Contacts of the helix formed by residues 708 - 743 (chain A) in PDB entry 3K23
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 708 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A GLY 3.6 0.6 - - - -
707A ASN* 1.3 84.9 + - - +
709A SER* 1.3 68.6 + - - -
710A GLN* 2.8 19.3 + - - +
711A ASN* 3.0 28.5 + - - +
712A TRP 4.3 0.2 + - - -
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Residues in contact with SER 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A SER* 1.3 76.0 + - - +
710A GLN* 1.3 62.7 + - - -
711A ASN 3.1 0.9 - - - -
712A TRP* 3.1 16.2 + - - +
713A GLN* 2.9 24.1 + - - +
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Residues in contact with GLN 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A GLU* 5.0 3.4 - - - +
707A ASN* 3.4 34.8 - - + +
708A SER* 2.8 9.9 + - - +
709A SER* 1.3 75.2 - - - +
711A ASN* 1.3 56.8 + - - +
713A GLN* 3.5 6.7 + - - +
714A ARG* 3.0 29.5 + - - +
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Residues in contact with ASN 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A ILE* 3.5 28.0 - - + +
702A VAL* 5.0 12.1 - - + +
705A GLU* 5.4 0.3 - - - +
706A GLY* 3.2 46.5 + - - -
707A ASN 3.7 1.7 + - - -
708A SER 3.0 16.7 + - - +
710A GLN* 1.3 74.6 - - - +
712A TRP* 1.3 66.1 + - - +
714A ARG* 3.1 4.0 + - - +
715A PHE* 2.9 23.7 + - - +
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Residues in contact with TRP 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A SER 4.3 0.6 + - - -
709A SER* 3.1 20.0 + - - +
711A ASN* 1.3 76.5 - - - +
713A GLN* 1.3 77.7 + - + +
715A PHE* 3.1 10.4 + + + +
716A TYR* 2.9 53.1 + + + -
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Residues in contact with GLN 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A SER 2.9 14.6 + - - +
710A GLN* 3.8 7.6 - - - +
712A TRP* 1.3 96.6 - - + +
714A ARG* 1.3 57.4 + - - +
716A TYR* 3.4 13.3 - - - +
717A GLN* 3.0 55.1 + - - +
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Residues in contact with ARG 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A LEU* 2.9 49.5 + - + +
657A GLN 3.3 11.3 + - - -
658A VAL* 3.7 6.9 - - - +
662A GLU* 2.7 38.7 + - - -
701A ILE* 3.6 27.1 - - + -
704A ARG* 3.3 20.8 - - - +
710A GLN 3.0 17.9 + - - +
711A ASN 3.1 4.5 + - - +
713A GLN* 1.3 75.6 - - - +
715A PHE* 1.3 59.9 + - - +
717A GLN* 3.3 6.9 + - - +
718A LEU* 2.9 42.9 + - + +
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Residues in contact with PHE 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694A ILE* 3.7 37.2 - - + -
697A LEU* 5.0 7.2 - - + -
698A GLY* 4.9 11.7 - - - -
701A ILE* 3.5 17.6 - - + +
711A ASN 2.9 13.1 + - - +
712A TRP* 3.4 11.9 - + + +
714A ARG* 1.3 76.2 - - - +
716A TYR* 1.3 59.6 + - - +
718A LEU* 4.0 2.3 - - - +
719A THR* 2.5 61.6 + - + +
774A PHE* 4.8 7.0 - + - -
775A HIS* 5.9 2.2 - + - -
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Residues in contact with TYR 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A TRP* 2.9 44.9 + + + +
713A GLN* 3.4 17.3 - - - +
715A PHE* 1.3 80.4 - - - +
717A GLN* 1.3 72.8 + - + +
719A THR* 3.2 6.2 + - - -
720A LYS* 2.9 69.3 + - + +
775A HIS* 3.7 21.3 + + - -
751E LYS* 4.6 8.7 + - - +
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Residues in contact with GLN 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A ARG* 3.2 32.8 + - - +
656A LEU* 3.6 30.9 - - + +
713A GLN* 3.0 41.1 + - - +
714A ARG* 4.0 5.9 + - - +
716A TYR* 1.3 92.1 - - + +
718A LEU* 1.3 66.6 + - - +
720A LYS* 3.7 4.9 - - - +
721A LEU* 3.2 21.5 + - - +
747E TYR* 4.4 7.6 + - + -
