ID code: '3V71' 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' --------------------------------------------------------------------------------- 2942 C1' C B 1 beta 2937 2943 2940 2962 C1' U B 3 beta 2957 2963 2960 2982 C1' G B 4 beta 2977 2983 2980 3005 C1' U B 5 beta 3000 3006 3003 3025 C1' A B 6 beta 3020 3026 3023 3047 C1' U B 7 beta 3042 3048 3045 3067 C1' C B 8 beta 3062 3068 3065 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2940 C2' C B 1 OK 2942 2938 2941 2960 C2' U B 3 OK 2962 2958 2961 2980 C2' G B 4 OK 2982 2978 2981 3003 C2' U B 5 OK 3005 3001 3004 3023 C2' A B 6 OK 3025 3021 3024 3045 C2' U B 7 OK 3047 3043 3046 3065 C2' C B 8 OK 3067 3063 3066 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2938 C3' C B 1 OK 2936 2939 2940 2958 C3' U B 3 OK 2956 2959 2960 2978 C3' G B 4 OK 2976 2979 2980 3001 C3' U B 5 OK 2999 3002 3003 3021 C3' A B 6 OK 3019 3022 3023 3043 C3' U B 7 OK 3041 3044 3045 3063 C3' C B 8 OK 3061 3064 3065 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2936 C4' C B 1 OK 2938 2935 2937 2956 C4' U B 3 OK 2958 2955 2957 2976 C4' G B 4 OK 2978 2975 2977 2999 C4' U B 5 OK 3001 2998 3000 3019 C4' A B 6 OK 3021 3018 3020 3041 C4' U B 7 OK 3043 3040 3042 3061 C4' C B 8 OK 3063 3060 3062 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2935 C5' C B 1 2934 2936 2955 C5' U B 3 2954 2956 2975 C5' G B 4 2974 2976 2998 C5' U B 5 2997 2999 3018 C5' A B 6 3017 3019 3040 C5' U B 7 3039 3041 3060 C5' C B 8 3059 3061 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2931 P C B 1 OK OK 2932 2933 2934 2951 P U B 3 distorted distorted 2939 2952 2953 2954 2971 P G B 4 distorted distorted 2959 2972 2973 2974 2994 P U B 5 distorted distorted 2979 2995 2996 2997 3014 P A B 6 distorted distorted 3002 3015 3016 3017 3036 P U B 7 distorted distorted 3022 3037 3038 3039 3056 P C B 8 distorted distorted 3044 3057 3058 3059 ---------------------------------------------------------------------------------