ID code: '1IPX' 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' --------------------------------------------------------------------------------- 12 C1' U A1868 beta 7 13 10 32 C1' G A1869 beta 27 33 30 53 C1' 5MU A1870 beta 59 44 54 73 C1' PSU A1871 beta 79 69 74 96 C1' C A1872 beta 91 97 94 116 C1' G A1873 beta 111 117 114 139 C1' 1MA A1874 beta 134 140 137 162 C1' U A1875 beta 157 163 160 182 C1' C A1876 beta 177 183 180 202 C1' C A1877 beta 197 203 200 222 C1' A A1878 beta 217 223 220 243 C1' H2U B1916 beta 240 246 244 263 C1' H2U B1917 beta 260 266 264 285 C1' G B1918 beta 280 286 283 308 C1' G B1919 beta 303 309 306 331 C1' G B1920 beta 326 332 329 354 C1' A B1921 beta 349 355 352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U A1868 OK 12 8 11 30 C2' G A1869 OK 32 28 31 54 C2' 5MU A1870 OK 53 56 55 74 C2' PSU A1871 OK 73 76 75 94 C2' C A1872 OK 96 92 95 114 C2' G A1873 OK 116 112 115 137 C2' 1MA A1874 OK 139 135 138 160 C2' U A1875 OK 162 158 161 180 C2' C A1876 OK 182 178 181 200 C2' C A1877 OK 202 198 201 220 C2' A A1878 OK 222 218 221 244 C2' H2U B1916 OK 243 241 245 264 C2' H2U B1917 OK 263 261 265 283 C2' G B1918 OK 285 281 284 306 C2' G B1919 OK 308 304 307 329 C2' G B1920 OK 331 327 330 352 C2' A B1921 OK 354 350 353 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U A1868 OK 6 9 10 28 C3' G A1869 OK 26 29 30 56 C3' 5MU A1870 OK 57 58 54 76 C3' PSU A1871 OK 77 78 74 92 C3' C A1872 OK 90 93 94 112 C3' G A1873 OK 110 113 114 135 C3' 1MA A1874 OK 133 136 137 158 C3' U A1875 OK 156 159 160 178 C3' C A1876 OK 176 179 180 198 C3' C A1877 OK 196 199 200 218 C3' A A1878 OK 216 219 220 241 C3' H2U B1916 OK 239 242 244 261 C3' H2U B1917 OK 259 262 264 281 C3' G B1918 OK 279 282 283 304 C3' G B1919 OK 302 305 306 327 C3' G B1920 OK 325 328 329 350 C3' A B1921 OK 348 351 352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U A1868 OK 8 5 7 26 C4' G A1869 OK 28 25 27 57 C4' 5MU A1870 OK 56 60 59 77 C4' PSU A1871 OK 76 80 79 90 C4' C A1872 OK 92 89 91 110 C4' G A1873 OK 112 109 111 133 C4' 1MA A1874 OK 135 132 134 156 C4' U A1875 OK 158 155 157 176 C4' C A1876 OK 178 175 177 196 C4' C A1877 OK 198 195 197 216 C4' A A1878 OK 218 215 217 239 C4' H2U B1916 OK 241 238 240 259 C4' H2U B1917 OK 261 258 260 279 C4' G B1918 OK 281 278 280 302 C4' G B1919 OK 304 301 303 325 C4' G B1920 OK 327 324 326 348 C4' A B1921 OK 350 347 349 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U A1868 4 6 25 C5' G A1869 24 26 60 C5' 5MU A1870 61 57 80 C5' PSU A1871 81 77 89 C5' C A1872 88 90 109 C5' G A1873 108 110 132 C5' 1MA A1874 131 133 155 C5' U A1875 154 156 175 C5' C A1876 174 176 195 C5' C A1877 194 196 215 C5' A A1878 214 216 238 C5' H2U B1916 237 239 258 C5' H2U B1917 257 259 278 C5' G B1918 277 279 301 C5' G B1919 300 302 324 C5' G B1920 323 325 347 C5' A B1921 346 348 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U A1868 OK OK 2 3 4 21 P G A1869 distorted distorted 9 22 23 24 62 P 5MU A1870 distorted distorted 29 63 64 61 82 P PSU A1871 distorted distorted 58 83 84 81 85 P C A1872 distorted distorted 78 86 87 88 105 P G A1873 distorted distorted 93 106 107 108 128 P 1MA A1874 distorted distorted 113 129 130 131 151 P U A1875 distorted distorted 136 152 153 154 171 P C A1876 distorted distorted 159 172 173 174 191 P C A1877 distorted distorted 179 192 193 194 211 P A A1878 distorted distorted 199 212 213 214 234 P H2U B1916 OK OK 235 236 237 254 P H2U B1917 distorted distorted 242 255 256 257 274 P G B1918 distorted distorted 262 275 276 277 297 P G B1919 distorted distorted 282 298 299 300 320 P G B1920 distorted distorted 305 321 322 323 343 P A B1921 distorted distorted 328 344 345 346 ---------------------------------------------------------------------------------