ID code: '2RPK' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' A A 4 alpha beta 107 129 113 110 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' C A 7 alpha beta 201 221 207 204 237 C1' A A 8 alpha beta 232 254 238 235 270 C1' U A 9 alpha beta 265 285 271 268 300 C1' G A 10 alpha beta 295 318 301 298 334 C1' A A 11 alpha beta 329 351 335 332 367 C1' C A 12 alpha beta 362 382 368 365 398 C1' A A 13 alpha beta 393 415 399 396 431 C1' G A 14 alpha beta 426 449 432 429 465 C1' G A 15 alpha beta 460 483 466 463 499 C1' A A 16 alpha beta 494 516 500 497 532 C1' U A 17 alpha beta 527 547 533 530 562 C1' C A 18 alpha beta 557 577 563 560 593 C1' C A 19 alpha beta 588 608 594 591 624 C1' C A 20 alpha beta 619 640 625 622 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' A A 4 OK OK 112 108 127 111 143 C2' U A 5 OK OK 145 141 158 144 173 C2' C A 6 OK OK 175 171 188 174 204 C2' C A 7 OK OK 206 202 219 205 235 C2' A A 8 OK OK 237 233 252 236 268 C2' U A 9 OK OK 270 266 283 269 298 C2' G A 10 OK OK 300 296 316 299 332 C2' A A 11 OK OK 334 330 349 333 365 C2' C A 12 OK OK 367 363 380 366 396 C2' A A 13 OK OK 398 394 413 397 429 C2' G A 14 OK OK 431 427 447 430 463 C2' G A 15 OK OK 465 461 481 464 497 C2' A A 16 OK OK 499 495 514 498 530 C2' U A 17 OK OK 532 528 545 531 560 C2' C A 18 OK OK 562 558 575 561 591 C2' C A 19 OK OK 593 589 606 592 622 C2' C A 20 OK OK 624 620 638 623 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' A A 4 OK OK 106 126 109 110 141 C3' U A 5 OK OK 139 157 142 143 171 C3' C A 6 OK OK 169 187 172 173 202 C3' C A 7 OK OK 200 218 203 204 233 C3' A A 8 OK OK 231 251 234 235 266 C3' U A 9 OK OK 264 282 267 268 296 C3' G A 10 OK OK 294 315 297 298 330 C3' A A 11 OK OK 328 348 331 332 363 C3' C A 12 OK OK 361 379 364 365 394 C3' A A 13 OK OK 392 412 395 396 427 C3' G A 14 OK OK 425 446 428 429 461 C3' G A 15 OK OK 459 480 462 463 495 C3' A A 16 OK OK 493 513 496 497 528 C3' U A 17 OK OK 526 544 529 530 558 C3' C A 18 OK OK 556 574 559 560 589 C3' C A 19 OK OK 587 605 590 591 620 C3' C A 20 OK OK 618 636 621 622 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' A A 4 OK OK 108 125 105 107 139 C4' U A 5 OK OK 141 156 138 140 169 C4' C A 6 OK OK 171 186 168 170 200 C4' C A 7 OK OK 202 217 199 201 231 C4' A A 8 OK OK 233 250 230 232 264 C4' U A 9 OK OK 266 281 263 265 294 C4' G A 10 OK OK 296 314 293 295 328 C4' A A 11 OK OK 330 347 327 329 361 C4' C A 12 OK OK 363 378 360 362 392 C4' A A 13 OK OK 394 411 391 393 425 C4' G A 14 OK OK 427 445 424 426 459 C4' G A 15 OK OK 461 479 458 460 493 C4' A A 16 OK OK 495 512 492 494 526 C4' U A 17 OK OK 528 543 525 527 556 C4' C A 18 OK OK 558 573 555 557 587 C4' C A 19 OK OK 589 604 586 588 618 C4' C A 20 OK OK 620 635 617 619 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' A A 4 OK OK 104 123 124 106 138 C5' U A 5 OK OK 137 154 155 139 168 C5' C A 6 OK OK 167 184 185 169 199 C5' C A 7 OK OK 198 215 216 200 230 C5' A A 8 OK OK 229 248 249 231 263 C5' U A 9 OK OK 262 279 280 264 293 C5' G A 10 OK OK 292 312 313 294 327 C5' A A 11 OK OK 326 345 346 328 360 C5' C A 12 OK OK 359 376 377 361 391 C5' A A 13 OK OK 390 409 410 392 424 C5' G A 14 OK OK 423 443 444 425 458 C5' G A 15 OK OK 457 477 478 459 492 C5' A A 16 OK OK 491 510 511 493 525 C5' U A 17 OK OK 524 541 542 526 555 C5' C A 18 OK OK 554 571 572 556 586 C5' C A 19 OK OK 585 602 603 587 617 C5' C A 20 OK OK 616 633 634 618 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P A A 4 distorted distorted 75 102 103 104 134 P U A 5 distorted distorted 109 135 136 137 164 P C A 6 distorted distorted 142 165 166 167 195 P C A 7 distorted distorted 172 196 197 198 226 P A A 8 distorted distorted 203 227 228 229 259 P U A 9 distorted distorted 234 260 261 262 289 P G A 10 distorted distorted 267 290 291 292 323 P A A 11 distorted distorted 297 324 325 326 356 P C A 12 distorted distorted 331 357 358 359 387 P A A 13 distorted distorted 364 388 389 390 420 P G A 14 distorted distorted 395 421 422 423 454 P G A 15 distorted distorted 428 455 456 457 488 P A A 16 distorted distorted 462 489 490 491 521 P U A 17 distorted distorted 496 522 523 524 551 P C A 18 distorted distorted 529 552 553 554 582 P C A 19 distorted distorted 559 583 584 585 613 P C A 20 distorted distorted 590 614 615 616 ---------------------------------------------------------------------------------