ID code: '1LDZ' 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' C A 2 alpha beta 39 59 45 42 75 C1' G A 3 alpha beta 70 93 76 73 109 C1' A A 4 alpha beta 104 126 110 107 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' C A 6 alpha beta 168 188 174 171 204 C1' G A 7 alpha beta 199 222 205 202 238 C1' A A 8 alpha beta 233 255 239 236 271 C1' G A 9 alpha beta 266 289 272 269 305 C1' C A 10 alpha beta 300 320 306 303 336 C1' C A 11 alpha beta 331 351 337 334 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' C A 14 alpha beta 429 449 435 432 465 C1' G A 15 alpha beta 460 483 466 463 499 C1' A A 16 alpha beta 494 516 500 497 532 C1' A A 17 alpha beta 527 549 533 530 565 C1' A A 18 alpha beta 560 582 566 563 598 C1' G A 19 alpha beta 593 616 599 596 632 C1' U A 20 alpha beta 627 647 633 630 662 C1' U A 21 alpha beta 657 677 663 660 692 C1' G A 22 alpha beta 687 710 693 690 726 C1' G A 23 alpha beta 721 744 727 724 760 C1' G A 24 alpha beta 755 778 761 758 794 C1' A A 25 alpha beta 789 812 795 792 828 C1' G A 26 alpha beta 823 846 829 826 862 C1' U A 27 alpha beta 857 877 863 860 892 C1' C A 28 alpha beta 887 907 893 890 923 C1' G A 29 alpha beta 918 941 924 921 957 C1' C A 30 alpha beta 952 973 958 955 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 2 OK OK 44 40 57 43 73 C2' G A 3 OK OK 75 71 91 74 107 C2' A A 4 OK OK 109 105 124 108 140 C2' C A 5 OK OK 142 138 155 141 171 C2' C A 6 OK OK 173 169 186 172 202 C2' G A 7 OK OK 204 200 220 203 236 C2' A A 8 OK OK 238 234 253 237 269 C2' G A 9 OK OK 271 267 287 270 303 C2' C A 10 OK OK 305 301 318 304 334 C2' C A 11 OK OK 336 332 349 335 365 C2' A A 12 OK OK 367 363 382 366 398 C2' G A 13 OK OK 400 396 416 399 432 C2' C A 14 OK OK 434 430 447 433 463 C2' G A 15 OK OK 465 461 481 464 497 C2' A A 16 OK OK 499 495 514 498 530 C2' A A 17 OK OK 532 528 547 531 563 C2' A A 18 OK OK 565 561 580 564 596 C2' G A 19 OK OK 598 594 614 597 630 C2' U A 20 OK OK 632 628 645 631 660 C2' U A 21 OK OK 662 658 675 661 690 C2' G A 22 OK OK 692 688 708 691 724 C2' G A 23 OK OK 726 722 742 725 758 C2' G A 24 OK OK 760 756 776 759 792 C2' A A 25 OK OK 794 790 810 793 826 C2' G A 26 OK OK 828 824 844 827 860 C2' U A 27 OK OK 862 858 875 861 890 C2' C A 28 OK OK 892 888 905 891 921 C2' G A 29 OK OK 923 919 939 922 955 C2' C A 30 OK OK 957 953 971 956 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' G A 3 OK OK 69 90 72 73 105 C3' A A 4 OK OK 103 123 106 107 138 C3' C A 5 OK OK 136 154 139 140 169 C3' C A 6 OK OK 167 185 170 171 200 C3' G A 7 OK OK 198 219 201 202 234 C3' A A 8 OK OK 232 252 235 236 267 C3' G A 9 OK OK 265 286 268 269 301 C3' C A 10 OK OK 299 317 302 303 332 C3' C A 11 OK OK 330 348 333 334 363 C3' A A 12 OK OK 361 381 364 365 396 C3' G A 13 OK OK 394 415 397 398 430 C3' C A 14 OK OK 428 446 431 432 461 C3' G A 15 OK OK 459 480 462 463 495 C3' A A 16 OK OK 493 513 496 497 528 C3' A A 17 OK OK 526 546 529 530 561 C3' A A 18 OK OK 559 579 562 563 594 C3' G A 19 OK OK 592 613 595 596 628 C3' U A 20 OK OK 626 644 629 630 658 C3' U A 21 OK OK 656 674 659 660 688 C3' G A 22 OK OK 686 707 689 690 722 C3' G A 23 OK OK 720 741 723 724 756 C3' G A 24 OK OK 754 775 757 758 790 C3' A A 25 OK OK 788 809 791 792 824 C3' G A 26 OK OK 822 843 825 826 858 C3' U A 27 OK OK 856 874 859 860 888 C3' C A 28 OK OK 886 904 889 890 919 C3' G A 29 OK OK 917 938 920 921 953 C3' C A 30 OK OK 951 969 954 955 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' G A 3 OK OK 71 89 68 70 103 C4' A A 4 OK OK 105 122 102 104 136 C4' C A 