ID code: '5EV2' 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' --------------------------------------------------------------------------------- 3065 C1' U B 2 alpha beta 3060 3080 3066 3063 3095 C1' U B 3 alpha beta 3090 3110 3096 3093 3124 C1' DU B 4 beta 3120 3125 3123 3143 C1' DU B 5 beta 3139 3144 3142 3163 C1' U B 6 alpha beta 3158 3178 3164 3161 3192 C1' DU B 7 beta 3188 3193 3191 3210 C1' BRU B 8 beta 3215 3201 3211 3231 C1' DU B 9 beta 3227 3232 3230 3243 C1' DIO A 401 3246 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3063 C2' U B 2 OK OK 3065 3061 3078 3064 3093 C2' U B 3 OK OK 3095 3091 3108 3094 3123 C2' DU B 4 3124 3121 3142 C2' DU B 5 3143 3140 3161 C2' U B 6 OK OK 3163 3159 3176 3162 3191 C2' DU B 7 3192 3189 3211 C2' BRU B 8 3210 3212 3230 C2' DU B 9 3231 3228 3244 C2' DIO A 401 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3061 C3' U B 2 OK OK 3059 3077 3062 3063 3091 C3' U B 3 OK OK 3089 3107 3092 3093 3121 C3' DU B 4 OK 3119 3122 3123 3140 C3' DU B 5 OK 3138 3141 3142 3159 C3' U B 6 OK OK 3157 3175 3160 3161 3189 C3' DU B 7 OK 3187 3190 3191 3212 C3' BRU B 8 OK 3213 3214 3211 3228 C3' DU B 9 OK 3226 3229 3230 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3059 C4' U B 2 OK OK 3061 3076 3058 3060 3089 C4' U B 3 OK OK 3091 3106 3088 3090 3119 C4' DU B 4 OK 3121 3118 3120 3138 C4' DU B 5 OK 3140 3137 3139 3157 C4' U B 6 OK OK 3159 3174 3156 3158 3187 C4' DU B 7 OK 3189 3186 3188 3213 C4' BRU B 8 OK 3212 3216 3215 3226 C4' DU B 9 OK 3228 3225 3227 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3058 C5' U B 2 OK OK 3057 3074 3075 3059 3088 C5' U B 3 OK OK 3087 3104 3105 3089 3118 C5' DU B 4 3117 3119 3137 C5' DU B 5 3136 3138 3156 C5' U B 6 OK OK 3155 3172 3173 3157 3186 C5' DU B 7 3185 3187 3216 C5' BRU B 8 3217 3213 3225 C5' DU B 9 3224 3226 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3054 P U B 2 OK OK 3055 3056 3057 3084 P U B 3 distorted distorted 3062 3085 3086 3087 3114 P DU B 4 distorted distorted 3092 3115 3116 3117 3133 P DU B 5 distorted distorted 3122 3134 3135 3136 3152 P U B 6 distorted distorted 3141 3153 3154 3155 3182 P DU B 7 distorted distorted 3160 3183 3184 3185 3218 P BRU B 8 distorted distorted 3190 3219 3220 3217 3221 P DU B 9 distorted distorted 3214 3222 3223 3224 ---------------------------------------------------------------------------------