ID code: '1LVJ' 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 16 alpha beta 8 31 14 11 48 C1' G A 17 alpha beta 43 66 49 46 82 C1' C A 18 alpha beta 77 97 83 80 113 C1' C A 19 alpha beta 108 128 114 111 144 C1' A A 20 alpha beta 139 161 145 142 177 C1' G A 21 alpha beta 172 195 178 175 211 C1' A A 22 alpha beta 206 228 212 209 244 C1' U A 23 alpha beta 239 259 245 242 274 C1' C A 24 alpha beta 269 289 275 272 305 C1' U A 25 alpha beta 300 320 306 303 335 C1' G A 26 alpha beta 330 353 336 333 369 C1' A A 27 alpha beta 364 386 370 367 402 C1' G A 28 alpha beta 397 420 403 400 436 C1' C A 29 alpha beta 431 451 437 434 467 C1' C A 30 alpha beta 462 482 468 465 498 C1' U A 31 alpha beta 493 513 499 496 528 C1' G A 32 alpha beta 523 546 529 526 562 C1' G A 33 alpha beta 557 580 563 560 596 C1' G A 34 alpha beta 591 614 597 594 630 C1' A A 35 alpha beta 625 647 631 628 663 C1' G A 36 alpha beta 658 681 664 661 697 C1' C A 37 alpha beta 692 712 698 695 728 C1' U A 38 alpha beta 723 743 729 726 758 C1' C A 39 alpha beta 753 773 759 756 789 C1' U A 40 alpha beta 784 804 790 787 819 C1' C A 41 alpha beta 814 834 820 817 850 C1' U A 42 alpha beta 845 865 851 848 880 C1' G A 43 alpha beta 875 898 881 878 914 C1' G A 44 alpha beta 909 932 915 912 948 C1' C A 45 alpha beta 943 963 949 946 979 C1' C A 46 alpha beta 974 995 980 977 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 16 OK OK 13 9 29 12 46 C2' G A 17 OK OK 48 44 64 47 80 C2' C A 18 OK OK 82 78 95 81 111 C2' C A 19 OK OK 113 109 126 112 142 C2' A A 20 OK OK 144 140 159 143 175 C2' G A 21 OK OK 177 173 193 176 209 C2' A A 22 OK OK 211 207 226 210 242 C2' U A 23 OK OK 244 240 257 243 272 C2' C A 24 OK OK 274 270 287 273 303 C2' U A 25 OK OK 305 301 318 304 333 C2' G A 26 OK OK 335 331 351 334 367 C2' A A 27 OK OK 369 365 384 368 400 C2' G A 28 OK OK 402 398 418 401 434 C2' C A 29 OK OK 436 432 449 435 465 C2' C A 30 OK OK 467 463 480 466 496 C2' U A 31 OK OK 498 494 511 497 526 C2' G A 32 OK OK 528 524 544 527 560 C2' G A 33 OK OK 562 558 578 561 594 C2' G A 34 OK OK 596 592 612 595 628 C2' A A 35 OK OK 630 626 645 629 661 C2' G A 36 OK OK 663 659 679 662 695 C2' C A 37 OK OK 697 693 710 696 726 C2' U A 38 OK OK 728 724 741 727 756 C2' C A 39 OK OK 758 754 771 757 787 C2' U A 40 OK OK 789 785 802 788 817 C2' C A 41 OK OK 819 815 832 818 848 C2' U A 42 OK OK 850 846 863 849 878 C2' G A 43 OK OK 880 876 896 879 912 C2' G A 44 OK OK 914 910 930 913 946 C2' C A 45 OK OK 948 944 961 947 977 C2' C A 46 OK OK 979 975 993 978 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 16 OK OK 7 28 10 11 44 C3' G A 17 OK OK 42 63 45 46 78 C3' C A 18 OK OK 76 94 79 80 109 C3' C A 19 OK OK 107 125 110 111 140 C3' A A 20 OK OK 138 158 141 142 173 C3' G A 21 OK OK 171 192 174 175 207 C3' A A 22 OK OK 205 225 208 209 240 C3' U A 23 OK OK 238 256 241 242 270 C3' C A 24 OK OK 268 286 271 272 301 C3' U A 25 OK OK 299 317 302 303 331 C3' G A 26 OK OK 329 350 332 333 365 C3' A A 27 OK OK 363 383 366 367 398 C3' G A 28 OK OK 396 417 399 400 432 C3' C A 29 OK OK 430 448 433 434 463 C3' C A 30 OK OK 461 479 464 465 494 C3' U A 31 OK OK 492 510 495 496 524 C3' G A 32 OK OK 522 543 525 526 558 C3' G A 33 OK OK 556 577 559 560 592 C3' G A 34 OK OK 590 611 593 594 626 C3' A A 35 OK OK 624 644 627 628 659 C3' G A 36 OK OK 657 678 660 661 693 C3' C A 37 OK OK 691 709 694 695 724 C3' U A 38 OK OK 722 740 725 726 754 C3' C A 39 OK OK 752 770 755 756 785 C3' U A 40 OK OK 783 801 786 787 815 C3' C A 41 OK OK 813 831 816 817 846 C3' U A 42 OK OK 844 862 847 848 876 C3' G A 43 OK OK 874 895 877 878 910 C3' G A 44 OK OK 908 929 911 912 944 C3' C A 45 OK OK 942 960 945 946 975 C3' C A 46 OK OK 973 991 976 977 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 16 OK OK 9 27 6 8 42 C4' G A 17 OK OK 44 62 41 43 76 C4' C A 18 OK OK 78 93 