ID code: '2M1O' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 alpha beta 8 31 14 11 48 C1' G A 2 alpha beta 43 66 49 46 82 C1' G A 3 alpha beta 77 100 83 80 116 C1' U A 4 alpha beta 111 131 117 114 146 C1' G A 5 alpha beta 141 164 147 144 180 C1' U A 6 alpha beta 175 195 181 178 210 C1' A A 7 alpha beta 205 228 211 208 246 C1' A B 17 alpha beta 241 263 247 244 280 C1' G B 18 alpha beta 275 298 281 278 314 C1' C B 19 alpha beta 309 329 315 312 345 C1' A B 20 alpha beta 340 362 346 343 378 C1' C B 21 alpha beta 373 393 379 376 409 C1' C B 22 alpha beta 404 424 410 407 440 C1' C B 23 alpha beta 435 456 441 438 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 29 12 46 C2' G A 2 OK OK 48 44 64 47 80 C2' G A 3 OK OK 82 78 98 81 114 C2' U A 4 OK OK 116 112 129 115 144 C2' G A 5 OK OK 146 142 162 145 178 C2' U A 6 OK OK 180 176 193 179 208 C2' A A 7 OK OK 210 206 226 209 244 C2' A B 17 OK OK 246 242 261 245 278 C2' G B 18 OK OK 280 276 296 279 312 C2' C B 19 OK OK 314 310 327 313 343 C2' A B 20 OK OK 345 341 360 344 376 C2' C B 21 OK OK 378 374 391 377 407 C2' C B 22 OK OK 409 405 422 408 438 C2' C B 23 OK OK 440 436 454 439 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' G A 2 OK OK 42 63 45 46 78 C3' G A 3 OK OK 76 97 79 80 112 C3' U A 4 OK OK 110 128 113 114 142 C3' G A 5 OK OK 140 161 143 144 176 C3' U A 6 OK OK 174 192 177 178 206 C3' A A 7 OK OK 204 224 207 208 242 C3' A B 17 OK OK 240 260 243 244 276 C3' G B 18 OK OK 274 295 277 278 310 C3' C B 19 OK OK 308 326 311 312 341 C3' A B 20 OK OK 339 359 342 343 374 C3' C B 21 OK OK 372 390 375 376 405 C3' C B 22 OK OK 403 421 406 407 436 C3' C B 23 OK OK 434 452 437 438 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' G A 2 OK OK 44 62 41 43 76 C4' G A 3 OK OK 78 96 75 77 110 C4' U A 4 OK OK 112 127 109 111 140 C4' G A 5 OK OK 142 160 139 141 174 C4' U A 6 OK OK 176 191 173 175 204 C4' A A 7 OK OK 206 223 203 205 240 C4' A B 17 OK OK 242 259 239 241 274 C4' G B 18 OK OK 276 294 273 275 308 C4' C B 19 OK OK 310 325 307 309 339 C4' A B 20 OK OK 341 358 338 340 372 C4' C B 21 OK OK 374 389 371 373 403 C4' C B 22 OK OK 405 420 402 404 434 C4' C B 23 OK OK 436 451 433 435 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' G A 2 OK OK 40 60 61 42 75 C5' G A 3 OK OK 74 94 95 76 109 C5' U A 4 OK OK 108 125 126 110 139 C5' G A 5 OK OK 138 158 159 140 173 C5' U A 6 OK OK 172 189 190 174 203 C5' A A 7 OK OK 202 221 222 204 239 C5' A B 17 OK OK 238 257 258 240 273 C5' G B 18 OK OK 272 292 293 274 307 C5' C B 19 OK OK 306 323 324 308 338 C5' A B 20 OK OK 337 356 357 339 371 C5' C B 21 OK OK 370 387 388 372 402 C5' C B 22 OK OK 401 418 419 403 433 C5' C B 23 OK OK 432 449 450 434 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 OK OK 3 4 5 37 P G A 2 distorted distorted 10 38 39 40 71 P G A 3 distorted distorted 45 72 73 74 105 P U A 4 distorted distorted 79 106 107 108 135 P G A 5 distorted distorted 113 136 137 138 169 P U A 6 distorted distorted 143 170 171 172 199 P A A 7 distorted distorted 177 200 201 202 235 P A B 17 OK OK 236 237 238 269 P G B 18 distorted distorted 243 270 271 272 303 P C B 19 distorted distorted 277 304 305 306 334 P A B 20 distorted distorted 311 335 336 337 367 P C B 21 distorted distorted 342 368 369 370 398 P C B 22 distorted distorted 375 399 400 401 429 P C B 23 distorted distorted 406 430 431 432 ---------------------------------------------------------------------------------