ID code: '5ELX' 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' --------------------------------------------------------------------------------- 3160 C1' U B 1 beta 3155 3161 3158 3180 C1' U B 2 beta 3175 3181 3178 3200 C1' U B 3 beta 3195 3201 3198 3220 C1' U B 4 beta 3215 3221 3218 3240 C1' U B 5 beta 3235 3241 3238 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3158 C2' U B 1 OK 3160 3156 3159 3178 C2' U B 2 OK 3180 3176 3179 3198 C2' U B 3 OK 3200 3196 3199 3218 C2' U B 4 OK 3220 3216 3219 3238 C2' U B 5 OK 3240 3236 3239 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3156 C3' U B 1 OK 3154 3157 3158 3176 C3' U B 2 OK 3174 3177 3178 3196 C3' U B 3 OK 3194 3197 3198 3216 C3' U B 4 OK 3214 3217 3218 3236 C3' U B 5 OK 3234 3237 3238 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3154 C4' U B 1 OK 3156 3153 3155 3174 C4' U B 2 OK 3176 3173 3175 3194 C4' U B 3 OK 3196 3193 3195 3214 C4' U B 4 OK 3216 3213 3215 3234 C4' U B 5 OK 3236 3233 3235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3153 C5' U B 1 3152 3154 3173 C5' U B 2 3172 3174 3193 C5' U B 3 3192 3194 3213 C5' U B 4 3212 3214 3233 C5' U B 5 3232 3234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3149 P U B 1 distorted distorted 3150 3151 3152 3169 P U B 2 distorted distorted 3157 3170 3171 3172 3189 P U B 3 distorted distorted 3177 3190 3191 3192 3209 P U B 4 distorted distorted 3197 3210 3211 3212 3229 P U B 5 distorted distorted 3217 3230 3231 3232 3249 P U B 6 distorted distorted 3237 3250 3251 3252 ---------------------------------------------------------------------------------