75 77 107 C4' C A 19 OK OK 109 124 106 108 138 C4' A A 20 OK OK 140 157 137 139 171 C4' G A 21 OK OK 173 191 170 172 205 C4' A A 22 OK OK 207 224 204 206 238 C4' U A 23 OK OK 240 255 237 239 268 C4' C A 24 OK OK 270 285 267 269 299 C4' U A 25 OK OK 301 316 298 300 329 C4' G A 26 OK OK 331 349 328 330 363 C4' A A 27 OK OK 365 382 362 364 396 C4' G A 28 OK OK 398 416 395 397 430 C4' C A 29 OK OK 432 447 429 431 461 C4' C A 30 OK OK 463 478 460 462 492 C4' U A 31 OK OK 494 509 491 493 522 C4' G A 32 OK OK 524 542 521 523 556 C4' G A 33 OK OK 558 576 555 557 590 C4' G A 34 OK OK 592 610 589 591 624 C4' A A 35 OK OK 626 643 623 625 657 C4' G A 36 OK OK 659 677 656 658 691 C4' C A 37 OK OK 693 708 690 692 722 C4' U A 38 OK OK 724 739 721 723 752 C4' C A 39 OK OK 754 769 751 753 783 C4' U A 40 OK OK 785 800 782 784 813 C4' C A 41 OK OK 815 830 812 814 844 C4' U A 42 OK OK 846 861 843 845 874 C4' G A 43 OK OK 876 894 873 875 908 C4' G A 44 OK OK 910 928 907 909 942 C4' C A 45 OK OK 944 959 941 943 973 C4' C A 46 OK OK 975 990 972 974 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 16 OK OK 5 25 26 7 41 C5' G A 17 OK OK 40 60 61 42 75 C5' C A 18 OK OK 74 91 92 76 106 C5' C A 19 OK OK 105 122 123 107 137 C5' A A 20 OK OK 136 155 156 138 170 C5' G A 21 OK OK 169 189 190 171 204 C5' A A 22 OK OK 203 222 223 205 237 C5' U A 23 OK OK 236 253 254 238 267 C5' C A 24 OK OK 266 283 284 268 298 C5' U A 25 OK OK 297 314 315 299 328 C5' G A 26 OK OK 327 347 348 329 362 C5' A A 27 OK OK 361 380 381 363 395 C5' G A 28 OK OK 394 414 415 396 429 C5' C A 29 OK OK 428 445 446 430 460 C5' C A 30 OK OK 459 476 477 461 491 C5' U A 31 OK OK 490 507 508 492 521 C5' G A 32 OK OK 520 540 541 522 555 C5' G A 33 OK OK 554 574 575 556 589 C5' G A 34 OK OK 588 608 609 590 623 C5' A A 35 OK OK 622 641 642 624 656 C5' G A 36 OK OK 655 675 676 657 690 C5' C A 37 OK OK 689 706 707 691 721 C5' U A 38 OK OK 720 737 738 722 751 C5' C A 39 OK OK 750 767 768 752 782 C5' U A 40 OK OK 781 798 799 783 812 C5' C A 41 OK OK 811 828 829 813 843 C5' U A 42 OK OK 842 859 860 844 873 C5' G A 43 OK OK 872 892 893 874 907 C5' G A 44 OK OK 906 926 927 908 941 C5' C A 45 OK OK 940 957 958 942 972 C5' C A 46 OK OK 971 988 989 973 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 16 OK OK 3 4 5 37 P G A 17 distorted distorted 10 38 39 40 71 P C A 18 distorted distorted 45 72 73 74 102 P C A 19 distorted distorted 79 103 104 105 133 P A A 20 distorted distorted 110 134 135 136 166 P G A 21 distorted distorted 141 167 168 169 200 P A A 22 distorted distorted 174 201 202 203 233 P U A 23 distorted distorted 208 234 235 236 263 P C A 24 distorted distorted 241 264 265 266 294 P U A 25 distorted distorted 271 295 296 297 324 P G A 26 distorted distorted 302 325 326 327 358 P A A 27 distorted distorted 332 359 360 361 391 P G A 28 distorted distorted 366 392 393 394 425 P C A 29 distorted distorted 399 426 427 428 456 P C A 30 distorted distorted 433 457 458 459 487 P U A 31 distorted distorted 464 488 489 490 517 P G A 32 distorted distorted 495 518 519 520 551 P G A 33 distorted distorted 525 552 553 554 585 P G A 34 distorted distorted 559 586 587 588 619 P A A 35 distorted distorted 593 620 621 622 652 P G A 36 distorted distorted 627 653 654 655 686 P C A 37 distorted distorted 660 687 688 689 717 P U A 38 distorted distorted 694 718 719 720 747 P C A 39 distorted distorted 725 748 749 750 778 P U A 40 distorted distorted 755 779 780 781 808 P C A 41 distorted distorted 786 809 810 811 839 P U A 42 distorted distorted 816 840 841 842 869 P G A 43 distorted distorted 847 870 871 872 903 P G A 44 distorted distorted 877 904 905 906 937 P C A 45 distorted distorted 911 938 939 940 968 P C A 46 distorted distorted 945 969 970 971 ---------------------------------------------------------------------------------