5 OK OK 138 153 135 137 167 C4' C A 6 OK OK 169 184 166 168 198 C4' G A 7 OK OK 200 218 197 199 232 C4' A A 8 OK OK 234 251 231 233 265 C4' G A 9 OK OK 267 285 264 266 299 C4' C A 10 OK OK 301 316 298 300 330 C4' C A 11 OK OK 332 347 329 331 361 C4' A A 12 OK OK 363 380 360 362 394 C4' G A 13 OK OK 396 414 393 395 428 C4' C A 14 OK OK 430 445 427 429 459 C4' G A 15 OK OK 461 479 458 460 493 C4' A A 16 OK OK 495 512 492 494 526 C4' A A 17 OK OK 528 545 525 527 559 C4' A A 18 OK OK 561 578 558 560 592 C4' G A 19 OK OK 594 612 591 593 626 C4' U A 20 OK OK 628 643 625 627 656 C4' U A 21 OK OK 658 673 655 657 686 C4' G A 22 OK OK 688 706 685 687 720 C4' G A 23 OK OK 722 740 719 721 754 C4' G A 24 OK OK 756 774 753 755 788 C4' A A 25 OK OK 790 808 787 789 822 C4' G A 26 OK OK 824 842 821 823 856 C4' U A 27 OK OK 858 873 855 857 886 C4' C A 28 OK OK 888 903 885 887 917 C4' G A 29 OK OK 919 937 916 918 951 C4' C A 30 OK OK 953 968 950 952 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 2 OK OK 36 53 54 38 68 C5' G A 3 OK OK 67 87 88 69 102 C5' A A 4 OK OK 101 120 121 103 135 C5' C A 5 OK OK 134 151 152 136 166 C5' C A 6 OK OK 165 182 183 167 197 C5' G A 7 OK OK 196 216 217 198 231 C5' A A 8 OK OK 230 249 250 232 264 C5' G A 9 OK OK 263 283 284 265 298 C5' C A 10 OK OK 297 314 315 299 329 C5' C A 11 OK OK 328 345 346 330 360 C5' A A 12 OK OK 359 378 379 361 393 C5' G A 13 OK OK 392 412 413 394 427 C5' C A 14 OK OK 426 443 444 428 458 C5' G A 15 OK OK 457 477 478 459 492 C5' A A 16 OK OK 491 510 511 493 525 C5' A A 17 OK OK 524 543 544 526 558 C5' A A 18 OK OK 557 576 577 559 591 C5' G A 19 OK OK 590 610 611 592 625 C5' U A 20 OK OK 624 641 642 626 655 C5' U A 21 OK OK 654 671 672 656 685 C5' G A 22 OK OK 684 704 705 686 719 C5' G A 23 OK OK 718 738 739 720 753 C5' G A 24 OK OK 752 772 773 754 787 C5' A A 25 OK OK 786 806 807 788 821 C5' G A 26 OK OK 820 840 841 822 855 C5' U A 27 OK OK 854 871 872 856 885 C5' C A 28 OK OK 884 901 902 886 916 C5' G A 29 OK OK 915 935 936 917 950 C5' C A 30 OK OK 949 966 967 951 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P G A 3 distorted distorted 41 65 66 67 98 P A A 4 distorted distorted 72 99 100 101 131 P C A 5 distorted distorted 106 132 133 134 162 P C A 6 distorted distorted 139 163 164 165 193 P G A 7 distorted distorted 170 194 195 196 227 P A A 8 distorted distorted 201 228 229 230 260 P G A 9 distorted distorted 235 261 262 263 294 P C A 10 distorted distorted 268 295 296 297 325 P C A 11 distorted distorted 302 326 327 328 356 P A A 12 distorted distorted 333 357 358 359 389 P G A 13 distorted distorted 364 390 391 392 423 P C A 14 distorted distorted 397 424 425 426 454 P G A 15 distorted distorted 431 455 456 457 488 P A A 16 distorted distorted 462 489 490 491 521 P A A 17 distorted distorted 496 522 523 524 554 P A A 18 distorted distorted 529 555 556 557 587 P G A 19 distorted distorted 562 588 589 590 621 P U A 20 distorted distorted 595 622 623 624 651 P U A 21 distorted distorted 629 652 653 654 681 P G A 22 distorted distorted 659 682 683 684 715 P G A 23 distorted distorted 689 716 717 718 749 P G A 24 distorted distorted 723 750 751 752 783 P A A 25 distorted distorted 757 784 785 786 817 P G A 26 distorted distorted 791 818 819 820 851 P U A 27 distorted distorted 825 852 853 854 881 P C A 28 distorted distorted 859 882 883 884 912 P G A 29 distorted distorted 889 913 914 915 946 P C A 30 distorted distorted 920 947 948 949 ---------------------------------------------------------------------------------