ID code: '124D' 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' --------------------------------------------------------------------------------- 8 C1' DG A 1 alpha beta 4 26 9 7 42 C1' DT A 2 alpha beta 38 58 43 41 74 C1' DC A 3 alpha beta 70 89 75 73 104 C1' DA A 4 alpha beta 100 121 105 103 136 C1' DC A 5 alpha beta 132 151 137 135 166 C1' DA A 6 alpha beta 162 183 167 165 198 C1' DT A 7 alpha beta 194 214 199 197 230 C1' DG A 8 alpha beta 226 249 231 229 263 C1' C B 9 alpha beta 258 278 264 261 295 C1' A B 10 alpha beta 290 312 296 293 328 C1' U B 11 alpha beta 323 343 329 326 358 C1' G B 12 alpha beta 353 376 359 356 392 C1' U B 13 alpha beta 387 407 393 390 422 C1' G B 14 alpha beta 417 440 423 420 456 C1' A B 15 alpha beta 451 473 457 454 489 C1' C B 16 alpha beta 484 505 490 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG A 1 OK OK 8 5 24 25 41 C2' DT A 2 OK OK 42 39 56 57 73 C2' DC A 3 OK OK 74 71 87 88 103 C2' DA A 4 OK OK 104 101 119 120 135 C2' DC A 5 OK OK 136 133 149 150 165 C2' DA A 6 OK OK 166 163 181 182 197 C2' DT A 7 OK OK 198 195 212 213 229 C2' DG A 8 OK OK 230 227 247 248 261 C2' C B 9 OK OK 263 259 276 262 293 C2' A B 10 OK OK 295 291 310 294 326 C2' U B 11 OK OK 328 324 341 327 356 C2' G B 12 OK OK 358 354 374 357 390 C2' U B 13 OK OK 392 388 405 391 420 C2' G B 14 OK OK 422 418 438 421 454 C2' A B 15 OK OK 456 452 471 455 487 C2' C B 16 OK OK 489 485 503 488 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG A 1 OK OK 3 23 6 7 39 C3' DT A 2 OK OK 37 55 40 41 71 C3' DC A 3 OK OK 69 86 72 73 101 C3' DA A 4 OK OK 99 118 102 103 133 C3' DC A 5 OK OK 131 148 134 135 163 C3' DA A 6 OK OK 161 180 164 165 195 C3' DT A 7 OK OK 193 211 196 197 227 C3' DG A 8 OK OK 225 245 228 229 259 C3' C B 9 OK OK 257 275 260 261 291 C3' A B 10 OK OK 289 309 292 293 324 C3' U B 11 OK OK 322 340 325 326 354 C3' G B 12 OK OK 352 373 355 356 388 C3' U B 13 OK OK 386 404 389 390 418 C3' G B 14 OK OK 416 437 419 420 452 C3' A B 15 OK OK 450 470 453 454 485 C3' C B 16 OK OK 483 501 486 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG A 1 OK OK 5 22 2 4 37 C4' DT A 2 OK OK 39 54 36 38 69 C4' DC A 3 OK OK 71 85 68 70 99 C4' DA A 4 OK OK 101 117 98 100 131 C4' DC A 5 OK OK 133 147 130 132 161 C4' DA A 6 OK OK 163 179 160 162 193 C4' DT A 7 OK OK 195 210 192 194 225 C4' DG A 8 OK OK 227 244 224 226 257 C4' C B 9 OK OK 259 274 256 258 289 C4' A B 10 OK OK 291 308 288 290 322 C4' U B 11 OK OK 324 339 321 323 352 C4' G B 12 OK OK 354 372 351 353 386 C4' U B 13 OK OK 388 403 385 387 416 C4' G B 14 OK OK 418 436 415 417 450 C4' A B 15 OK OK 452 469 449 451 483 C4' C B 16 OK OK 485 500 482 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG A 1 OK OK 1 20 21 3 36 C5' DT A 2 OK OK 35 52 53 37 68 C5' DC A 3 OK OK 67 83 84 69 98 C5' DA A 4 OK OK 97 115 116 99 130 C5' DC A 5 OK OK 129 145 146 131 160 C5' DA A 6 OK OK 159 177 178 161 192 C5' DT A 7 OK OK 191 208 209 193 224 C5' DG A 8 OK OK 223 242 243 225 256 C5' C B 9 OK OK 255 272 273 257 288 C5' A B 10 OK OK 287 306 307 289 321 C5' U B 11 OK OK 320 337 338 322 351 C5' G B 12 OK OK 350 370 371 352 385 C5' U B 13 OK OK 384 401 402 386 415 C5' G B 14 OK OK 414 434 435 416 449 C5' A B 15 OK OK 448 467 468 450 482 C5' C B 16 OK OK 481 498 499 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P DT A 2 distorted distorted 6 33 34 35 64 P DC A 3 distorted distorted 40 65 66 67 94 P DA A 4 distorted distorted 72 95 96 97 126 P DC A 5 distorted distorted 102 127 128 129 156 P DA A 6 distorted distorted 134 157 158 159 188 P DT A 7 distorted distorted 164 189 190 191 220 P DG A 8 distorted distorted 196 221 222 223 284 P A B 10 distorted distorted 260 285 286 287 317 P U B 11 distorted distorted 292 318 319 320 347 P G B 12 distorted distorted 325 348 349 350 381 P U B 13 distorted distorted 355 382 383 384 411 P G B 14 distorted distorted 389 412 413 414 445 P A B 15 distorted distorted 419 446 447 448 478 P C B 16 distorted distorted 453 479 480 481 ---------------------------------------------------------------------------------