ID code: '1QDJ' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 alpha beta 4 24 9 7 42 C1' G A 2 alpha beta 38 58 43 41 75 C1' G A 3 alpha beta 71 91 76 74 108 C1' G A 4 alpha beta 104 124 109 107 141 C1' T A 5 alpha beta 137 157 142 140 173 C1' T A 6 alpha beta 169 189 174 172 205 C1' T A 7 alpha beta 201 221 206 204 237 C1' T A 8 alpha beta 233 253 238 236 269 C1' G A 9 alpha beta 265 285 270 268 302 C1' G A 10 alpha beta 298 318 303 301 335 C1' G A 11 alpha beta 331 351 336 334 368 C1' G A 12 alpha beta 364 385 369 367 400 C1' G B 1 alpha beta 396 416 401 399 433 C1' G B 2 alpha beta 429 449 434 432 466 C1' G B 3 alpha beta 462 482 467 465 499 C1' G B 4 alpha beta 495 515 500 498 532 C1' T B 5 alpha beta 528 548 533 531 564 C1' T B 6 alpha beta 560 580 565 563 596 C1' T B 7 alpha beta 592 612 597 595 628 C1' T B 8 alpha beta 624 644 629 627 660 C1' G B 9 alpha beta 656 676 661 659 693 C1' G B 10 alpha beta 689 709 694 692 726 C1' G B 11 alpha beta 722 742 727 725 759 C1' G B 12 alpha beta 755 776 760 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 29 30 41 C2' G A 2 OK OK 42 39 63 64 74 C2' G A 3 OK OK 75 72 96 97 107 C2' G A 4 OK OK 108 105 129 130 140 C2' T A 5 OK OK 141 138 155 156 172 C2' T A 6 OK OK 173 170 187 188 204 C2' T A 7 OK OK 205 202 219 220 236 C2' T A 8 OK OK 237 234 251 252 268 C2' G A 9 OK OK 269 266 290 291 301 C2' G A 10 OK OK 302 299 323 324 334 C2' G A 11 OK OK 335 332 356 357 367 C2' G A 12 OK OK 368 365 390 391 399 C2' G B 1 OK OK 400 397 421 422 432 C2' G B 2 OK OK 433 430 454 455 465 C2' G B 3 OK OK 466 463 487 488 498 C2' G B 4 OK OK 499 496 520 521 531 C2' T B 5 OK OK 532 529 546 547 563 C2' T B 6 OK OK 564 561 578 579 595 C2' T B 7 OK OK 596 593 610 611 627 C2' T B 8 OK OK 628 625 642 643 659 C2' G B 9 OK OK 660 657 681 682 692 C2' G B 10 OK OK 693 690 714 715 725 C2' G B 11 OK OK 726 723 747 748 758 C2' G B 12 OK OK 759 756 781 782 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 23 6 7 39 C3' G A 2 OK OK 37 57 40 41 72 C3' G A 3 OK OK 70 90 73 74 105 C3' G A 4 OK OK 103 123 106 107 138 C3' T A 5 OK OK 136 154 139 140 170 C3' T A 6 OK OK 168 186 171 172 202 C3' T A 7 OK OK 200 218 203 204 234 C3' T A 8 OK OK 232 250 235 236 266 C3' G A 9 OK OK 264 284 267 268 299 C3' G A 10 OK OK 297 317 300 301 332 C3' G A 11 OK OK 330 350 333 334 365 C3' G A 12 OK OK 363 383 366 367 397 C3' G B 1 OK OK 395 415 398 399 430 C3' G B 2 OK OK 428 448 431 432 463 C3' G B 3 OK OK 461 481 464 465 496 C3' G B 4 OK OK 494 514 497 498 529 C3' T B 5 OK OK 527 545 530 531 561 C3' T B 6 OK OK 559 577 562 563 593 C3' T B 7 OK OK 591 609 594 595 625 C3' T B 8 OK OK 623 641 626 627 657 C3' G B 9 OK OK 655 675 658 659 690 C3' G B 10 OK OK 688 708 691 692 723 C3' G B 11 OK OK 721 741 724 725 756 C3' G B 12 OK OK 754 774 757 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 22 2 4 37 