ID code: '2M12' 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' U A 4 alpha beta 107 127 113 110 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' U A 6 alpha beta 171 191 177 174 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' U A 8 alpha beta 234 254 240 237 269 C1' U A 9 alpha beta 264 284 270 267 299 C1' G A 10 alpha beta 294 317 300 297 333 C1' G A 11 alpha beta 328 351 334 331 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' A A 13 alpha beta 395 417 401 398 433 C1' A A 14 alpha beta 428 450 434 431 466 C1' U A 15 alpha beta 461 481 467 464 496 C1' G A 16 alpha beta 491 514 497 494 530 C1' A A 17 alpha beta 525 547 531 528 563 C1' G A 18 alpha beta 558 581 564 561 597 C1' C A 19 alpha beta 592 612 598 595 628 C1' A A 20 alpha beta 623 645 629 626 661 C1' C A 21 alpha beta 656 676 662 659 692 C1' C A 22 alpha beta 687 707 693 690 723 C1' C A 23 alpha beta 718 739 724 721 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 4 OK OK 112 108 125 111 140 C2' G A 5 OK OK 142 138 158 141 174 C2' U A 6 OK OK 176 172 189 175 204 C2' A A 7 OK OK 206 202 221 205 237 C2' U A 8 OK OK 239 235 252 238 267 C2' U A 9 OK OK 269 265 282 268 297 C2' G A 10 OK OK 299 295 315 298 331 C2' G A 11 OK OK 333 329 349 332 365 C2' A A 12 OK OK 367 363 382 366 398 C2' A A 13 OK OK 400 396 415 399 431 C2' A A 14 OK OK 433 429 448 432 464 C2' U A 15 OK OK 466 462 479 465 494 C2' G A 16 OK OK 496 492 512 495 528 C2' A A 17 OK OK 530 526 545 529 561 C2' G A 18 OK OK 563 559 579 562 595 C2' C A 19 OK OK 597 593 610 596 626 C2' A A 20 OK OK 628 624 643 627 659 C2' C A 21 OK OK 661 657 674 660 690 C2' C A 22 OK OK 692 688 705 691 721 C2' C A 23 OK OK 723 719 737 722 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 106 124 109 110 138 C3' G A 5 OK OK 136 157 139 140 172 C3' U A 6 OK OK 170 188 173 174 202 C3' A A 7 OK OK 200 220 203 204 235 C3' U A 8 OK OK 233 251 236 237 265 C3' U A 9 OK OK 263 281 266 267 295 C3' G A 10 OK OK 293 314 296 297 329 C3' G A 11 OK OK 327 348 330 331 363 C3' A A 12 OK OK 361 381 364 365 396 C3' A A 13 OK OK 394 414 397 398 429 C3' A A 14 OK OK 427 447 430 431 462 C3' U A 15 OK OK 460 478 463 464 492 C3' G A 16 OK OK 490 511 493 494 526 C3' A A 17 OK OK 524 544 527 528 559 C3' G A 18 OK OK 557 578 560 561 593 C3' C A 19 OK OK 591 609 594 595 624 C3' A A 20 OK OK 622 642 625 626 657 C3' C A 21 OK OK 655 673 658 659 688 C3' C A 22 OK OK 686 704 689 690 719 C3' C A 23 OK OK 717 735 720 721 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 108 123 105 107 136 C4' G A 5 OK OK 138 156 135 137 170 C4' U A 6 OK OK 172 187 169 171 200 C4' A A 7 OK OK 202 219 199 201 233 C4' U A 8 OK OK 235 250 232 234 263 C4' U A 9 OK OK 265 280 262 264 293 C4' G A 10 OK OK 295 313 292 294 327 C4' G A 11 OK OK 329 347 326 328 361 C4' A A 12 OK OK 363 380 360 362 394 C4' A A 13 OK OK 396 413 393 395 427 C4' A A 14 OK OK 429 446 426 428 460 C4' U A 15 OK OK 462 477 459 461 490 C4' G A 16 OK OK 492 510 489 491 524 C4' A A 17 OK OK 526 543 523 525 557 C4' G A 18 OK OK 559 577 556 558 591 C4' C A 19 OK OK 593 608 590 592 622 C4' A A 20 OK OK 624 641 621 623 655 C4' C A 21 OK OK 657 672 654 656 686 C4' C A 22 OK OK 688 703 685 687 717 C4' C A 23 OK OK 719 734 716 718 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 104 121 122 106 135 C5' G A 5 OK OK 134 154 155 136 169 C5' U A 6 OK OK 168 185 186 170 199 C5' A A 7 OK OK 198 217 218 200 232 C5' U A 8 OK OK 231 248 249 233 262 C5' U A 9 OK OK 261 278 279 263 292 C5' G A 10 OK OK 291 311 312 293 326 C5' G A 11 OK OK 325 345 346 327 360 C5' A A 12 OK OK 359 378 379 361 393 C5' A A 13 OK OK 392 411 412 394 426 C5' A A 14 OK OK 425 444 445 427 459 C5' U A 15 OK OK 458 475 476 460 489 C5' G A 16 OK OK 488 508 509 490 523 C5' A A 17 OK OK 522 541 542 524 556 C5' G A 18 OK OK 555 575 576 557 590 C5' C A 19 OK OK 589 606 607 591 621 C5' A A 20 OK OK 620 639 640 622 654 C5' C A 21 OK OK 653 670 671 655 685 C5' C A 22 OK OK 684 701 702 686 716 C5' C A 23 OK OK 715 732 733 717 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 4 distorted distorted 75 102 103 104 131 P G A 5 distorted distorted 109 132 133 134 165 P U A 6 distorted distorted 139 166 167 168 195 P A A 7 distorted distorted 173 196 197 198 228 P U A 8 distorted distorted 203 229 230 231 258 P U A 9 distorted distorted 236 259 260 261 288 P G A 10 distorted distorted 266 289 290 291 322 P G A 11 distorted distorted 296 323 324 325 356 P A A 12 distorted distorted 330 357 358 359 389 P A A 13 distorted distorted 364 390 391 392 422 P A A 14 distorted distorted 397 423 424 425 455 P U A 15 distorted distorted 430 456 457 458 485 P G A 16 distorted distorted 463 486 487 488 519 P A A 17 distorted distorted 493 520 521 522 552 P G A 18 distorted distorted 527 553 554 555 586 P C A 19 distorted distorted 560 587 588 589 617 P A A 20 distorted distorted 594 618 619 620 650 P C A 21 distorted distorted 625 651 652 653 681 P C A 22 distorted distorted 658 682 683 684 712 P C A 23 distorted distorted 689 713 714 715 ---------------------------------------------------------------------------------