ID code: '2N0R' 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' --------------------------------------------------------------------------------- 12 C1' C A 2 alpha beta 7 27 13 10 43 C1' U A 3 alpha beta 38 58 44 41 73 C1' G A 4 alpha beta 68 91 74 71 107 C1' A A 5 alpha beta 102 124 108 105 140 C1' G A 6 alpha beta 135 158 141 138 174 C1' C A 7 alpha beta 169 189 175 172 205 C1' U A 8 alpha beta 200 220 206 203 235 C1' C A 9 alpha beta 230 250 236 233 266 C1' G A 10 alpha beta 261 284 267 264 300 C1' A A 11 alpha beta 295 317 301 298 333 C1' A A 12 alpha beta 328 350 334 331 366 C1' A A 13 alpha beta 361 383 367 364 399 C1' G A 14 alpha beta 394 417 400 397 433 C1' A A 15 alpha beta 428 450 434 431 466 C1' G A 16 alpha beta 461 484 467 464 500 C1' C A 17 alpha beta 495 515 501 498 531 C1' A A 18 alpha beta 526 548 532 529 564 C1' A A 19 alpha beta 559 581 565 562 597 C1' U A 20 alpha beta 592 612 598 595 627 C1' G A 21 alpha beta 622 645 628 625 661 C1' A A 22 alpha beta 656 678 662 659 694 C1' U A 23 alpha beta 689 709 695 692 724 C1' G A 24 alpha beta 719 742 725 722 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C A 2 OK OK 12 8 25 11 41 C2' U A 3 OK OK 43 39 56 42 71 C2' G A 4 OK OK 73 69 89 72 105 C2' A A 5 OK OK 107 103 122 106 138 C2' G A 6 OK OK 140 136 156 139 172 C2' C A 7 OK OK 174 170 187 173 203 C2' U A 8 OK OK 205 201 218 204 233 C2' C A 9 OK OK 235 231 248 234 264 C2' G A 10 OK OK 266 262 282 265 298 C2' A A 11 OK OK 300 296 315 299 331 C2' A A 12 OK OK 333 329 348 332 364 C2' A A 13 OK OK 366 362 381 365 397 C2' G A 14 OK OK 399 395 415 398 431 C2' A A 15 OK OK 433 429 448 432 464 C2' G A 16 OK OK 466 462 482 465 498 C2' C A 17 OK OK 500 496 513 499 529 C2' A A 18 OK OK 531 527 546 530 562 C2' A A 19 OK OK 564 560 579 563 595 C2' U A 20 OK OK 597 593 610 596 625 C2' G A 21 OK OK 627 623 643 626 659 C2' A A 22 OK OK 661 657 676 660 692 C2' U A 23 OK OK 694 690 707 693 722 C2' G A 24 OK OK 724 720 740 723 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A 2 OK OK 6 24 9 10 39 C3' U A 3 OK OK 37 55 40 41 69 C3' G A 4 OK OK 67 88 70 71 103 C3' A A 5 OK OK 101 121 104 105 136 C3' G A 6 OK OK 134 155 137 138 170 C3' C A 7 OK OK 168 186 171 172 201 C3' U A 8 OK OK 199 217 202 203 231 C3' C A 9 OK OK 229 247 232 233 262 C3' G A 10 OK OK 260 281 263 264 296 C3' A A 11 OK OK 294 314 297 298 329 C3' A A 12 OK OK 327 347 330 331 362 C3' A A 13 OK OK 360 380 363 364 395 C3' G A 14 OK OK 393 414 396 397 429 C3' A A 15 OK OK 427 447 430 431 462 C3' G A 16 OK OK 460 481 463 464 496 C3' C A 17 OK OK 494 512 497 498 527 C3' A A 18 OK OK 525 545 528 529 560 C3' A A 19 OK OK 558 578 561 562 593 C3' U A 20 OK OK 591 609 594 595 623 C3' G A 21 OK OK 621 642 624 625 657 C3' A A 22 OK OK 655 675 658 659 690 C3' U A 23 OK OK 688 706 691 692 720 C3' G A 24 OK OK 718 739 721 722 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A 2 OK