* 2.9 13.4 + - - +
631C GLU* 1.3 89.7 + - - +
633C PRO* 1.3 68.6 - - - +
634C ASN* 3.0 13.9 + - + +
635C ILE* 3.1 40.3 - - + +
----------------------------------------------------------
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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