Contacts of the helix formed by residues 690 - 717 (chain F) in PDB entry 6NYY
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 SER 690 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687E LYS* 5.2 1.6 - - - +
691E GLU* 3.3 14.8 - - - -
694E ALA* 3.3 31.4 + - - +
695E ARG* 3.7 8.7 - - - -
698E ASP* 2.7 20.9 + - - +
687F LYS* 5.3 1.0 - - - +
689F TYR* 1.3 84.3 - - - +
691F GLU* 1.3 62.3 + - - +
692F ALA* 3.5 3.2 + - - +
693F THR* 3.2 19.0 + - - -
694F ALA* 3.3 19.2 + - - +
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Residues in contact with GLU 691 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A GLU* 5.4 3.5 - - - +
690A SER* 3.2 15.3 - - - -
691A GLU* 2.4 48.5 + - + +
692A ALA 4.1 1.8 + - - +
691E GLU* 2.6 29.7 + - + +
687F LYS* 5.8 1.6 + - - +
690F SER* 1.3 70.6 - - - +
692F ALA* 1.3 54.5 + - - +
693F THR 3.1 1.6 - - - -
694F ALA* 3.0 5.8 + - - +
695F ARG* 2.6 37.3 + - + +
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Residues in contact with ALA 692 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691E GLU* 4.3 0.8 + - - -
695E ARG* 3.7 45.5 - - + +
699E ASP* 5.8 1.3 - - - +
690F SER* 3.5 3.0 + - - +
691F GLU* 1.3 78.3 - - - +
693F THR* 1.3 60.3 + - - +
695F ARG* 3.9 11.0 - - - +
696F LEU* 3.3 22.2 + - - +
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Residues in contact with THR 693 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698E ASP* 3.2 22.2 + - - +
699E ASP* 5.6 0.5 + - - -
702E ARG* 3.8 22.9 + - - +
670F VAL* 5.7 2.2 - - + -
673F ILE* 6.4 0.2 - - + -
675F PHE* 5.1 6.3 - - + -
689F TYR* 3.7 30.7 - - + -
690F SER* 3.2 18.5 + - - -
691F GLU 3.1 0.4 - - - -
692F ALA* 1.3 76.5 - - - +
694F ALA* 1.3 53.1 + - - +
696F LEU* 2.9 8.4 + - + +
697F ILE* 2.8 50.9 + - + +
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Residues in contact with ALA 694 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A SER* 3.5 18.1 - - - -
687F LYS* 3.7 22.4 - - + +
689F TYR* 3.6 22.4 - - + -
690F SER 3.3 16.3 + - - +
691F GLU* 3.0 10.4 + - - +
693F THR* 1.3 74.8 - - - +
695F ARG* 1.3 65.1 + - - +
697F ILE* 4.0 3.9 - - - +
698F ASP* 3.1 22.5 + - - +
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Residues in contact with ARG 695 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A SER* 3.8 10.9 - - - +
692A ALA* 3.7 31.7 - - + +
691F GLU* 2.6 24.3 + - + +
692F ALA* 4.0 11.7 - - - +
694F ALA* 1.3 71.0 - - - +
696F LEU* 1.3 61.7 + - - +
698F ASP* 4.1 1.3 - - - +
699F ASP* 3.0 42.9 + - - +
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Residues in contact with LEU 696 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702E ARG* 4.2 26.9 - - - +
669F LYS* 3.7 39.0 - - + +
670F VAL* 4.4 11.6 - - + +
692F ALA 3.3 13.6 + - - +
693F THR* 2.9 9.9 + - + +
695F ARG* 1.3 78.9 - - - +
697F ILE* 1.3 63.0 + - - +
699F ASP* 3.6 7.9 + - + +
700F GLU* 3.3 34.7 + - + +
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Residues in contact with ILE 697 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658F TYR* 4.1 20.2 - - + -
661F ILE* 4.0 11.3 - - + +
662F VAL* 3.8 29.4 - - + -
670F VAL* 4.1 26.5 - - + -
675F PHE* 5.4 3.6 - - + -
689F TYR* 3.8 29.4 - - + +
693F THR* 2.8 40.8 + - + +
694F ALA* 3.4 5.4 + - - +
695F ARG 3.3 0.2 - - - -
696F LEU* 1.3 72.9 - - + +
698F ASP* 1.3 60.2 + - - +
700F GLU* 3.0 17.3 + - - +
701F VAL* 3.0 14.8 + - + +
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Residues in contact with ASP 698 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A PHE* 5.6 0.2 - - - -
689A TYR* 3.6 6.9 - - - +
690A SER* 2.8 36.3 + - - +
693A THR* 3.1 22.4 + - - +
658F TYR* 2.3 40.5 + - - -
687F LYS* 4.8 1.6 + - - -
694F ALA 3.1 11.9 + - - +
695F ARG 4.3 1.8 - - - +
697F ILE* 1.3 76.4 - - - +
699F ASP* 1.3 63.7 + - - +
700F GLU 3.3 0.5 + - - -
701F VAL* 4.2 4.0 - - - +
702F ARG* 3.4 32.7 + - - +
