ID code: '1F84' 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' C A 4 alpha beta 104 124 110 107 140 C1' G A 5 alpha beta 135 158 141 138 174 C1' A A 6 alpha beta 169 191 175 172 207 C1' G A 7 alpha beta 202 225 208 205 241 C1' U A 8 alpha beta 236 256 242 239 271 C1' A A 9 alpha beta 266 288 272 269 304 C1' G A 10 alpha beta 299 322 305 302 338 C1' U A 11 alpha beta 333 353 339 336 368 C1' G A 12 alpha beta 363 386 369 366 402 C1' U A 13 alpha beta 397 417 403 400 432 C1' U A 14 alpha beta 427 447 433 430 462 C1' G A 15 alpha beta 457 480 463 460 496 C1' G A 16 alpha beta 491 514 497 494 530 C1' G A 17 alpha beta 525 548 531 528 564 C1' U A 18 alpha beta 559 579 565 562 594 C1' C A 19 alpha beta 589 609 595 592 625 C1' G A 20 alpha beta 620 643 626 623 659 C1' C A 21 alpha beta 654 674 660 657 690 C1' G A 22 alpha beta 685 708 691 688 724 C1' A A 23 alpha beta 719 741 725 722 757 C1' A A 24 alpha beta 752 774 758 755 790 C1' A A 25 alpha beta 785 807 791 788 823 C1' G A 26 alpha beta 818 841 824 821 857 C1' G A 27 alpha beta 852 875 858 855 891 C1' C A 28 alpha beta 886 906 892 889 922 C1' C A 29 alpha beta 917 938 923 920 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 4 OK OK 109 105 122 108 138 C2' G A 5 OK OK 140 136 156 139 172 C2' A A 6 OK OK 174 170 189 173 205 C2' G A 7 OK OK 207 203 223 206 239 C2' U A 8 OK OK 241 237 254 240 269 C2' A A 9 OK OK 271 267 286 270 302 C2' G A 10 OK OK 304 300 320 303 336 C2' U A 11 OK OK 338 334 351 337 366 C2' G A 12 OK OK 368 364 384 367 400 C2' U A 13 OK OK 402 398 415 401 430 C2' U A 14 OK OK 432 428 445 431 460 C2' G A 15 OK OK 462 458 478 461 494 C2' G A 16 OK OK 496 492 512 495 528 C2' G A 17 OK OK 530 526 546 529 562 C2' U A 18 OK OK 564 560 577 563 592 C2' C A 19 OK OK 594 590 607 593 623 C2' G A 20 OK OK 625 621 641 624 657 C2' C A 21 OK OK 659 655 672 658 688 C2' G A 22 OK OK 690 686 706 689 722 C2' A A 23 OK OK 724 720 739 723 755 C2' A A 24 OK OK 757 753 772 756 788 C2' A A 25 OK OK 790 786 805 789 821 C2' G A 26 OK OK 823 819 839 822 855 C2' G A 27 OK OK 857 853 873 856 889 C2' C A 28 OK OK 891 887 904 890 920 C2' C A 29 OK OK 922 918 936 921 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 103 121 106 107 136 C3' G A 5 OK OK 134 155 137 138 170 C3' A A 6 OK OK 168 188 171 172 203 C3' G A 7 OK OK 201 222 204 205 237 C3' U A 8 OK OK 235 253 238 239 267 C3' A A 9 OK OK 265 285 268 269 300 C3' G A 10 OK OK 298 319 301 302 334 C3' U A 11 OK OK 332 350 335 336 364 C3' G A 12 OK OK 362 383 365 366 398 C3' U A 13 OK OK 396 414 399 400 428 C3' U A 14 OK OK 426 444 429 430 458 C3' G A 15 OK OK 456 477 459 460 492 C3' G A 16 OK OK 490 511 493 494 526 C3' G A 17 OK OK 524 545 527 528 560 C3' U A 18 OK OK 558 576 561 562 590 C3' C A 19 OK OK 588 606 591 592 621 C3' G A 20 OK OK 619 640 622 623 655 C3' C A 21 OK OK 653 671 656 657 686 C3' G A 22 OK OK 684 705 687 688 720 C3' A A 23 OK OK 718 738 721 722 753 C3' A A 24 OK OK 751 771 754 755 786 C3' A A 25 OK OK 784 804 787 788 819 C3' G A 26 OK OK 817 838 820 821 853 C3' G A 27 OK OK 851 872 854 855 887 C3' C A 28 OK OK 885 903 888 889 918 C3' C A 29 OK OK 916 934 919 920 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 105 120 102 104 134 C4' G A 5 OK OK 136 154 133 135 168 C4' A A 