ID code: '5KIE' 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' DA A 1 alpha beta 4 25 9 7 41 C1' DT A 2 alpha beta 37 57 42 40 73 C1' DG A 3 alpha beta 69 91 74 72 106 C1' DG A 4 alpha beta 102 124 107 105 139 C1' DA A 5 alpha beta 135 156 140 138 172 C1' G A 6 alpha beta 167 190 173 170 205 C1' DC A 7 alpha beta 201 220 206 204 235 C1' DT A 8 alpha beta 231 251 236 234 267 C1' DC A 9 alpha beta 263 283 268 266 296 C1' DG B 10 alpha beta 292 314 297 295 330 C1' DA B 11 alpha beta 326 347 331 329 362 C1' DG B 12 alpha beta 358 380 363 361 395 C1' DC B 13 alpha beta 391 410 396 394 425 C1' DT B 14 alpha beta 421 441 426 424 457 C1' DC B 15 alpha beta 453 472 458 456 487 C1' DC B 16 alpha beta 483 502 488 486 517 C1' DA B 17 alpha beta 513 534 518 516 549 C1' DT B 18 alpha beta 545 566 550 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DA A 1 OK OK 8 5 23 24 40 C2' DT A 2 OK OK 41 38 55 56 72 C2' DG A 3 OK OK 73 70 89 90 105 C2' DG A 4 OK OK 106 103 122 123 138 C2' DA A 5 OK OK 139 136 154 155 170 C2' G A 6 OK OK 172 168 188 171 204 C2' DC A 7 OK OK 205 202 218 219 234 C2' DT A 8 OK OK 235 232 249 250 266 C2' DC A 9 OK OK 267 264 281 282 295 C2' DG B 10 OK OK 296 293 312 313 329 C2' DA B 11 OK OK 330 327 345 346 361 C2' DG B 12 OK OK 362 359 378 379 394 C2' DC B 13 OK OK 395 392 408 409 424 C2' DT B 14 OK OK 425 422 439 440 456 C2' DC B 15 OK OK 457 454 470 471 486 C2' DC B 16 OK OK 487 484 500 501 516 C2' DA B 17 OK OK 517 514 532 533 548 C2' DT B 18 OK OK 549 546 564 565 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DA A 1 OK OK 3 22 6 7 38 C3' DT A 2 OK OK 36 54 39 40 70 C3' DG A 3 OK OK 68 88 71 72 103 C3' DG A 4 OK OK 101 121 104 105 136 C3' DA A 5 OK OK 134 153 137 138 168 C3' G A 6 OK OK 166 187 169 170 202 C3' DC A 7 OK OK 200 217 203 204 232 C3' DT A 8 OK OK 230 248 233 234 264 C3' DC A 9 OK OK 262 279 265 266 293 C3' DG B 10 OK OK 291 311 294 295 327 C3' DA B 11 OK OK 325 344 328 329 359 C3' DG B 12 OK OK 357 377 360 361 392 C3' DC B 13 OK OK 390 407 393 394 422 C3' DT B 14 OK OK 420 438 423 424 454 C3' DC B 15 OK OK 452 469 455 456 484 C3' DC B 16 OK OK 482 499 485 486 514 C3' DA B 17 OK OK 512 531 515 516 546 C3' DT B 18 OK OK 544 562 547 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DA A 1 OK OK 5 21 2 4 36 C4' DT A 2 OK OK 38 53 35 37 68 C4' DG A 3 OK OK 70 87 67 69 101 C4' DG A 4 OK OK 103 120 100 102 134 C4' DA A 5 OK OK 136 152 133 135 166 C4' G A 6 OK OK 168 186 165 167 200 C4' DC A 7 OK OK 202 216 199 201 230 C4' DT A 8 OK OK 232 247 229 231 262 C4' DC A 9 OK OK 264 278 261 263 291 C4' DG B 10 OK OK 293 310 290 292 325 C4' DA B 11 OK OK 327 343 324 326 357 C4' DG B 12 OK OK 359 376 356 358 390 C4' DC B 13 OK OK 392 406 389 391 420 C4' DT B 14 OK OK 422 437 419 421 452 C4' DC B 15 OK OK 454 468 451 453 482 C4' DC B 16 OK OK 484 498 481 483 512 C4' DA B 17 OK OK 514 530 511 513 544 C4' DT B 18 OK OK 546 561 543 545 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DA A 1 OK OK 1 19 20 3 35 C5' DT A 2 OK OK 34 51 52 36 67 C5' DG A 3 OK OK 66 85 86 68 100 C5' DG A 4 OK OK 99 118 119 101 133 C5' DA A 5 OK OK 132 150 151 134 165 C5' G A 6 OK OK 164 184 185 166 199 C5' DC A 7 OK OK 198 214 215 200 229 C5' DT A 8 OK OK 228 245 246 230 261 C5' DC A 9 OK OK 260 276 277 262 290 C5' DG B 10 OK OK 289 308 309 291 324 C5' DA B 11 OK OK 323 341 342 325 356 C5' DG B 12 OK OK 355 374 375 357 389 C5' DC B 13 OK OK 388 404 405 390 419 C5' DT B 14 OK OK 418 435 436 420 451 C5' DC B 15 OK OK 450 466 467 452 481 C5' DC B 16 OK OK 480 496 497 482 511 C5' DA B 17 OK OK 510 528 529 512 543 C5' DT B 18 OK OK 542 559 560 544 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 31 P DT A 2 distorted distorted 6 32 33 34 63 P DG A 3 distorted distorted 39 64 65 66 96 P DG A 4 distorted distorted 71 97 98 99 129 P DA A 5 distorted distorted 104 130 131 132 161 P G A 6 distorted distorted 137 162 163 164 195 P DC A 7 distorted distorted 169 196 197 198 225 P DT A 8 distorted distorted 203 226 227 228 257 P DC A 9 distorted distorted 233 258 259 260 320 P DA B 11 distorted distorted 294 321 322 323 352 P DG B 12 distorted distorted 328 353 354 355 385 P DC B 13 distorted distorted 360 386 387 388 415 P DT B 14 distorted distorted 393 416 417 418 447 P DC B 15 distorted distorted 423 448 449 450 477 P DC B 16 distorted distorted 455 478 479 480 507 P DA B 17 distorted distorted 485 508 509 510 539 P DT B 18 distorted distorted 515 540 541 542 ---------------------------------------------------------------------------------