C4' G A 2 OK OK 39 56 36 38 70 C4' G A 3 OK OK 72 89 69 71 103 C4' G A 4 OK OK 105 122 102 104 136 C4' T A 5 OK OK 138 153 135 137 168 C4' T A 6 OK OK 170 185 167 169 200 C4' T A 7 OK OK 202 217 199 201 232 C4' T A 8 OK OK 234 249 231 233 264 C4' G A 9 OK OK 266 283 263 265 297 C4' G A 10 OK OK 299 316 296 298 330 C4' G A 11 OK OK 332 349 329 331 363 C4' G A 12 OK OK 365 382 362 364 395 C4' G B 1 OK OK 397 414 394 396 428 C4' G B 2 OK OK 430 447 427 429 461 C4' G B 3 OK OK 463 480 460 462 494 C4' G B 4 OK OK 496 513 493 495 527 C4' T B 5 OK OK 529 544 526 528 559 C4' T B 6 OK OK 561 576 558 560 591 C4' T B 7 OK OK 593 608 590 592 623 C4' T B 8 OK OK 625 640 622 624 655 C4' G B 9 OK OK 657 674 654 656 688 C4' G B 10 OK OK 690 707 687 689 721 C4' G B 11 OK OK 723 740 720 722 754 C4' G B 12 OK OK 756 773 753 755 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 20 21 3 36 C5' G A 2 OK OK 35 54 55 37 69 C5' G A 3 OK OK 68 87 88 70 102 C5' G A 4 OK OK 101 120 121 103 135 C5' T A 5 OK OK 134 151 152 136 167 C5' T A 6 OK OK 166 183 184 168 199 C5' T A 7 OK OK 198 215 216 200 231 C5' T A 8 OK OK 230 247 248 232 263 C5' G A 9 OK OK 262 281 282 264 296 C5' G A 10 OK OK 295 314 315 297 329 C5' G A 11 OK OK 328 347 348 330 362 C5' G A 12 OK OK 361 380 381 363 394 C5' G B 1 OK distorted 393 412 413 395 427 C5' G B 2 OK OK 426 445 446 428 460 C5' G B 3 OK OK 459 478 479 461 493 C5' G B 4 OK OK 492 511 512 494 526 C5' T B 5 OK OK 525 542 543 527 558 C5' T B 6 OK OK 557 574 575 559 590 C5' T B 7 OK OK 589 606 607 591 622 C5' T B 8 OK OK 621 638 639 623 654 C5' G B 9 OK OK 653 672 673 655 687 C5' G B 10 OK OK 686 705 706 688 720 C5' G B 11 OK OK 719 738 739 721 753 C5' G B 12 OK OK 752 771 772 754 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 65 P G A 3 distorted distorted 40 66 67 68 98 P G A 4 distorted distorted 73 99 100 101 131 P T A 5 distorted distorted 106 132 133 134 163 P T A 6 distorted distorted 139 164 165 166 195 P T A 7 distorted distorted 171 196 197 198 227 P T A 8 distorted distorted 203 228 229 230 259 P G A 9 distorted distorted 235 260 261 262 292 P G A 10 distorted distorted 267 293 294 295 325 P G A 11 distorted distorted 300 326 327 328 358 P G A 12 distorted distorted 333 359 360 361 423 P G B 2 distorted distorted 398 424 425 426 456 P G B 3 distorted distorted 431 457 458 459 489 P G B 4 distorted distorted 464 490 491 492 522 P T B 5 distorted distorted 497 523 524 525 554 P T B 6 distorted distorted 530 555 556 557 586 P T B 7 distorted distorted 562 587 588 589 618 P T B 8 distorted distorted 594 619 620 621 650 P G B 9 distorted distorted 626 651 652 653 683 P G B 10 distorted distorted 658 684 685 686 716 P G B 11 distorted distorted 691 717 718 719 749 P G B 12 distorted distorted 724 750 751 752 ---------------------------------------------------------------------------------