ID code: '5BTE' 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' --------------------------------------------------------------------------------- 2995 C1' U D 2 beta 2990 2996 2993 3015 C1' U37 D 3 beta 3010 3016 3013 3035 C1' U37 D 4 beta 3030 3036 3033 3055 C1' U D 5 beta 3050 3056 3053 3075 C1' U D 6 beta 3070 3076 3073 3095 C1' U D 7 beta 3090 3096 3093 3117 C1' U C 2 beta 3112 3118 3115 3137 C1' U37 C 3 beta 3132 3138 3135 3157 C1' U37 C 4 beta 3152 3158 3155 3177 C1' U C 5 beta 3172 3178 3175 3197 C1' U C 6 beta 3192 3198 3195 3217 C1' U C 7 beta 3212 3218 3215 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2993 C2' U D 2 OK 2995 2991 2994 3013 C2' U37 D 3 OK 3015 3011 3014 3033 C2' U37 D 4 OK 3035 3031 3034 3053 C2' U D 5 OK 3055 3051 3054 3073 C2' U D 6 OK 3075 3071 3074 3093 C2' U D 7 OK 3095 3091 3094 3115 C2' U C 2 OK 3117 3113 3116 3135 C2' U37 C 3 OK 3137 3133 3136 3155 C2' U37 C 4 OK 3157 3153 3156 3175 C2' U C 5 OK 3177 3173 3176 3195 C2' U C 6 OK 3197 3193 3196 3215 C2' U C 7 OK 3217 3213 3216 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2991 C3' U D 2 OK 2989 2992 2993 3011 C3' U37 D 3 OK 3009 3012 3013 3031 C3' U37 D 4 OK 3029 3032 3033 3051 C3' U D 5 OK 3049 3052 3053 3071 C3' U D 6 OK 3069 3072 3073 3091 C3' U D 7 OK 3089 3092 3093 3113 C3' U C 2 OK 3111 3114 3115 3133 C3' U37 C 3 OK 3131 3134 3135 3153 C3' U37 C 4 OK 3151 3154 3155 3173 C3' U C 5 OK 3171 3174 3175 3193 C3' U C 6 OK 3191 3194 3195 3213 C3' U C 7 OK 3211 3214 3215 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2989 C4' U D 2 OK 2991 2988 2990 3009 C4' U37 D 3 OK 3011 3008 3010 3029 C4' U37 D 4 OK 3031 3028 3030 3049 C4' U D 5 OK 3051 3048 3050 3069 C4' U D 6 OK 3071 3068 3070 3089 C4' U D 7 OK 3091 3088 3090 3111 C4' U C 2 OK 3113 3110 3112 3131 C4' U37 C 3 OK 3133 3130 3132 3151 C4' U37 C 4 OK 3153 3150 3152 3171 C4' U C 5 OK 3173 3170 3172 3191 C4' U C 6 OK 3193 3190 3192 3211 C4' U C 7 OK 3213 3210 3212 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2988 C5' U D 2 2987 2989 3008 C5' U37 D 3 3007 3009 3028 C5' U37 D 4 3027 3029 3048 C5' U D 5 3047 3049 3068 C5' U D 6 3067 3069 3088 C5' U D 7 3087 3089 3110 C5' U C 2 3109 3111 3130 C5' U37 C 3 3129 3131 3150 C5' U37 C 4 3149 3151 3170 C5' U C 5 3169 3171 3190 C5' U C 6 3189 3191 3210 C5' U C 7 3209 3211 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2984 P U D 2 distorted distorted 2985 2986 2987 3004 P U37 D 3 2992 3006 3007 3024 P U37 D 4 3012 3026 3027 3044 P U D 5 distorted distorted 3032 3045 3046 3047 3064 P U D 6 distorted distorted 3052 3065 3066 3067 3084 P U D 7 distorted distorted 3072 3085 3086 3087 3106 P U C 2 distorted distorted 3107 3108 3109 3126 P U37 C 3 3114 3128 3129 3146 P U37 C 4 3134 3148 3149 3166 P U C 5 distorted distorted 3154 3167 3168 3169 3186 P U C 6 distorted distorted 3174 3187 3188 3189 3206 P U C 7 distorted distorted 3194 3207 3208 3209 ---------------------------------------------------------------------------------