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Residues in contact with LEU 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A LEU* 4.0 13.5 - - + -
658A VAL* 3.6 24.0 - - + -
662A GLU* 4.0 12.3 - - - +
666A MET* 3.5 34.0 - - + +
697A LEU* 4.3 18.8 - - + -
701A ILE* 3.7 27.6 - - + -
714A ARG* 2.9 34.7 + - + +
715A PHE* 4.0 2.9 - - - +
717A GLN* 1.3 78.5 - - + +
719A THR* 1.3 63.2 + - - +
721A LEU* 3.1 7.8 + - - +
722A LEU* 3.1 24.1 + - - +
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Residues in contact with THR 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A LEU* 4.4 13.0 - - + -
715A PHE* 2.5 48.6 + - + +
716A TYR* 3.2 7.4 + - - -
718A LEU* 1.3 72.6 - - - +
720A LYS* 1.3 63.1 - - - +
722A LEU* 3.2 11.1 + - + +
723A ASP* 3.1 25.6 + - - +
774A PHE* 3.3 46.1 - - + -
775A HIS* 3.2 11.5 + - - -
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Residues in contact with LYS 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A TYR* 2.9 55.1 + - + +
717A GLN* 3.7 8.7 - - - +
719A THR* 1.3 74.2 - - - +
721A LEU* 1.3 65.2 + - - +
723A ASP* 3.0 18.2 + - + +
724A SER* 3.0 13.2 + - - -
775A HIS* 3.7 37.9 + - + +
747E TYR* 6.3 1.1 - - + -
751E LYS* 3.0 54.1 - - + +
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A PHE* 4.8 6.5 - - + -
648A TYR* 4.5 9.4 - - + +
649A VAL* 4.9 7.4 - - + +
652A GLU* 3.8 39.0 - - + +
653A LEU* 4.0 27.4 - - + -
656A LEU* 4.1 15.5 - - + -
666A MET* 4.1 14.4 - - + -
717A GLN 3.2 10.4 + - - +
718A LEU 3.1 9.3 + - - +
720A LYS* 1.3 76.8 - - - +
722A LEU* 1.3 64.5 + - - +
724A SER* 2.4 28.6 + - - +
725A MET* 3.2 18.6 + - - +
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Residues in contact with LEU 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A TYR* 5.5 0.2 - - - -
606A PHE* 4.3 11.4 - - + -
666A MET* 3.4 42.4 - - + +
669A LEU* 4.0 31.0 - - + -
670A LEU* 3.7 25.8 - - + +
697A LEU* 4.8 2.5 - - + -
718A LEU 3.1 15.3 + - - +
719A THR* 3.5 11.2 - - - +
720A LYS 3.2 0.2 - - - -
721A LEU* 1.3 74.7 - - - +
723A ASP* 1.3 64.7 + - - +
725A MET* 3.0 24.3 - - + +
726A HIS* 3.9 5.3 + - - -
774A PHE* 3.9 27.4 - - + -
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Residues in contact with ASP 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A THR 3.1 11.1 + - - -
720A LYS* 3.0 14.5 + - + +
722A LEU* 1.3 75.7 - - - +
724A SER* 1.3 62.8 + - - +
726A HIS* 2.9 31.5 + - + +
727A GLU* 4.1 0.7 + - - +
772A LEU 4.6 0.2 - - - +
773A LEU* 3.3 23.4 - - + +
774A PHE* 2.8 28.9 + - - -
775A HIS* 3.1 38.2 + - - +
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Residues in contact with SER 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TYR* 3.9 22.8 + - - -
720A LYS 3.0 6.7 + - - -
721A LEU* 2.4 41.6 + - - +
723A ASP* 1.3 73.6 - - - +
725A MET* 1.3 62.0 + - - +
727A GLU* 3.1 10.3 + - - +
728A VAL* 3.0 22.7 + - - +
747E TYR 5.9 0.7 - - - -
750E ASP* 4.1 24.6 - - - +
751E LYS* 6.3 0.7 - - - -
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Residues in contact with MET 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A TYR* 3.9 23.3 - - + +
605A ALA* 3.9 14.4 - - + -
606A PHE* 3.8 42.6 - - + +
648A TYR* 6.3 0.2 - - - -
649A VAL* 3.5 29.8 - - + -
670A LEU* 4.0 14.4 - - + -
721A LEU* 3.2 17.2 + - - +
722A LEU* 3.0 23.1 - - + +
724A SER* 1.3 76.5 - - - +
726A HIS* 1.3 61.8 + - - +
728A VAL* 3.0 5.0 + - + +
729A VAL* 2.9 35.2 + - + +
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Residues in contact with HIS 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A TYR* 2.7 39.7 + + - +
673A SER* 3.4 27.9 + - - -
674A SER* 4.0 2.9 - - - -
722A LEU 4.4 3.1 + - - -