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Residues in contact with ASP 699 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695F ARG* 3.0 37.1 + - - +
696F LEU* 3.9 11.3 - - + +
697F ILE 3.2 0.2 - - - -
698F ASP* 1.3 76.2 - - - +
700F GLU* 1.3 63.6 + - - +
702F ARG* 3.2 23.9 + - - +
703F ILE* 3.3 30.2 + - + +
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Residues in contact with GLU 700 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661F ILE* 3.6 6.4 - - + +
667F ASN* 3.4 33.5 - - - +
669F LYS* 3.3 38.7 + - + +
670F VAL* 4.4 6.1 - - + -
696F LEU* 3.3 20.7 + - + +
697F ILE 3.0 8.7 + - - +
699F ASP* 1.3 83.7 - - - +
701F VAL* 1.3 63.3 + - - +
702F ARG 3.3 0.9 - - - -
703F ILE* 3.9 25.4 - - - +
704F LEU* 3.2 22.3 + - - +
----------------------------------------------------------
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Residues in contact with VAL 701 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A ILE* 4.5 10.1 - - + -
654F THR 5.0 0.9 - - - +
657F ALA* 3.4 37.2 - - + +
658F TYR* 3.9 44.2 - - + +
661F ILE* 3.7 7.6 - - + -
697F ILE* 3.0 15.6 + - + +
698F ASP* 3.7 5.6 + - - +
700F GLU* 1.3 76.4 - - - +
702F ARG* 1.3 57.5 + - - +
704F LEU* 3.0 5.0 + - - +
705F ILE* 2.9 42.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG 702 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A GLU 5.6 0.4 - - - -
669A LYS 3.4 19.2 + - - -
670A VAL* 2.8 31.9 + - - +
671A GLY* 4.5 4.5 - - - -
673A ILE* 4.4 14.6 - - + +
693A THR* 3.8 30.1 + - - +
696A LEU* 4.3 16.3 - - - +
698F ASP* 3.4 23.6 + - - +
699F ASP* 3.2 29.2 + - - +
700F GLU 3.3 0.2 - - - -
701F VAL* 1.3 80.3 - - - +
703F ILE* 1.3 59.3 + - + +
705F ILE* 3.8 3.8 + - - +
706F ASN* 2.7 47.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 703 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669F LYS* 5.5 5.8 - - - +
699F ASP* 3.3 22.1 + - + +
700F GLU* 3.8 27.2 + - - +
701F VAL 3.3 0.2 - - - -
702F ARG* 1.3 78.4 - - + +
704F LEU* 1.3 59.3 + - - +
706F ASN* 3.5 4.9 + - - +
707F ASP* 3.0 51.8 + - - +
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Residues in contact with LEU 704 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618F LYS* 5.9 4.9 - - - -
622F LEU* 4.6 13.6 - - + +
625F MET* 3.8 8.5 - - + +
657F ALA* 3.7 27.8 - - + +
660F GLN* 3.4 42.0 - - + +
661F ILE* 4.6 8.7 - - + -
700F GLU 3.2 17.7 + - - +
701F VAL 3.0 6.3 + - - +
703F ILE* 1.3 79.4 - - - +
705F ILE* 1.3 60.8 + - - +
707F ASP* 3.6 8.9 + - + +
708F ALA* 3.1 20.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 705 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A GLN* 3.7 33.0 - - + +
673A ILE* 4.0 24.2 - - + -
625F MET* 3.8 12.6 - - + -
629F LEU* 3.9 7.3 - - + +
653F VAL* 3.7 40.4 - - + +
654F THR* 4.6 3.4 - - - -
657F ALA* 4.1 4.5 - - + -
701F VAL* 2.9 37.2 + - + +
702F ARG* 4.5 3.6 - - - +
704F LEU* 1.3 74.6 - - - +
706F ASN* 1.3 55.6 + - - +
708F ALA* 3.0 3.8 + - - +
709F TYR* 2.6 33.3 + - - +
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Residues in contact with ASN 706 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A GLU 5.5 3.1 + - - +
671A GLY* 4.8 8.8 - - - -
672A GLN* 4.7 12.7 + - - +
702F ARG* 2.7 38.1 + - - +
703F ILE* 4.0 5.0 - - - +
705F ILE* 1.3 76.9 - - - +
707F ASP* 1.3 59.7 + - - +
709F TYR* 3.5 15.3 - - + +
710F LYS* 2.8 45.0 + - - +
----------------------------------------------------------
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Residues in contact with ASP 707 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622F LEU* 5.1 7.4 - - + +
703F ILE* 3.0 38.4 + - - +
704F LEU* 3.9 9.9 - - + +
706F ASN* 1.3 79.1 - - - +
708F ALA* 1.3 57.8 + - - +
710F LYS* 4.0 12.0 + - - +
711F ARG* 3.2 27.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 708 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622F LEU* 3.8 20.3 - - + +
625F MET* 3.8 19.5 - - + -
626F CYS* 3.3 18.9 - - - -
629F LEU* 3.7 13.1 - - + +
