ID code: '2LV0' 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' C A 4 alpha beta 107 127 113 110 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' A A 6 alpha beta 168 190 174 171 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' U A 8 alpha beta 234 254 240 237 269 C1' G A 9 alpha beta 264 287 270 267 303 C1' U A 10 alpha beta 298 318 304 301 333 C1' U A 11 alpha beta 328 348 334 331 363 C1' G A 12 alpha beta 358 381 364 361 397 C1' A A 13 alpha beta 392 414 398 395 430 C1' A A 14 alpha beta 425 447 431 428 463 C1' A A 15 alpha beta 458 480 464 461 496 C1' A A 16 alpha beta 491 513 497 494 529 C1' A A 17 alpha beta 524 546 530 527 562 C1' U A 18 alpha beta 557 577 563 560 592 C1' U A 19 alpha beta 587 607 593 590 622 C1' A A 20 alpha beta 617 639 623 620 655 C1' G A 21 alpha beta 650 673 656 653 689 C1' C A 22 alpha beta 684 704 690 687 720 C1' C A 23 alpha beta 715 735 721 718 751 C1' C A 24 alpha beta 746 767 752 749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 4 OK OK 112 108 125 111 141 C2' U A 5 OK OK 143 139 156 142 171 C2' A A 6 OK OK 173 169 188 172 204 C2' A A 7 OK OK 206 202 221 205 237 C2' U A 8 OK OK 239 235 252 238 267 C2' G A 9 OK OK 269 265 285 268 301 C2' U A 10 OK OK 303 299 316 302 331 C2' U A 11 OK OK 333 329 346 332 361 C2' G A 12 OK OK 363 359 379 362 395 C2' A A 13 OK OK 397 393 412 396 428 C2' A A 14 OK OK 430 426 445 429 461 C2' A A 15 OK OK 463 459 478 462 494 C2' A A 16 OK OK 496 492 511 495 527 C2' A A 17 OK OK 529 525 544 528 560 C2' U A 18 OK OK 562 558 575 561 590 C2' U A 19 OK OK 592 588 605 591 620 C2' A A 20 OK OK 622 618 637 621 653 C2' G A 21 OK OK 655 651 671 654 687 C2' C A 22 OK OK 689 685 702 688 718 C2' C A 23 OK OK 720 716 733 719 749 C2' C A 24 OK OK 751 747 765 750 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 106 124 109 110 139 C3' U A 5 OK OK 137 155 140 141 169 C3' A A 6 OK OK 167 187 170 171 202 C3' A A 7 OK OK 200 220 203 204 235 C3' U A 8 OK OK 233 251 236 237 265 C3' G A 9 OK OK 263 284 266 267 299 C3' U A 10 OK OK 297 315 300 301 329 C3' U A 11 OK OK 327 345 330 331 359 C3' G A 12 OK OK 357 378 360 361 393 C3' A A 13 OK OK 391 411 394 395 426 C3' A A 14 OK OK 424 444 427 428 459 C3' A A 15 OK OK 457 477 460 461 492 C3' A A 16 OK OK 490 510 493 494 525 C3' A A 17 OK OK 523 543 526 527 558 C3' U A 18 OK OK 556 574 559 560 588 C3' U A 19 OK OK 586 604 589 590 618 C3' A A 20 OK OK 616 636 619 620 651 C3' G A 21 OK OK 649 670 652 653 685 C3' C A 22 OK OK 683 701 686 687 716 C3' C A 23 OK OK 714 732 717 718 747 C3' C A 24 OK OK 745 763 748 749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 108 123 105 107 137 C4' U A 5 OK OK 139 154 136 138 167 C4' A A 6 OK OK 169 186 166 168 200 C4' A A 7 OK OK 202 219 199 201 233 C4' U A 8 OK OK 235 250 232 234 263 C4' G A 9 OK OK 265 283 262 264 297 C4' U A 10 OK OK 299 314 296 298 327 C4' U A 11 OK OK 329 344 326 328 357 C4' G A 12 OK OK 359 377 356 358 391 C4' A A 13 OK OK 393 410 390 392 424 C4' A A 14 OK OK 426 443 423 425 457 C4' A A 15 OK OK 459 476 456 458 490 C4' A A 16 OK OK 492 509 489 491 523 C4' A A 17 OK OK 525 542 522 524 556 C4' U A 18 OK OK 558 573 555 557 586 C4' U A 19 OK OK 588 603 585 587 616 C4' A A 20 OK OK 618 635 615 617 649 C4' G A 21 OK OK 651 669 648 650 683 C4' C A 22 OK OK 685 700 682 684 714 C4' C A 23 OK OK 716 731 713 715 745 C4' C A 24 OK OK 747 762 744 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 104 121 122 106 136 C5' U A 5 OK OK 135 152 153 137 166 C5' A A 6 OK OK 165 184 185 167 199 C5' A A 7 OK OK 198 217 218 200 232 C5' U A 8 OK OK 231 248 249 233 262 C5' G A 9 OK OK 261 281 282 263 296 C5' U A 10 OK OK 295 312 313 297 326 C5' U A 11 OK OK 325 342 343 327 356 C5' G A 12 OK OK 355 375 376 357 390 C5' A A 13 OK OK 389 408 409 391 423 C5' A A 14 OK OK 422 441 442 424 456 C5' A A 15 OK OK 455 474 475 457 489 C5' A A 16 OK OK 488 507 508 490 522 C5' A A 17 OK OK 521 540 541 523 555 C5' U A 18 OK OK 554 571 572 556 585 C5' U A 19 OK OK 584 601 602 586 615 C5' A A 20 OK OK 614 633 634 616 648 C5' G A 21 OK OK 647 667 668 649 682 C5' C A 22 OK OK 681 698 699 683 713 C5' C A 23 OK OK 712 729 730 714 744 C5' C A 24 OK OK 743 760 761 745 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 C A 4 distorted distorted 75 102 103 104 132 P U A 5 distorted distorted 109 133 134 135 162 P A A 6 distorted distorted 140 163 164 165 195 P A A 7 distorted distorted 170 196 197 198 228 P U A 8 distorted distorted 203 229 230 231 258 P G A 9 distorted distorted 236 259 260 261 292 P U A 10 distorted distorted 266 293 294 295 322 P U A 11 distorted distorted 300 323 324 325 352 P G A 12 distorted distorted 330 353 354 355 386 P A A 13 distorted distorted 360 387 388 389 419 P A A 14 distorted distorted 394 420 421 422 452 P A A 15 distorted distorted 427 453 454 455 485 P A A 16 distorted distorted 460 486 487 488 518 P A A 17 distorted distorted 493 519 520 521 551 P U A 18 distorted distorted 526 552 553 554 581 P U A 19 distorted distorted 559 582 583 584 611 P A A 20 distorted distorted 589 612 613 614 644 P G A 21 distorted distorted 619 645 646 647 678 P C A 22 distorted distorted 652 679 680 681 709 P C A 23 distorted distorted 686 710 711 712 740 P C A 24 distorted distorted 717 741 742 743 ---------------------------------------------------------------------------------