ID code: '4DW7' 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' --------------------------------------------------------------------------------- 2802 C1' U A1110 beta 2797 2803 2800 2819 C1' C A1111 beta 2814 2820 2817 2854 C1' U B 210 beta 2849 2855 2852 2871 C1' C B 213 beta 2866 2872 2869 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2800 C2' U A1110 OK 2802 2798 2801 2817 C2' C A1111 OK 2819 2815 2818 2852 C2' U B 210 OK 2854 2850 2853 2869 C2' C B 213 OK 2871 2867 2870 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2798 C3' U A1110 OK 2796 2799 2800 2815 C3' C A1111 OK 2813 2816 2817 2850 C3' U B 210 OK 2848 2851 2852 2867 C3' C B 213 OK 2865 2868 2869 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2796 C4' U A1110 OK 2798 2795 2797 2813 C4' C A1111 OK 2815 2812 2814 2848 C4' U B 210 OK 2850 2847 2849 2865 C4' C B 213 OK 2867 2864 2866 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2795 C5' U A1110 2794 2796 2812 C5' C A1111 2811 2813 2847 C5' U B 210 2846 2848 2864 C5' C B 213 2863 2865 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2791 P U A1110 distorted distorted 2816 2792 2793 2794 2843 P U B 210 OK OK 2868 2844 2845 2846 ---------------------------------------------------------------------------------