ID code: '1NXR' 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' DC A 1 alpha beta 4 23 9 7 39 C1' DA A 2 alpha beta 35 56 40 38 71 C1' DG A 3 alpha beta 67 89 72 70 104 C1' DT A 4 alpha beta 100 120 105 103 136 C1' DC A 5 alpha beta 132 151 137 135 166 C1' DC A 6 alpha beta 162 181 167 165 196 C1' DT A 7 alpha beta 192 212 197 195 228 C1' DC A 8 alpha beta 224 244 229 227 258 C1' G B 1 alpha beta 253 276 259 256 293 C1' A B 2 alpha beta 288 310 294 291 326 C1' G B 3 alpha beta 321 344 327 324 360 C1' G B 4 alpha beta 355 378 361 358 394 C1' A B 5 alpha beta 389 411 395 392 427 C1' C B 6 alpha beta 422 442 428 425 458 C1' U B 7 alpha beta 453 473 459 456 488 C1' G B 8 alpha beta 483 507 489 486 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DC A 1 OK OK 8 5 21 22 38 C2' DA A 2 OK OK 39 36 54 55 70 C2' DG A 3 OK OK 71 68 87 88 103 C2' DT A 4 OK OK 104 101 118 119 135 C2' DC A 5 OK OK 136 133 149 150 165 C2' DC A 6 OK OK 166 163 179 180 195 C2' DT A 7 OK OK 196 193 210 211 227 C2' DC A 8 OK OK 228 225 242 243 256 C2' G B 1 OK OK 258 254 274 257 291 C2' A B 2 OK OK 293 289 308 292 324 C2' G B 3 OK OK 326 322 342 325 358 C2' G B 4 OK OK 360 356 376 359 392 C2' A B 5 OK OK 394 390 409 393 425 C2' C B 6 OK OK 427 423 440 426 456 C2' U B 7 OK OK 458 454 471 457 486 C2' G B 8 OK OK 488 484 505 487 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC A 1 OK OK 3 20 6 7 36 C3' DA A 2 OK OK 34 53 37 38 68 C3' DG A 3 OK OK 66 86 69 70 101 C3' DT A 4 OK OK 99 117 102 103 133 C3' DC A 5 OK OK 131 148 134 135 163 C3' DC A 6 OK OK 161 178 164 165 193 C3' DT A 7 OK OK 191 209 194 195 225 C3' DC A 8 OK OK 223 240 226 227 254 C3' G B 1 OK OK 252 273 255 256 289 C3' A B 2 OK OK 287 307 290 291 322 C3' G B 3 OK OK 320 341 323 324 356 C3' G B 4 OK OK 354 375 357 358 390 C3' A B 5 OK OK 388 408 391 392 423 C3' C B 6 OK OK 421 439 424 425 454 C3' U B 7 OK OK 452 470 455 456 484 C3' G B 8 OK OK 482 503 485 486 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC A 1 OK OK 5 19 2 4 34 C4' DA A 2 OK OK 36 52 33 35 66 C4' DG A 3 OK OK 68 85 65 67 99 C4' DT A 4 OK OK 101 116 98 100 131 C4' DC A 5 OK OK 133 147 130 132 161 C4' DC A 6 OK OK 163 177 160 162 191 C4' DT A 7 OK OK 193 208 190 192 223 C4' DC A 8 OK OK 225 239 222 224 252 C4' G B 1 OK OK 254 272 251 253 287 C4' A B 2 OK OK 289 306 286 288 320 C4' G B 3 OK OK 322 340 319 321 354 C4' G B 4 OK OK 356 374 353 355 388 C4' A B 5 OK OK 390 407 387 389 421 C4' C B 6 OK OK 423 438 420 422 452 C4' U B 7 OK OK 454 469 451 453 482 C4' G B 8 OK OK 484 502 481 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC A 1 OK OK 1 17 18 3 33 C5' DA A 2 OK OK 32 50 51 34 65 C5' DG A 3 OK OK 64 83 84 66 98 C5' DT A 4 OK OK 97 114 115 99 130 C5' DC A 5 OK OK 129 145 146 131 160 C5' DC A 6 OK OK 159 175 176 161 190 C5' DT A 7 OK OK 189 206 207 191 222 C5' DC A 8 OK OK 221 237 238 223 251 C5' G B 1 OK OK 250 270 271 252 286 C5' A B 2 OK OK 285 304 305 287 319 C5' G B 3 OK OK 318 338 339 320 353 C5' G B 4 OK OK 352 372 373 354 387 C5' A B 5 OK OK 386 405 406 388 420 C5' C B 6 OK OK 419 436 437 421 451 C5' U B 7 OK OK 450 467 468 452 481 C5' G B 8 OK OK 480 500 501 482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P DA A 2 distorted distorted 6 30 31 32 61 P DG A 3 distorted distorted 37 62 63 64 94 P DT A 4 distorted distorted 69 95 96 97 126 P DC A 5 distorted distorted 102 127 128 129 156 P DC A 6 distorted distorted 134 157 158 159 186 P DT A 7 distorted distorted 164 187 188 189 218 P DC A 8 distorted distorted 194 219 220 221 282 P A B 2 distorted distorted 255 283 284 285 315 P G B 3 distorted distorted 290 316 317 318 349 P G B 4 distorted distorted 323 350 351 352 383 P A B 5 distorted distorted 357 384 385 386 416 P C B 6 distorted distorted 391 417 418 419 447 P U B 7 distorted distorted 424 448 449 450 477 P G B 8 distorted distorted 455 478 479 480 ---------------------------------------------------------------------------------