ID code: '2M22' 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' C A 3 alpha beta 73 93 79 76 109 C1' A A 4 alpha beta 104 126 110 107 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' A A 6 alpha beta 171 193 177 174 209 C1' U A 7 alpha beta 204 224 210 207 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' U A 9 alpha beta 265 285 271 268 300 C1' G A 10 alpha beta 295 318 301 298 334 C1' U A 11 alpha beta 329 349 335 332 364 C1' A A 12 alpha beta 359 381 365 362 397 C1' A A 13 alpha beta 392 414 398 395 430 C1' U A 14 alpha beta 425 445 431 428 460 C1' A A 15 alpha beta 455 477 461 458 493 C1' G A 16 alpha beta 488 511 494 491 527 C1' A A 17 alpha beta 522 544 528 525 560 C1' A A 18 alpha beta 555 577 561 558 593 C1' C A 19 alpha beta 588 608 594 591 624 C1' U A 20 alpha beta 619 639 625 622 654 C1' G A 21 alpha beta 649 672 655 652 688 C1' C A 22 alpha beta 683 703 689 686 719 C1' C A 23 alpha beta 714 735 720 717 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' A A 4 OK OK 109 105 124 108 140 C2' G A 5 OK OK 142 138 158 141 174 C2' A A 6 OK OK 176 172 191 175 207 C2' U A 7 OK OK 209 205 222 208 237 C2' C A 8 OK OK 239 235 252 238 268 C2' U A 9 OK OK 270 266 283 269 298 C2' G A 10 OK OK 300 296 316 299 332 C2' U A 11 OK OK 334 330 347 333 362 C2' A A 12 OK OK 364 360 379 363 395 C2' A A 13 OK OK 397 393 412 396 428 C2' U A 14 OK OK 430 426 443 429 458 C2' A A 15 OK OK 460 456 475 459 491 C2' G A 16 OK OK 493 489 509 492 525 C2' A A 17 OK OK 527 523 542 526 558 C2' A A 18 OK OK 560 556 575 559 591 C2' C A 19 OK OK 593 589 606 592 622 C2' U A 20 OK OK 624 620 637 623 652 C2' G A 21 OK OK 654 650 670 653 686 C2' C A 22 OK OK 688 684 701 687 717 C2' C A 23 OK OK 719 715 733 718 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' A A 4 OK OK 103 123 106 107 138 C3' G A 5 OK OK 136 157 139 140 172 C3' A A 6 OK OK 170 190 173 174 205 C3' U A 7 OK OK 203 221 206 207 235 C3' C A 8 OK OK 233 251 236 237 266 C3' U A 9 OK OK 264 282 267 268 296 C3' G A 10 OK OK 294 315 297 298 330 C3' U A 11 OK OK 328 346 331 332 360 C3' A A 12 OK OK 358 378 361 362 393 C3' A A 13 OK OK 391 411 394 395 426 C3' U A 14 OK OK 424 442 427 428 456 C3' A A 15 OK OK 454 474 457 458 489 C3' G A 16 OK OK 487 508 490 491 523 C3' A A 17 OK OK 521 541 524 525 556 C3' A A 18 OK OK 554 574 557 558 589 C3' C A 19 OK OK 587 605 590 591 620 C3' U A 20 OK OK 618 636 621 622 650 C3' G A 21 OK OK 648 669 651 652 684 C3' C A 22 OK OK 682 700 685 686 715 C3' C A 23 OK OK 713 731 716 717 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' A A 4 OK OK 105 122 102 104 136 C4' G A 5 OK OK 138 156 135 137 170 C4' A A 6 OK OK 172 189 169 171 203 C4' U A 7 OK OK 205 220 202 204 233 C4' C A 8 OK OK 235 250 232 234 264 C4' U A 9 OK OK 266 281 263 265 294 C4' G A 10 OK OK 296 314 293 295 328 C4' U A 11 OK OK 330 345 327 329 358 C4' A A 12 OK OK 360 377 357 359 391 C4' A A 13 OK OK 393 410 390 392 424 C4' U A 14 OK OK 426 441 423 425 454 C4' A A 15 OK OK 456 473 453 455 487 C4' G A 16 OK OK 489 507 486 488 521 C4' A A 17 OK OK 523 540 520 522 554 C4' A A 18 OK OK 556 573 553 555 587 C4' C A 19 OK OK 589 604 586 588 618 C4' U A 20 OK OK 620 635 617 619 648 C4' G A 21 OK OK 650 668 647 649 682 C4' C A 22 OK OK 684 699 681 683 713 C4' C A 23 OK OK 715 730 712 714 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' A A 4 OK OK 101 120 121 103 135 C5' G A 5 OK OK 134 154 155 136 169 C5' A A 6 OK OK 168 187 188 170 202 C5' U A 7 OK OK 201 218 219 203 232 C5' C A 8 OK OK 231 248 249 233 263 C5' U A 9 OK OK 262 279 280 264 293 C5' G A 10 OK OK 292 312 313 294 327 C5' U A 11 OK OK 326 343 344 328 357 C5' A A 12 OK OK 356 375 376 358 390 C5' A A 13 OK OK 389 408 409 391 423 C5' U A 14 OK OK 422 439 440 424 453 C5' A A 15 OK OK 452 471 472 454 486 C5' G A 16 OK OK 485 505 506 487 520 C5' A A 17 OK OK 519 538 539 521 553 C5' A A 18 OK OK 552 571 572 554 586 C5' C A 19 OK OK 585 602 603 587 617 C5' U A 20 OK OK 616 633 634 618 647 C5' G A 21 OK OK 646 666 667 648 681 C5' C A 22 OK OK 680 697 698 682 712 C5' C A 23 OK OK 711 728 729 713 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P A A 4 distorted distorted 75 99 100 101 131 P G A 5 distorted distorted 106 132 133 134 165 P A A 6 distorted distorted 139 166 167 168 198 P U A 7 distorted distorted 173 199 200 201 228 P C A 8 distorted distorted 206 229 230 231 259 P U A 9 distorted distorted 236 260 261 262 289 P G A 10 distorted distorted 267 290 291 292 323 P U A 11 distorted distorted 297 324 325 326 353 P A A 12 distorted distorted 331 354 355 356 386 P A A 13 distorted distorted 361 387 388 389 419 P U A 14 distorted distorted 394 420 421 422 449 P A A 15 distorted distorted 427 450 451 452 482 P G A 16 distorted distorted 457 483 484 485 516 P A A 17 distorted distorted 490 517 518 519 549 P A A 18 distorted distorted 524 550 551 552 582 P C A 19 distorted distorted 557 583 584 585 613 P U A 20 distorted distorted 590 614 615 616 643 P G A 21 distorted distorted 621 644 645 646 677 P C A 22 distorted distorted 651 678 679 680 708 P C A 23 distorted distorted 685 709 710 711 ---------------------------------------------------------------------------------