723A ASP* 2.9 30.0 + - - +
725A MET* 1.3 78.6 - - - +
727A GLU* 1.3 62.3 + - - +
729A VAL* 3.4 2.4 + - - +
730A GLU* 3.3 20.4 + - - +
771A LYS* 3.5 36.4 - - + +
772A LEU 2.6 21.7 + - - -
773A LEU* 3.1 23.3 - - + +
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Residues in contact with GLU 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A HIS* 4.7 3.5 + - + -
723A ASP 4.1 0.8 + - - +
724A SER* 3.1 12.3 + - - +
726A HIS* 1.3 75.7 - - - +
728A VAL* 1.3 58.9 + - - +
730A GLU* 3.8 11.4 + - + +
731A ASN* 2.5 42.3 + - - +
585B ARG* 4.9 11.8 + - - -
749E LEU 4.7 2.9 - - - +
750E ASP* 4.1 41.0 - - + +
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Residues in contact with VAL 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ALA* 4.8 7.0 - - + -
645A HIS* 4.0 39.4 + - + +
646A MET* 5.3 0.7 - - - -
648A TYR* 4.2 24.9 - - + -
649A VAL* 4.3 14.6 - - + -
724A SER 3.0 18.8 + - - +
725A MET* 3.0 10.1 + - + +
727A GLU* 1.3 74.1 - - - +
729A VAL* 1.3 67.2 + - - +
731A ASN* 3.3 6.4 + - - +
732A LEU* 3.1 38.2 + - + +
750E ASP* 4.4 6.3 - - - +
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Residues in contact with VAL 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A MET* 3.5 27.1 - - + +
602A TYR* 3.4 55.9 - - + +
605A ALA* 4.5 8.3 - - + -
725A MET* 2.9 21.6 + - + +
726A HIS 4.0 2.0 - - - +
728A VAL* 1.3 74.7 - - - +
730A GLU* 1.3 55.8 + - - +
732A LEU* 3.0 7.3 + - - -
733A LEU* 2.5 52.5 + - + +
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Residues in contact with GLU 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A HIS 3.3 13.5 + - - +
727A GLU* 3.9 14.8 - - - +
728A VAL 3.2 0.2 - - - -
729A VAL* 1.3 78.6 - - - +
731A ASN* 1.3 63.8 + - - +
733A LEU* 3.1 17.2 + - + +
734A ASN* 2.7 36.5 + - - +
764A TYR* 3.3 34.4 + - + +
771A LYS* 2.9 31.6 + - - +
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Residues in contact with ASN 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A ASP* 3.7 25.5 - - + +
645A HIS* 3.7 34.9 + - + +
727A GLU* 2.5 35.5 + - - +
728A VAL 3.3 7.1 + - - +
730A GLU* 1.3 79.5 + - - +
732A LEU* 1.3 62.8 + - + +
734A ASN* 4.0 5.9 + - - +
735A TYR* 3.7 13.2 + - - +
589B LEU* 5.6 0.7 - - - +
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Residues in contact with LEU 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A JZN 3.8 25.2 - - + +
601A MET* 4.0 15.9 - - + -
605A ALA* 3.9 27.1 - - + -
641A ASP 4.9 0.7 - - - +
642A GLN* 3.8 35.0 - - + +
645A HIS* 4.9 5.2 - - + -
646A MET* 3.9 25.6 - - + -
728A VAL* 3.1 23.0 + - + +
729A VAL* 3.0 8.6 + - - +
731A ASN* 1.3 79.2 - - - +
733A LEU* 1.3 63.6 + - - +
734A ASN 3.3 0.2 - - - -
735A TYR* 3.7 3.5 + - + +
736A CYS* 3.2 22.9 + - - +
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Residues in contact with LEU 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A TYR 5.4 6.3 - - - +
600A TRP* 3.7 27.4 - - + +
601A MET* 3.4 27.6 - - + -
602A TYR* 5.6 1.1 - - + -
729A VAL* 2.5 39.6 + - + +
730A GLU* 3.1 8.0 + - + +
732A LEU* 1.3 73.6 - - - +
734A ASN* 1.3 64.1 + - - +
736A CYS* 3.4 5.0 + - + +
737A PHE* 3.0 52.7 + - + -
764A TYR* 5.5 12.3 - - + -
769A ILE* 6.5 0.9 - - + -
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Residues in contact with ASN 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A GLU* 2.7 41.5 + - - +
731A ASN* 4.3 6.2 - - - +
733A LEU* 1.3 74.3 - - - +
735A TYR* 1.3 55.6 + - - +
737A PHE* 2.8 15.1 + - - +
738A GLN* 2.6 48.2 + - + +
764A TYR* 4.1 23.6 + - - -
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Residues in contact with TYR 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A JZN 4.1 26.7 - + + +
