ID code: '3VAH' 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' --------------------------------------------------------------------------------- 2886 C1' DU P 2 beta 2882 2887 2885 2905 C1' DU P 3 beta 2901 2906 2904 2923 C1' BRU P 4 beta 2928 2914 2924 2944 C1' DC P 5 beta 2940 2945 2943 2963 C1' DU P 6 beta 2959 2964 2962 2982 C1' DU P 7 beta 2978 2983 2981 2994 C1' DIO A 401 2997 3010 C1' DIO B 401 3013 3016 C1' DIO B 402 3019 3022 C1' DIO B 403 3025 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2885 C2' DU P 2 2886 2883 2904 C2' DU P 3 2905 2902 2924 C2' BRU P 4 2923 2925 2943 C2' DC P 5 2944 2941 2962 C2' DU P 6 2963 2960 2981 C2' DU P 7 2982 2979 2995 C2' DIO A 401 3011 C2' DIO B 401 3017 C2' DIO B 402 3023 C2' DIO B 403 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2883 C3' DU P 2 OK 2881 2884 2885 2902 C3' DU P 3 OK 2900 2903 2904 2925 C3' BRU P 4 OK 2926 2927 2924 2941 C3' DC P 5 OK 2939 2942 2943 2960 C3' DU P 6 OK 2958 2961 2962 2979 C3' DU P 7 OK 2977 2980 2981 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2881 C4' DU P 2 OK 2883 2880 2882 2900 C4' DU P 3 OK 2902 2899 2901 2926 C4' BRU P 4 OK 2925 2929 2928 2939 C4' DC P 5 OK 2941 2938 2940 2958 C4' DU P 6 OK 2960 2957 2959 2977 C4' DU P 7 OK 2979 2976 2978 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2880 C5' DU P 2 2879 2881 2899 C5' DU P 3 2898 2900 2929 C5' BRU P 4 2930 2926 2938 C5' DC P 5 2937 2939 2957 C5' DU P 6 2956 2958 2976 C5' DU P 7 2975 2977 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2689 P DU E 1 2724 P DU E 2 2725 P DU E 2 2796 P BRU E 3 2797 P BRU E 3 2802 P DC E 4 2803 P DC E 4 2840 P DU E 5 2841 P DU E 5 2895 P DU P 3 distorted distorted 2884 2896 2897 2898 2931 P BRU P 4 distorted distorted 2903 2932 2933 2930 2934 P DC P 5 distorted distorted 2927 2935 2936 2937 2953 P DU P 6 distorted distorted 2942 2954 2955 2956 2972 P DU P 7 distorted distorted 2961 2973 2974 2975 ---------------------------------------------------------------------------------