ID code: '4U3O' 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' --------------------------------------------------------------------------------- 9 C1' U A 1 beta 4 10 7 29 C1' C A 2 beta 24 30 27 49 C1' G A 3 beta 44 50 47 72 C1' U A 4 beta 67 73 70 92 C1' A A 5 beta 87 93 90 114 C1' C A 6 beta 109 115 112 134 C1' G A 7 beta 129 135 132 157 C1' A A 8 beta 152 158 155 177 C1' U B 1 beta 172 178 175 197 C1' C B 2 beta 192 198 195 217 C1' G B 3 beta 212 218 215 240 C1' U B 4 beta 235 241 238 260 C1' A B 5 beta 255 261 258 282 C1' C B 6 beta 277 283 280 302 C1' G B 7 beta 297 303 300 325 C1' A B 8 beta 320 326 323 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK 9 5 8 27 C2' C A 2 OK 29 25 28 47 C2' G A 3 OK 49 45 48 70 C2' U A 4 OK 72 68 71 90 C2' A A 5 OK 92 88 91 112 C2' C A 6 OK 114 110 113 132 C2' G A 7 OK 134 130 133 155 C2' A A 8 OK 157 153 156 175 C2' U B 1 OK 177 173 176 195 C2' C B 2 OK 197 193 196 215 C2' G B 3 OK 217 213 216 238 C2' U B 4 OK 240 236 239 258 C2' A B 5 OK 260 256 259 280 C2' C B 6 OK 282 278 281 300 C2' G B 7 OK 302 298 301 323 C2' A B 8 OK 325 321 324 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK 3 6 7 25 C3' C A 2 OK 23 26 27 45 C3' G A 3 OK 43 46 47 68 C3' U A 4 OK 66 69 70 88 C3' A A 5 OK 86 89 90 110 C3' C A 6 OK 108 111 112 130 C3' G A 7 OK 128 131 132 153 C3' A A 8 OK 151 154 155 173 C3' U B 1 OK 171 174 175 193 C3' C B 2 OK 191 194 195 213 C3' G B 3 OK 211 214 215 236 C3' U B 4 OK 234 237 238 256 C3' A B 5 OK 254 257 258 278 C3' C B 6 OK 276 279 280 298 C3' G B 7 OK 296 299 300 321 C3' A B 8 OK 319 322 323 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK 5 2 4 23 C4' C A 2 OK 25 22 24 43 C4' G A 3 OK 45 42 44 66 C4' U A 4 OK 68 65 67 86 C4' A A 5 OK 88 85 87 108 C4' C A 6 OK 110 107 109 128 C4' G A 7 OK 130 127 129 151 C4' A A 8 OK 153 150 152 171 C4' U B 1 OK 173 170 172 191 C4' C B 2 OK 193 190 192 211 C4' G B 3 OK 213 210 212 234 C4' U B 4 OK 236 233 235 254 C4' A B 5 OK 256 253 255 276 C4' C B 6 OK 278 275 277 296 C4' G B 7 OK 298 295 297 319 C4' A B 8 OK 321 318 320 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 1 3 22 C5' C A 2 21 23 42 C5' G A 3 41 43 65 C5' U A 4 64 66 85 C5' A A 5 84 86 107 C5' C A 6 106 108 127 C5' G A 7 126 128 150 C5' A A 8 149 151 170 C5' U B 1 169 171 190 C5' C B 2 189 191 210 C5' G B 3 209 211 233 C5' U B 4 232 234 253 C5' A B 5 252 254 275 C5' C B 6 274 276 295 C5' G B 7 294 296 318 C5' A B 8 317 319 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C A 2 distorted distorted 6 19 20 21 38 P G A 3 distorted distorted 26 39 40 41 61 P U A 4 distorted distorted 46 62 63 64 81 P A A 5 distorted distorted 69 82 83 84 103 P C A 6 distorted distorted 89 104 105 106 123 P G A 7 distorted distorted 111 124 125 126 146 P A A 8 distorted distorted 131 147 148 149 186 P C B 2 distorted distorted 174 187 188 189 206 P G B 3 distorted distorted 194 207 208 209 229 P U B 4 distorted distorted 214 230 231 232 249 P A B 5 distorted distorted 237 250 251 252 271 P C B 6 distorted distorted 257 272 273 274 291 P G B 7 distorted distorted 279 292 293 294 314 P A B 8 distorted distorted 299 315 316 317 ---------------------------------------------------------------------------------