ID code: '2VOO' 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' --------------------------------------------------------------------------------- 2925 C1' U C -3 beta 2920 2926 2923 2945 C1' U C -2 beta 2940 2946 2943 2965 C1' U C -1 beta 2960 2966 2963 2983 C1' U D -3 beta 2978 2984 2981 3003 C1' U D -2 beta 2998 3004 3001 3023 C1' U D -1 beta 3018 3024 3021 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2923 C2' U C -3 OK 2925 2921 2924 2943 C2' U C -2 OK 2945 2941 2944 2963 C2' U C -1 OK 2965 2961 2964 2981 C2' U D -3 OK 2983 2979 2982 3001 C2' U D -2 OK 3003 2999 3002 3021 C2' U D -1 OK 3023 3019 3022 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2921 C3' U C -3 OK 2919 2922 2923 2941 C3' U C -2 OK 2939 2942 2943 2961 C3' U C -1 OK 2959 2962 2963 2979 C3' U D -3 OK 2977 2980 2981 2999 C3' U D -2 OK 2997 3000 3001 3019 C3' U D -1 OK 3017 3020 3021 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2919 C4' U C -3 OK 2921 2918 2920 2939 C4' U C -2 OK 2941 2938 2940 2959 C4' U C -1 OK 2961 2958 2960 2977 C4' U D -3 OK 2979 2976 2978 2997 C4' U D -2 OK 2999 2996 2998 3017 C4' U D -1 OK 3019 3016 3018 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2918 C5' U C -3 2917 2919 2938 C5' U C -2 2937 2939 2958 C5' U C -1 2957 2959 2976 C5' U D -3 2975 2977 2996 C5' U D -2 2995 2997 3016 C5' U D -1 3015 3017 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2934 P U C -2 OK OK 2922 2935 2936 2937 2954 P U C -1 OK OK 2942 2955 2956 2957 2992 P U D -2 OK OK 2980 2993 2994 2995 3012 P U D -1 OK OK 3000 3013 3014 3015 ---------------------------------------------------------------------------------