6 OK OK 170 187 167 169 201 C4' G A 7 OK OK 203 221 200 202 235 C4' U A 8 OK OK 237 252 234 236 265 C4' A A 9 OK OK 267 284 264 266 298 C4' G A 10 OK OK 300 318 297 299 332 C4' U A 11 OK OK 334 349 331 333 362 C4' G A 12 OK OK 364 382 361 363 396 C4' U A 13 OK OK 398 413 395 397 426 C4' U A 14 OK OK 428 443 425 427 456 C4' G A 15 OK OK 458 476 455 457 490 C4' G A 16 OK OK 492 510 489 491 524 C4' G A 17 OK OK 526 544 523 525 558 C4' U A 18 OK OK 560 575 557 559 588 C4' C A 19 OK OK 590 605 587 589 619 C4' G A 20 OK OK 621 639 618 620 653 C4' C A 21 OK OK 655 670 652 654 684 C4' G A 22 OK OK 686 704 683 685 718 C4' A A 23 OK OK 720 737 717 719 751 C4' A A 24 OK OK 753 770 750 752 784 C4' A A 25 OK OK 786 803 783 785 817 C4' G A 26 OK OK 819 837 816 818 851 C4' G A 27 OK OK 853 871 850 852 885 C4' C A 28 OK OK 887 902 884 886 916 C4' C A 29 OK OK 918 933 915 917 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 101 118 119 103 133 C5' G A 5 OK OK 132 152 153 134 167 C5' A A 6 OK OK 166 185 186 168 200 C5' G A 7 OK OK 199 219 220 201 234 C5' U A 8 OK OK 233 250 251 235 264 C5' A A 9 OK OK 263 282 283 265 297 C5' G A 10 OK OK 296 316 317 298 331 C5' U A 11 OK OK 330 347 348 332 361 C5' G A 12 OK OK 360 380 381 362 395 C5' U A 13 OK OK 394 411 412 396 425 C5' U A 14 OK OK 424 441 442 426 455 C5' G A 15 OK OK 454 474 475 456 489 C5' G A 16 OK OK 488 508 509 490 523 C5' G A 17 OK OK 522 542 543 524 557 C5' U A 18 OK OK 556 573 574 558 587 C5' C A 19 OK OK 586 603 604 588 618 C5' G A 20 OK OK 617 637 638 619 652 C5' C A 21 OK OK 651 668 669 653 683 C5' G A 22 OK OK 682 702 703 684 717 C5' A A 23 OK OK 716 735 736 718 750 C5' A A 24 OK OK 749 768 769 751 783 C5' A A 25 OK OK 782 801 802 784 816 C5' G A 26 OK OK 815 835 836 817 850 C5' G A 27 OK OK 849 869 870 851 884 C5' C A 28 OK OK 883 900 901 885 915 C5' C A 29 OK OK 914 931 932 916 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 C A 4 distorted distorted 75 99 100 101 129 P G A 5 distorted distorted 106 130 131 132 163 P A A 6 distorted distorted 137 164 165 166 196 P G A 7 distorted distorted 171 197 198 199 230 P U A 8 distorted distorted 204 231 232 233 260 P A A 9 distorted distorted 238 261 262 263 293 P G A 10 distorted distorted 268 294 295 296 327 P U A 11 distorted distorted 301 328 329 330 357 P G A 12 distorted distorted 335 358 359 360 391 P U A 13 distorted distorted 365 392 393 394 421 P U A 14 distorted distorted 399 422 423 424 451 P G A 15 distorted distorted 429 452 453 454 485 P G A 16 distorted distorted 459 486 487 488 519 P G A 17 distorted distorted 493 520 521 522 553 P U A 18 distorted distorted 527 554 555 556 583 P C A 19 distorted distorted 561 584 585 586 614 P G A 20 distorted distorted 591 615 616 617 648 P C A 21 distorted distorted 622 649 650 651 679 P G A 22 distorted distorted 656 680 681 682 713 P A A 23 distorted distorted 687 714 715 716 746 P A A 24 distorted distorted 721 747 748 749 779 P A A 25 distorted distorted 754 780 781 782 812 P G A 26 distorted distorted 787 813 814 815 846 P G A 27 distorted distorted 820 847 848 849 880 P C A 28 distorted distorted 854 881 882 883 911 P C A 29 distorted distorted 888 912 913 914 ---------------------------------------------------------------------------------