Contacts of the helix formed by residues 690 - 717 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687D LYS* 5.4 1.3 - - - +
691D GLU* 3.3 13.5 - - - -
694D ALA* 3.3 30.5 + - - -
695D ARG* 3.8 4.0 - - - -
698D ASP* 2.8 16.3 + - - +
687E LYS* 4.7 3.0 - - - -
689E TYR* 1.3 92.9 - - - +
691E GLU* 1.3 60.2 + - - +
692E ALA* 3.4 6.6 + - - +
693E THR* 3.0 28.4 + - - -
694E ALA* 3.5 8.1 + - - +
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Residues in contact with GLU 691 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D GLU* 2.5 32.1 + - + +
687E LYS* 4.3 17.5 + - - -
690E SER* 1.3 70.3 - - - +
692E ALA* 1.3 59.5 + - - +
693E THR 3.2 1.8 - - - -
694E ALA* 3.1 1.7 + - - +
695E ARG* 2.8 31.0 + - + +
690F SER* 3.3 12.9 - - - -
691F GLU* 2.6 46.2 + - + +
692F ALA 4.3 1.0 + - - -
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Residues in contact with ALA 692 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D GLU* 4.2 1.6 + - - +
695D ARG* 3.7 44.6 - - + +
702D ARG* 6.0 2.9 - - - +
690E SER* 3.4 4.5 + - - +
691E GLU* 1.3 76.6 - - - +
693E THR* 1.3 61.8 + - - +
695E ARG* 3.9 9.0 - - - +
696E LEU* 3.2 21.1 + - - +
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Residues in contact with THR 693 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D ASP* 3.4 21.4 - - + +
702D ARG* 3.7 21.1 + - - +
670E VAL* 5.4 5.8 - - + -
675E PHE* 5.3 4.7 - - + -
689E TYR* 3.7 23.6 - - + -
690E SER* 3.0 25.4 + - - -
692E ALA* 1.3 78.4 - - - +
694E ALA* 1.3 58.2 + - - +
696E LEU* 2.9 9.6 + - + +
697E ILE* 2.8 40.4 + - + +
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Residues in contact with ALA 694 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687E LYS* 3.8 16.8 - - + -
689E TYR* 3.6 21.1 - - + -
690E SER 3.5 16.1 + - - +
691E GLU* 3.1 8.3 + - - +
693E THR* 1.3 76.2 - - - +
695E ARG* 1.3 64.0 + - - +
697E ILE* 4.0 4.8 - - - +
698E ASP* 3.2 22.3 + - - +
689F TYR 5.6 0.4 - - - -
690F SER* 3.3 24.5 - - - +
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Residues in contact with ARG 695 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691E GLU* 2.8 19.8 + - + +
692E ALA* 3.9 9.0 - - - +
694E ALA* 1.3 75.3 - - - +
696E LEU* 1.3 62.8 + - - +
698E ASP* 3.8 1.4 + - - +
699E ASP* 2.9 42.8 + - - +
690F SER* 3.7 10.6 - - - +
692F ALA* 3.7 31.7 - - + +
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Residues in contact with LEU 696 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702D ARG* 4.2 25.1 - - - +
669E LYS* 4.0 42.6 - - + +
670E VAL* 4.3 12.1 - - + -
692E ALA 3.2 14.3 + - - +
693E THR* 2.9 11.4 + - + +
695E ARG* 1.3 76.2 - - - +
697E ILE* 1.3 63.2 + - - +
699E ASP* 3.6 7.8 + - + +
700E GLU* 3.3 34.0 + - + +
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Residues in contact with ILE 697 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658E TYR* 3.9 20.9 - - + -
661E ILE* 4.3 9.4 - - + +
662E VAL* 3.7 31.2 - - + -
670E VAL* 4.0 26.9 - - + -
675E PHE* 5.5 1.6 - - + -
689E TYR* 3.7 39.9 - - + +
693E THR* 2.8 31.0 + - + +
694E ALA* 3.5 5.6 + - - +
695E ARG 3.4 0.2 - - - -
696E LEU* 1.3 72.5 - - - +
698E ASP* 1.3 60.9 + - - +
700E GLU* 3.0 5.2 + - - +
701E VAL* 3.0 27.5 + - + +
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Residues in contact with ASP 698 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658E TYR* 2.3 40.2 + - - +
694E ALA* 3.2 11.5 + - - +
695E ARG 4.4 1.8 - - - +
697E ILE* 1.3 77.1 - - - +
699E ASP* 1.3 63.7 + - - +
701E VAL* 4.0 5.8 - - - +
702E ARG* 3.4 30.6 + - - +
673F ILE* 5.3 1.6 - - - +
689F TYR* 3.4 7.3 - - - -
690F SER* 2.7 39.8 + - - +
693F THR* 3.2 20.0 + - - +
----------------------------------------------------------
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Residues in contact with ASP 699 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695E ARG* 2.9 38.4 + - - +
696E LEU* 4.0 9.3 - - + +
