ID code: '4II9' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 2750 C1' C C 8 beta 2745 2751 2748 2770 C1' C C 9 beta 2765 2771 2768 2795 C1' A9Z C 10 beta 2796 2797 2787 2822 C1' UDP B 101 beta 2827 2814 2823 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2748 C2' C C 8 OK 2750 2746 2749 2768 C2' C C 9 OK 2770 2766 2769 2787 C2' A9Z C 10 2795 2785 2823 C2' UDP B 101 OK 2822 2825 2824 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2746 C3' C C 8 OK 2744 2747 2748 2766 C3' C C 9 OK 2764 2767 2768 2785 C3' A9Z C 10 OK 2784 2786 2787 2825 C3' UDP B 101 OK 2826 2828 2823 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2744 C4' C C 8 OK 2746 2743 2745 2764 C4' C C 9 OK 2766 2763 2765 2784 C4' A9Z C 10 OK 2785 2783 2796 2826 C4' UDP B 101 OK 2825 2829 2827 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2743 C5' C C 8 2742 2744 2763 C5' C C 9 2762 2764 2783 C5' A9Z C 10 2782 2784 2829 C5' UDP B 101 2830 2826 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2739 P C C 8 distorted distorted 2740 2741 2742 2759 P C C 9 distorted distorted 2747 2760 2761 2762 2780 P A9Z C 10 distorted distorted 2767 2779 2781 2782 ---------------------------------------------------------------------------------