OK 8 23 5 7 37 C4' U A 3 OK OK 39 54 36 38 67 C4' G A 4 OK OK 69 87 66 68 101 C4' A A 5 OK OK 103 120 100 102 134 C4' G A 6 OK OK 136 154 133 135 168 C4' C A 7 OK OK 170 185 167 169 199 C4' U A 8 OK OK 201 216 198 200 229 C4' C A 9 OK OK 231 246 228 230 260 C4' G A 10 OK OK 262 280 259 261 294 C4' A A 11 OK OK 296 313 293 295 327 C4' A A 12 OK OK 329 346 326 328 360 C4' A A 13 OK OK 362 379 359 361 393 C4' G A 14 OK OK 395 413 392 394 427 C4' A A 15 OK OK 429 446 426 428 460 C4' G A 16 OK OK 462 480 459 461 494 C4' C A 17 OK OK 496 511 493 495 525 C4' A A 18 OK OK 527 544 524 526 558 C4' A A 19 OK OK 560 577 557 559 591 C4' U A 20 OK OK 593 608 590 592 621 C4' G A 21 OK OK 623 641 620 622 655 C4' A A 22 OK OK 657 674 654 656 688 C4' U A 23 OK OK 690 705 687 689 718 C4' G A 24 OK OK 720 738 717 719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A 2 OK OK 4 21 22 6 36 C5' U A 3 OK OK 35 52 53 37 66 C5' G A 4 OK OK 65 85 86 67 100 C5' A A 5 OK OK 99 118 119 101 133 C5' G A 6 OK OK 132 152 153 134 167 C5' C A 7 OK OK 166 183 184 168 198 C5' U A 8 OK OK 197 214 215 199 228 C5' C A 9 OK OK 227 244 245 229 259 C5' G A 10 OK OK 258 278 279 260 293 C5' A A 11 OK OK 292 311 312 294 326 C5' A A 12 OK OK 325 344 345 327 359 C5' A A 13 OK OK 358 377 378 360 392 C5' G A 14 OK OK 391 411 412 393 426 C5' A A 15 OK OK 425 444 445 427 459 C5' G A 16 OK OK 458 478 479 460 493 C5' C A 17 OK OK 492 509 510 494 524 C5' A A 18 OK OK 523 542 543 525 557 C5' A A 19 OK OK 556 575 576 558 590 C5' U A 20 OK OK 589 606 607 591 620 C5' G A 21 OK OK 619 639 640 621 654 C5' A A 22 OK OK 653 672 673 655 687 C5' U A 23 OK OK 686 703 704 688 717 C5' G A 24 OK OK 716 736 737 718 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A 2 distorted distorted 2 3 4 32 P U A 3 distorted distorted 9 33 34 35 62 P G A 4 distorted distorted 40 63 64 65 96 P A A 5 distorted distorted 70 97 98 99 129 P G A 6 distorted distorted 104 130 131 132 163 P C A 7 distorted distorted 137 164 165 166 194 P U A 8 distorted distorted 171 195 196 197 224 P C A 9 distorted distorted 202 225 226 227 255 P G A 10 distorted distorted 232 256 257 258 289 P A A 11 distorted distorted 263 290 291 292 322 P A A 12 distorted distorted 297 323 324 325 355 P A A 13 distorted distorted 330 356 357 358 388 P G A 14 distorted distorted 363 389 390 391 422 P A A 15 distorted distorted 396 423 424 425 455 P G A 16 distorted distorted 430 456 457 458 489 P C A 17 distorted distorted 463 490 491 492 520 P A A 18 distorted distorted 497 521 522 523 553 P A A 19 distorted distorted 528 554 555 556 586 P U A 20 distorted distorted 561 587 588 589 616 P G A 21 distorted distorted 594 617 618 619 650 P A A 22 distorted distorted 624 651 652 653 683 P U A 23 distorted distorted 658 684 685 686 713 P G A 24 distorted distorted 691 714 715 716 ---------------------------------------------------------------------------------