ID code: '1FQZ' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 alpha beta 8 31 14 11 48 C1' C A 2 alpha beta 43 63 49 46 79 C1' C A 3 alpha beta 74 94 80 77 110 C1' G A 4 alpha beta 105 128 111 108 144 C1' A A 5 alpha beta 139 161 145 142 177 C1' G A 6 alpha beta 172 195 178 175 211 C1' U A 7 alpha beta 206 226 212 209 241 C1' A A 8 alpha beta 236 258 242 239 274 C1' G A 9 alpha beta 269 292 275 272 308 C1' U A 10 alpha beta 303 323 309 306 338 C1' G A 11 alpha beta 333 356 339 336 372 C1' U A 12 alpha beta 367 387 373 370 402 C1' U A 13 alpha beta 397 417 403 400 432 C1' G A 14 alpha beta 427 450 433 430 466 C1' G A 15 alpha beta 461 484 467 464 500 C1' G A 16 alpha beta 495 518 501 498 534 C1' U A 17 alpha beta 529 549 535 532 564 C1' C A 18 alpha beta 559 579 565 562 595 C1' G A 19 alpha beta 590 613 596 593 629 C1' C A 20 alpha beta 624 644 630 627 660 C1' G A 21 alpha beta 655 678 661 658 694 C1' A A 22 alpha beta 689 711 695 692 727 C1' A A 23 alpha beta 722 744 728 725 760 C1' A A 24 alpha beta 755 777 761 758 793 C1' G A 25 alpha beta 788 811 794 791 827 C1' G A 26 alpha beta 822 845 828 825 861 C1' C A 27 alpha beta 856 877 862 859 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 29 12 46 C2' C A 2 OK OK 48 44 61 47 77 C2' C A 3 OK OK 79 75 92 78 108 C2' G A 4 OK OK 110 106 126 109 142 C2' A A 5 OK OK 144 140 159 143 175 C2' G A 6 OK OK 177 173 193 176 209 C2' U A 7 OK OK 211 207 224 210 239 C2' A A 8 OK OK 241 237 256 240 272 C2' G A 9 OK OK 274 270 290 273 306 C2' U A 10 OK OK 308 304 321 307 336 C2' G A 11 OK OK 338 334 354 337 370 C2' U A 12 OK OK 372 368 385 371 400 C2' U A 13 OK OK 402 398 415 401 430 C2' G A 14 OK OK 432 428 448 431 464 C2' G A 15 OK OK 466 462 482 465 498 C2' G A 16 OK OK 500 496 516 499 532 C2' U A 17 OK OK 534 530 547 533 562 C2' C A 18 OK OK 564 560 577 563 593 C2' G A 19 OK OK 595 591 611 594 627 C2' C A 20 OK OK 629 625 642 628 658 C2' G A 21 OK OK 660 656 676 659 692 C2' A A 22 OK OK 694 690 709 693 725 C2' A A 23 OK OK 727 723 742 726 758 C2' A A 24 OK OK 760 756 775 759 791 C2' G A 25 OK OK 793 789 809 792 825 C2' G A 26 OK OK 827 823 843 826 859 C2' C A 27 OK OK 861 857 875 860 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' C A 2 OK OK 42 60 45 46 75 C3' C A 3 OK OK 73 91 76 77 106 C3' G A 4 OK OK 104 125 107 108 140 C3' A A 5 OK OK 138 158 141 142 173 C3' G A 6 OK OK 171 192 174 175 207 C3' U A 7 OK OK 205 223 208 209 237 C3' A A 8 OK OK 235 255 238 239 270 C3' G A 9 OK OK 268 289 271 272 304 C3' U A 10 OK OK 302 320 305 306 334 C3' G A 11 OK OK 332 353 335 336 368 C3' U A 12 OK OK 366 384 369 370 398 C3' U A 13 OK OK 396 414 399 400 428 C3' G A 14 OK OK 426 447 429 430 462 C3' G A 15 OK OK 460 481 463 464 496 C3' G A 16 OK OK 494 515 497 498 530 C3' U A 17 OK OK 528 546 531 532 560 C3' C A 18 OK OK 558 576 561 562 591 C3' G A 19 OK OK 589 610 592 593 625 C3' C A 20 OK OK 623 641 626 627 656 C3' G A 21 OK OK 654 675 657 658 690 C3' A A 22 OK OK 688 708 691 692 723 C3' A A 23 OK OK 721 741 724 725 756 C3' A A 24 OK OK 754 774 757 758 789 C3' G A 25 OK OK 787 808 790 791 823 C3' G A 26 OK OK 821 842 824 825 857 C3' C A 27 OK OK 855 873 858 859 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' C A 2 OK OK 44 59 41 43 73 C4' C A 3 OK OK 75 90 72 74 