697E ILE 3.2 0.8 - - - -
698E ASP* 1.3 77.0 - - - +
700E GLU* 1.3 62.3 + - + +
702E ARG* 3.3 23.3 + - - +
703E ILE* 3.3 30.5 + - + +
692F ALA* 6.0 1.3 - - - +
693F THR* 5.6 0.3 + - - -
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Residues in contact with GLU 700 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661E ILE* 3.4 10.0 - - + +
667E ASN* 3.3 36.1 + - - +
669E LYS* 3.3 32.1 + - + +
670E VAL* 4.8 0.9 - - + -
696E LEU* 3.3 23.8 - - + +
697E ILE 3.0 7.8 + - - +
699E ASP* 1.3 80.3 - - - +
701E VAL* 1.3 63.4 + - - +
702E ARG 3.3 0.7 - - - -
703E ILE* 3.6 32.1 - - - +
704E LEU* 3.1 22.7 + - - +
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Residues in contact with VAL 701 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654E THR* 5.0 0.7 - - - +
657E ALA* 3.7 24.5 - - + +
658E TYR* 3.8 44.0 - - + +
661E ILE* 3.8 17.3 - - + -
697E ILE* 3.0 16.1 + - + +
698E ASP* 3.6 6.5 + - - +
700E GLU* 1.3 77.2 - - - +
702E ARG* 1.3 58.2 + - - +
704E LEU* 3.1 4.1 + - - +
705E ILE* 2.9 43.5 + - + +
673F ILE* 4.2 13.0 - - + -
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Residues in contact with ARG 702 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698E ASP* 3.4 21.8 + - - +
699E ASP* 3.3 27.7 + - - +
700E GLU 3.3 0.4 - - - -
701E VAL* 1.3 76.4 - - - +
703E ILE* 1.3 64.3 + - + +
705E ILE* 4.6 3.3 - - - +
706E ASN* 2.9 42.6 + - - +
668F GLU 5.9 0.2 - - - -
669F LYS 3.9 11.0 + - - -
670F VAL* 2.6 33.1 + - - +
671F GLY* 4.9 3.1 - - - -
673F ILE* 4.5 18.3 - - + +
693F THR* 3.8 32.1 + - - +
696F LEU* 4.2 21.1 - - - +
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Residues in contact with ILE 703 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669E LYS* 5.2 5.8 - - - +
699E ASP* 3.3 22.2 + - + +
700E GLU* 3.6 31.2 + - - +
701E VAL 3.3 0.4 - - - -
702E ARG* 1.3 77.4 - - + +
704E LEU* 1.3 57.1 + - - +
706E ASN* 3.8 2.6 - - - +
707E ASP* 2.9 50.8 + - - +
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Residues in contact with LEU 704 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618E LYS* 6.0 6.1 - - - -
622E LEU* 4.7 9.5 - - + +
625E MET* 3.8 18.8 - - + +
657E ALA* 3.8 32.3 - - + +
660E GLN* 3.3 26.7 - - + +
661E ILE* 4.4 8.7 - - + -
700E GLU 3.1 17.2 + - - +
701E VAL* 3.1 6.8 + - - +
703E ILE* 1.3 79.6 - - - +
705E ILE* 1.3 57.3 + - - +
707E ASP* 3.4 8.6 + - + +
708E ALA* 3.1 24.6 + - - +
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Residues in contact with ILE 705 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625E MET* 4.7 1.8 - - - -
629E LEU* 3.9 7.6 - - + +
653E VAL* 3.7 40.8 - - + +
654E THR* 4.8 0.2 - - - -
657E ALA* 4.3 8.7 - - + -
701E VAL* 2.9 30.6 + - + +
702E ARG* 4.6 3.1 - - - +
704E LEU* 1.3 74.2 - - - +
706E ASN* 1.3 56.4 + - - +
708E ALA* 3.0 7.8 + - - +
709E TYR* 2.5 33.4 + - - +
672F GLN* 3.7 35.0 - - + +
673F ILE* 3.7 32.1 - - + -
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Residues in contact with ASN 706 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702E ARG* 2.9 36.1 + - - +
703E ILE* 4.2 3.4 - - - +
705E ILE* 1.3 78.3 - - - +
707E ASP* 1.3 58.2 + - - +
709E TYR* 3.8 20.8 - - - +
710E LYS* 3.0 46.7 + - - +
668F GLU 5.6 2.6 + - - +
671F GLY* 4.9 8.7 - - - -
672F GLN* 4.9 11.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 707 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622E LEU* 5.0 7.0 - - + +
703E ILE* 2.9 40.9 + - - +
704E LEU* 3.7 10.2 - - + +
706E ASN* 1.3 79.2 - - - +
708E ALA* 1.3 57.8 + - - +
710E LYS* 4.6 8.3 + - - +
711E ARG* 3.4 24.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 708 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622E LEU* 3.8 14.8 - - + -
625E MET* 4.1 14.6 - - + -
626E CYS* 3.4 21.5 - - - -
629E LEU* 3.5 14.2 - - + +
704E LEU 3.1 12.5 + - - +
705E ILE* 3.0 9.9 + - - +
707E ASP* 1.3 74.6 - - - +
709E TYR* 1.3 58.4 + - - +
711E ARG 4.0 0.9 - - - -
