ID code: '1PBM' 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' C A 1 alpha beta 4 24 10 7 41 C1' G A 2 alpha beta 36 59 42 39 75 C1' C A 3 alpha beta 70 90 76 73 106 C1' G A 4 alpha beta 101 124 107 104 140 C1' C A 5 alpha beta 135 155 141 138 171 C1' G A 6 alpha beta 166 190 172 169 204 C1' C B 7 alpha beta 199 219 205 202 236 C1' G B 8 alpha beta 231 254 237 234 270 C1' C B 9 alpha beta 265 285 271 268 301 C1' G B 10 alpha beta 296 319 302 299 335 C1' C B 11 alpha beta 330 350 336 333 366 C1' G B 12 alpha beta 361 385 367 364 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK OK 9 5 22 8 39 C2' G A 2 OK OK 41 37 57 40 73 C2' C A 3 OK OK 75 71 88 74 104 C2' G A 4 OK OK 106 102 122 105 138 C2' C A 5 OK OK 140 136 153 139 169 C2' G A 6 OK OK 171 167 188 170 202 C2' C B 7 OK OK 204 200 217 203 234 C2' G B 8 OK OK 236 232 252 235 268 C2' C B 9 OK OK 270 266 283 269 299 C2' G B 10 OK OK 301 297 317 300 333 C2' C B 11 OK OK 335 331 348 334 364 C2' G B 12 OK OK 366 362 383 365 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' G A 2 OK OK 35 56 38 39 71 C3' C A 3 OK OK 69 87 72 73 102 C3' G A 4 OK OK 100 121 103 104 136 C3' C A 5 OK OK 134 152 137 138 167 C3' G A 6 OK OK 165 186 168 169 200 C3' C B 7 OK OK 198 216 201 202 232 C3' G B 8 OK OK 230 251 233 234 266 C3' C B 9 OK OK 264 282 267 268 297 C3' G B 10 OK OK 295 316 298 299 331 C3' C B 11 OK OK 329 347 332 333 362 C3' G B 12 OK OK 360 381 363 364 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' G A 2 OK OK 37 55 34 36 69 C4' C A 3 OK OK 71 86 68 70 100 C4' G A 4 OK OK 102 120 99 101 134 C4' C A 5 OK OK 136 151 133 135 165 C4' G A 6 OK OK 167 185 164 166 198 C4' C B 7 OK OK 200 215 197 199 230 C4' G B 8 OK OK 232 250 229 231 264 C4' C B 9 OK OK 266 281 263 265 295 C4' G B 10 OK OK 297 315 294 296 329 C4' C B 11 OK OK 331 346 328 330 360 C4' G B 12 OK OK 362 380 359 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 34 C5' G A 2 OK OK 33 53 54 35 68 C5' C A 3 OK OK 67 84 85 69 99 C5' G A 4 OK OK 98 118 119 100 133 C5' C A 5 OK OK 132 149 150 134 164 C5' G A 6 OK OK 163 183 184 165 197 C5' C B 7 OK OK 196 213 214 198 229 C5' G B 8 OK OK 228 248 249 230 263 C5' C B 9 OK OK 262 279 280 264 294 C5' G B 10 OK OK 293 313 314 295 328 C5' C B 11 OK OK 327 344 345 329 359 C5' G B 12 OK OK 358 378 379 360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P G A 2 distorted distorted 6 31 32 33 64 P C A 3 distorted distorted 38 65 66 67 95 P G A 4 distorted distorted 72 96 97 98 129 P C A 5 distorted distorted 103 130 131 132 160 P G A 6 distorted distorted 137 161 162 163 225 P G B 8 distorted distorted 201 226 227 228 259 P C B 9 distorted distorted 233 260 261 262 290 P G B 10 distorted distorted 267 291 292 293 324 P C B 11 distorted distorted 298 325 326 327 355 P G B 12 distorted distorted 332 356 357 358 ---------------------------------------------------------------------------------