704F LEU 3.1 13.5 + - - +
705F ILE 3.0 8.6 + - - +
707F ASP* 1.3 76.3 - - - +
709F TYR* 1.3 60.1 + - - +
711F ARG 3.9 0.4 - - - -
712F THR* 2.8 25.8 + - - -
----------------------------------------------------------
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Residues in contact with TYR 709 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A GLN* 4.6 34.2 + - + -
629F LEU* 4.0 14.8 - - + -
632F ARG* 5.3 8.1 - - + -
633F VAL* 3.6 27.6 - - + -
636F GLU* 2.3 37.6 + - - -
705F ILE 2.6 18.0 + - - +
706F ASN* 3.2 19.9 + - - +
708F ALA* 1.3 73.1 - - - +
710F LYS* 1.3 65.9 + - + +
712F THR* 3.2 4.4 + - - -
713F VAL* 3.0 48.3 + - + +
----------------------------------------------------------
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Residues in contact with LYS 710 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706F ASN* 2.8 31.7 + - - +
707F ASP* 4.3 12.0 + - - +
709F TYR* 1.3 77.8 - - + +
711F ARG* 1.3 61.2 + - - +
713F VAL* 4.0 7.4 - - - +
714F ALA* 3.3 23.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 711 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585F LEU* 3.9 20.1 - - + +
619F GLU* 5.3 4.6 + - - +
622F LEU* 3.5 30.2 - - - +
623F ASP* 3.1 30.4 + - - -
626F CYS* 3.7 21.1 - - - -
707F ASP 3.2 17.6 + - - +
709F TYR 3.2 1.0 - - - -
710F LYS* 1.3 77.0 - - - +
712F THR* 1.3 59.9 + - - +
714F ALA* 3.6 4.1 + - - +
715F LEU* 2.9 28.8 + - + +
----------------------------------------------------------
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Residues in contact with THR 712 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581F ALA* 4.6 5.4 - - + -
626F CYS* 3.3 36.1 + - + +
629F LEU* 3.8 8.7 - - - +
630F GLY* 3.7 21.8 - - - -
633F VAL* 3.8 12.7 - - + +
708F ALA 2.8 18.6 + - - -
709F TYR 3.2 5.1 + - - -
711F ARG* 1.3 75.5 - - - +
713F VAL* 1.3 60.3 + - - +
715F LEU* 3.7 5.6 - - + +
716F LEU* 2.9 39.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 713 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633F VAL* 3.7 23.6 - - + -
636F GLU* 5.7 0.9 - - - +
637F ILE* 4.6 5.1 - - + +
709F TYR* 3.0 44.8 + - + +
710F LYS* 4.2 7.9 - - - +
712F THR* 1.3 75.7 - - - +
714F ALA* 1.3 59.7 + - + +
716F LEU* 3.3 0.9 + - - +
717F THR* 2.8 41.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 714 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710F LYS 3.3 17.1 + - - +
711F ARG* 4.1 4.0 - - - +
713F VAL* 1.3 80.1 - - + +
715F LEU* 1.3 61.5 + - - +
717F THR* 4.0 10.1 - - - +
718F GLU* 3.8 21.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 715 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580F VAL* 6.5 0.2 - - + -
581F ALA* 4.1 24.5 - - + -
584F TYR* 4.3 25.6 - - + +
585F LEU* 3.9 35.7 - - + -
711F ARG* 2.9 20.3 + - + +
712F THR* 3.7 8.1 - - + +
713F VAL 3.2 0.2 - - - -
714F ALA* 1.3 78.7 - - - +
716F LEU* 1.3 66.5 + - + +
718F GLU* 3.4 9.7 + - - +
719F LYS* 3.2 30.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 716 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577F GLY* 4.4 5.4 - - - +
580F VAL* 4.2 15.9 - - + -
581F ALA* 4.3 15.7 - - + +
630F GLY 3.5 24.9 - - - +
633F VAL* 4.0 16.6 - - + -
634F SER* 4.2 12.1 - - - +
637F ILE* 3.8 15.8 - - + +
712F THR* 2.9 27.3 + - + +
715F LEU* 1.3 81.6 - - + +
717F THR* 1.3 61.4 + - - +
719F LYS* 3.2 4.5 - - + +
720F LYS* 2.9 30.0 + - - +
723F VAL* 3.7 25.9 - - + +
----------------------------------------------------------
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Residues in contact with THR 717 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637F ILE* 4.0 15.1 - - - +
713F VAL* 2.8 28.4 + - + +
714F ALA* 4.0 13.2 - - - +
716F LEU* 1.3 76.7 - - - +
718F GLU* 1.3 63.3 + - + +
720F LYS* 4.0 19.8 - - - +
----------------------------------------------------------
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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