ID code: '4M7A' 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' --------------------------------------------------------------------------------- 8115 C1' G O 108 beta 8110 8116 8113 8138 C1' U O 109 beta 8133 8139 8136 8158 C1' U O 110 beta 8153 8159 8156 8178 C1' U O 111 beta 8173 8179 8176 8198 C1' U O 112 beta 8193 8199 8196 8219 C1' G P 108 beta 8214 8220 8217 8242 C1' U P 109 beta 8237 8243 8240 8262 C1' U P 110 beta 8257 8263 8260 8282 C1' U P 111 beta 8277 8283 8280 8302 C1' U P 112 beta 8297 8303 8300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8113 C2' G O 108 OK 8115 8111 8114 8136 C2' U O 109 OK 8138 8134 8137 8156 C2' U O 110 OK 8158 8154 8157 8176 C2' U O 111 OK 8178 8174 8177 8196 C2' U O 112 OK 8198 8194 8197 8217 C2' G P 108 OK 8219 8215 8218 8240 C2' U P 109 OK 8242 8238 8241 8260 C2' U P 110 OK 8262 8258 8261 8280 C2' U P 111 OK 8282 8278 8281 8300 C2' U P 112 OK 8302 8298 8301 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8111 C3' G O 108 OK 8109 8112 8113 8134 C3' U O 109 OK 8132 8135 8136 8154 C3' U O 110 OK 8152 8155 8156 8174 C3' U O 111 OK 8172 8175 8176 8194 C3' U O 112 OK 8192 8195 8196 8215 C3' G P 108 OK 8213 8216 8217 8238 C3' U P 109 OK 8236 8239 8240 8258 C3' U P 110 OK 8256 8259 8260 8278 C3' U P 111 OK 8276 8279 8280 8298 C3' U P 112 OK 8296 8299 8300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8109 C4' G O 108 OK 8111 8108 8110 8132 C4' U O 109 OK 8134 8131 8133 8152 C4' U O 110 OK 8154 8151 8153 8172 C4' U O 111 OK 8174 8171 8173 8192 C4' U O 112 OK 8194 8191 8193 8213 C4' G P 108 OK 8215 8212 8214 8236 C4' U P 109 OK 8238 8235 8237 8256 C4' U P 110 OK 8258 8255 8257 8276 C4' U P 111 OK 8278 8275 8277 8296 C4' U P 112 OK 8298 8295 8297 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8108 C5' G O 108 8107 8109 8131 C5' U O 109 8130 8132 8151 C5' U O 110 8150 8152 8171 C5' U O 111 8170 8172 8191 C5' U O 112 8190 8192 8212 C5' G P 108 8211 8213 8235 C5' U P 109 8234 8236 8255 C5' U P 110 8254 8256 8275 C5' U P 111 8274 8276 8295 C5' U P 112 8294 8296 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8104 P G O 108 OK OK 8105 8106 8107 8127 P U O 109 distorted distorted 8112 8128 8129 8130 8147 P U O 110 distorted distorted 8135 8148 8149 8150 8167 P U O 111 distorted distorted 8155 8168 8169 8170 8187 P U O 112 distorted distorted 8175 8188 8189 8190 8208 P G P 108 distorted distorted 8209 8210 8211 8231 P U P 109 distorted distorted 8216 8232 8233 8234 8251 P U P 110 distorted distorted 8239 8252 8253 8254 8271 P U P 111 distorted distorted 8259 8272 8273 8274 8291 P U P 112 distorted distorted 8279 8292 8293 8294 ---------------------------------------------------------------------------------