712E THR* 2.6 32.7 + - - -
----------------------------------------------------------
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Residues in contact with TYR 709 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629E LEU* 3.8 15.9 - - + -
632E ARG* 4.4 12.7 + - + +
633E VAL* 3.8 23.6 - - + -
636E GLU* 2.3 38.9 + - - -
705E ILE 2.5 18.3 + - - +
706E ASN* 3.4 21.5 + - - +
708E ALA* 1.3 73.8 - - - +
710E LYS* 1.3 67.0 + - + +
711E ARG 3.2 0.4 - - - -
712E THR* 3.3 4.0 + - - -
713E VAL* 3.1 43.8 + - + +
672F GLN* 4.2 36.0 + - + -
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Residues in contact with LYS 710 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706E ASN* 3.0 32.0 + - - +
707E ASP* 4.7 8.4 + - - +
709E TYR* 1.3 82.2 - - + +
711E ARG* 1.3 61.6 + - - +
713E VAL* 3.8 7.8 - - - +
714E ALA* 3.1 24.4 + - - +
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Residues in contact with ARG 711 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585E LEU* 4.5 14.4 - - + +
622E LEU* 4.3 21.9 - - - +
623E ASP* 3.8 24.6 + - - -
626E CYS* 3.7 23.8 - - + -
707E ASP 3.4 19.1 + - - +
709E TYR 3.2 0.6 - - - -
710E LYS* 1.3 78.8 - - - +
712E THR* 1.3 61.5 + - - +
714E ALA* 3.7 5.9 + - - +
715E LEU* 3.4 19.9 + - - +
----------------------------------------------------------
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Residues in contact with THR 712 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581E ALA* 4.7 5.2 - - + -
626E CYS* 3.3 39.5 - - + +
629E LEU* 4.0 3.4 - - - +
630E GLY* 3.7 24.2 - - - +
633E VAL* 3.9 13.4 - - + +
708E ALA 2.6 23.5 + - - -
709E TYR 3.3 5.0 + - - -
710E LYS 3.3 0.6 - - - -
711E ARG* 1.3 76.5 - - - +
713E VAL* 1.3 63.9 + - - +
715E LEU* 3.3 5.6 + - + +
716E LEU* 3.1 30.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 713 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633E VAL* 3.7 26.7 - - + -
636E GLU* 5.8 0.7 - - - +
637E ILE* 5.2 4.7 - - + -
709E TYR* 3.1 35.4 + - + +
710E LYS* 3.8 7.9 - - - +
711E ARG 3.4 0.2 - - - -
712E THR* 1.3 76.4 - - - +
714E ALA* 1.3 58.1 + - - +
716E LEU 3.3 0.2 + - - -
717E THR* 2.9 47.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA 714 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710E LYS 3.1 17.5 + - - +
711E ARG* 4.0 6.7 - - - +
712E THR 3.3 0.2 - - - -
713E VAL* 1.3 76.2 - - - +
715E LEU* 1.3 56.9 + - - +
717E THR* 4.4 7.2 - - - -
718E GLU* 3.3 35.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 715 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580E VAL 4.8 0.2 - - - +
581E ALA* 3.8 35.7 - - + -
584E TYR* 4.2 28.5 - - + +
585E LEU* 4.2 25.1 - - + -
711E ARG 3.4 12.7 + - - +
712E THR* 3.3 10.9 + - + +
713E VAL 3.1 0.8 - - - -
714E ALA* 1.3 78.4 - - - +
716E LEU* 1.3 63.1 + - + +
717E THR 3.4 0.2 - - - -
718E GLU* 3.4 3.9 + - - +
719E LYS* 3.1 41.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 716 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577E GLY* 4.3 4.7 - - - +
580E VAL* 4.1 15.9 - - + -
581E ALA* 4.1 20.9 - - + +
630E GLY* 3.6 33.4 - - - +
633E VAL* 3.8 19.5 - - + -
634E SER* 4.1 11.4 - - - +
637E ILE* 4.0 15.2 - - + +
712E THR* 3.1 15.0 + - + +
715E LEU* 1.3 80.9 - - + +
717E THR* 1.3 62.8 + - - +
718E GLU 3.2 0.2 - - - -
719E LYS* 3.2 3.9 - - - +
720E LYS* 3.0 28.2 + - - +
723E VAL* 3.7 26.5 - - + +
----------------------------------------------------------
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Residues in contact with THR 717 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637E ILE* 3.8 24.0 - - - +
713E VAL* 2.9 31.9 + - + +
714E ALA* 4.4 7.4 - - - -
716E LEU* 1.3 77.4 - - - +
718E GLU* 1.3 67.4 + - + +
719E LYS 3.4 0.2 - - - -
720E LYS* 4.1 16.0 - - - +
----------------------------------------------------------
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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