560A MET* 4.1 22.6 - - + +
638A GLY 2.5 38.1 + - - -
639A MET* 4.8 2.9 - - - -
641A ASP* 3.7 30.5 - - - +
642A GLN* 5.4 2.2 - - + -
731A ASN 3.7 15.6 + - - +
732A LEU* 3.7 6.5 + - - +
733A LEU 3.5 0.2 - - - -
734A ASN* 1.3 77.3 - - - +
736A CYS* 1.3 59.2 + - - +
738A GLN* 3.2 9.5 + - + +
739A THR* 2.8 50.8 + - - -
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Residues in contact with CYS 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A JZN 3.4 44.2 - - + +
600A TRP* 3.9 17.5 - - - -
601A MET* 4.2 2.9 - - + -
732A LEU 3.2 12.3 + - - +
733A LEU* 3.4 11.0 - - + +
734A ASN 3.1 0.4 - - - -
735A TYR* 1.3 80.4 - - - +
737A PHE* 1.3 58.8 + - - +
739A THR* 3.6 3.0 + - - -
740A PHE* 3.0 27.2 + - - +
749A PHE* 4.5 3.0 - - - -
757A ILE* 3.6 26.7 - - - -
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Residues in contact with PHE 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A TRP* 5.1 2.0 - + - -
733A LEU* 3.0 52.0 + - + -
734A ASN* 2.8 19.8 + - - +
736A CYS* 1.3 72.3 - - + +
738A GLN* 1.3 62.7 + - - +
740A PHE* 2.9 6.0 + - - +
741A LEU* 2.6 52.4 + - + +
757A ILE* 3.9 29.8 - - + -
760A GLN* 5.1 8.3 - - + -
761A ILE* 3.9 32.3 - - + -
764A TYR* 4.6 26.5 - + + -
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Residues in contact with GLN 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A ASN* 2.6 32.0 + - + +
735A TYR* 3.5 9.6 - - + +
737A PHE* 1.3 76.7 - - - +
739A THR* 1.3 55.8 + - - +
741A LEU* 5.0 6.2 - - - +
742A ASP* 2.7 50.1 + - + +
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Residues in contact with THR 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A JZN 4.2 15.7 - - + -
560A MET* 4.7 6.8 - - - -
735A TYR* 2.8 38.4 + - - -
736A CYS 3.8 4.5 - - - -
738A GLN* 1.3 75.2 - - - +
740A PHE* 1.3 59.3 + - - +
742A ASP* 5.0 0.4 - - - -
743A LYS* 2.8 31.7 + - - +
747A ILE* 3.8 30.6 - - + +
749A PHE* 4.3 7.6 - - + -
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Residues in contact with PHE 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A CYS 3.0 17.8 + - - +
737A PHE* 2.9 9.6 + - - +
739A THR* 1.3 78.5 - - - +
741A LEU* 1.3 81.7 + - + +
743A LYS* 3.6 10.9 - - - +
749A PHE* 4.0 30.3 - + + -
754A ALA* 3.9 30.7 - - + -
757A ILE* 3.5 33.4 - - + -
758A THR* 3.5 27.6 - - + -
761A ILE* 4.8 2.2 - - + -
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Residues in contact with LEU 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A PHE* 2.6 29.0 + - + +
738A GLN* 5.0 6.5 - - - +
740A PHE* 1.3 94.1 - - + +
742A ASP* 1.3 55.8 + - - +
743A LYS 2.8 27.1 + - - +
761A ILE* 3.4 32.5 - - + -
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Residues in contact with ASP 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A GLN* 2.7 35.9 + - + +
739A THR* 5.0 0.7 - - - -
741A LEU* 1.3 73.0 - - - +
743A LYS* 1.3 62.4 + - - +
745A MET* 3.8 12.4 - - - +
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Residues in contact with LYS 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739A THR* 2.8 24.5 + - + +
740A PHE* 3.6 11.0 - - - +
741A LEU 2.8 12.3 + - - +
742A ASP* 1.3 86.5 - - - +
745A MET* 2.9 51.3 - - - +
746A SER* 4.9 1.3 - - - -
747A ILE* 3.4 19.1 - - + +
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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
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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) + - + + + + + -
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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