104 C4' G A 4 OK OK 106 124 103 105 138 C4' A A 5 OK OK 140 157 137 139 171 C4' G A 6 OK OK 173 191 170 172 205 C4' U A 7 OK OK 207 222 204 206 235 C4' A A 8 OK OK 237 254 234 236 268 C4' G A 9 OK OK 270 288 267 269 302 C4' U A 10 OK OK 304 319 301 303 332 C4' G A 11 OK OK 334 352 331 333 366 C4' U A 12 OK OK 368 383 365 367 396 C4' U A 13 OK OK 398 413 395 397 426 C4' G A 14 OK OK 428 446 425 427 460 C4' G A 15 OK OK 462 480 459 461 494 C4' G A 16 OK OK 496 514 493 495 528 C4' U A 17 OK OK 530 545 527 529 558 C4' C A 18 OK OK 560 575 557 559 589 C4' G A 19 OK OK 591 609 588 590 623 C4' C A 20 OK OK 625 640 622 624 654 C4' G A 21 OK OK 656 674 653 655 688 C4' A A 22 OK OK 690 707 687 689 721 C4' A A 23 OK OK 723 740 720 722 754 C4' A A 24 OK OK 756 773 753 755 787 C4' G A 25 OK OK 789 807 786 788 821 C4' G A 26 OK OK 823 841 820 822 855 C4' C A 27 OK OK 857 872 854 856 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' C A 2 OK OK 40 57 58 42 72 C5' C A 3 OK OK 71 88 89 73 103 C5' G A 4 OK OK 102 122 123 104 137 C5' A A 5 OK OK 136 155 156 138 170 C5' G A 6 OK OK 169 189 190 171 204 C5' U A 7 OK OK 203 220 221 205 234 C5' A A 8 OK OK 233 252 253 235 267 C5' G A 9 OK OK 266 286 287 268 301 C5' U A 10 OK OK 300 317 318 302 331 C5' G A 11 OK OK 330 350 351 332 365 C5' U A 12 OK OK 364 381 382 366 395 C5' U A 13 OK OK 394 411 412 396 425 C5' G A 14 OK OK 424 444 445 426 459 C5' G A 15 OK OK 458 478 479 460 493 C5' G A 16 OK OK 492 512 513 494 527 C5' U A 17 OK OK 526 543 544 528 557 C5' C A 18 OK OK 556 573 574 558 588 C5' G A 19 OK OK 587 607 608 589 622 C5' C A 20 OK OK 621 638 639 623 653 C5' G A 21 OK OK 652 672 673 654 687 C5' A A 22 OK OK 686 705 706 688 720 C5' A A 23 OK OK 719 738 739 721 753 C5' A A 24 OK OK 752 771 772 754 786 C5' G A 25 OK OK 785 805 806 787 820 C5' G A 26 OK OK 819 839 840 821 854 C5' C A 27 OK OK 853 870 871 855 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 OK OK 3 4 5 37 P C A 2 distorted distorted 10 38 39 40 68 P C A 3 distorted distorted 45 69 70 71 99 P G A 4 distorted distorted 76 100 101 102 133 P A A 5 distorted distorted 107 134 135 136 166 P G A 6 distorted distorted 141 167 168 169 200 P U A 7 distorted distorted 174 201 202 203 230 P A A 8 distorted distorted 208 231 232 233 263 P G A 9 distorted distorted 238 264 265 266 297 P U A 10 distorted distorted 271 298 299 300 327 P G A 11 distorted distorted 305 328 329 330 361 P U A 12 distorted distorted 335 362 363 364 391 P U A 13 distorted distorted 369 392 393 394 421 P G A 14 distorted distorted 399 422 423 424 455 P G A 15 distorted distorted 429 456 457 458 489 P G A 16 distorted distorted 463 490 491 492 523 P U A 17 distorted distorted 497 524 525 526 553 P C A 18 distorted distorted 531 554 555 556 584 P G A 19 distorted distorted 561 585 586 587 618 P C A 20 distorted distorted 592 619 620 621 649 P G A 21 distorted distorted 626 650 651 652 683 P A A 22 distorted distorted 657 684 685 686 716 P A A 23 distorted distorted 691 717 718 719 749 P A A 24 distorted distorted 724 750 751 752 782 P G A 25 distorted distorted 757 783 784 785 816 P G A 26 distorted distorted 790 817 818 819 850 P C A 27 distorted distorted 824 851 852 853 ---------------------------------------------------------------------------------