ID code: '1MFY' 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' A A 1 alpha beta 4 26 10 7 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' U A 3 alpha beta 72 92 78 75 107 C1' A A 4 alpha beta 102 124 108 105 140 C1' G A 5 alpha beta 135 158 141 138 174 C1' A A 6 alpha beta 169 191 175 172 207 C1' A A 7 alpha beta 202 224 208 205 240 C1' A A 8 alpha beta 235 257 241 238 273 C1' C A 9 alpha beta 268 288 274 271 304 C1' A A 10 alpha beta 299 321 305 302 337 C1' A A 11 alpha beta 332 354 338 335 370 C1' G A 12 alpha beta 365 388 371 368 404 C1' G A 13 alpha beta 399 422 405 402 438 C1' C A 14 alpha beta 433 453 439 436 469 C1' U A 15 alpha beta 464 484 470 467 499 C1' U A 16 alpha beta 494 514 500 497 529 C1' C A 17 alpha beta 524 544 530 527 560 C1' G A 18 alpha beta 555 578 561 558 594 C1' G A 19 alpha beta 589 612 595 592 628 C1' C A 20 alpha beta 623 643 629 626 659 C1' C A 21 alpha beta 654 674 660 657 690 C1' U A 22 alpha beta 685 705 691 688 720 C1' G A 23 alpha beta 715 738 721 718 754 C1' C A 24 alpha beta 749 769 755 752 785 C1' U A 25 alpha beta 780 800 786 783 815 C1' U A 26 alpha beta 810 830 816 813 845 C1' U A 27 alpha beta 840 860 846 843 875 C1' C A 28 alpha beta 870 890 876 873 906 C1' G A 29 alpha beta 901 924 907 904 940 C1' C A 30 alpha beta 935 955 941 938 971 C1' U A 31 alpha beta 966 987 972 969 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A A 1 OK OK 9 5 24 8 41 C2' G A 2 OK OK 43 39 59 42 75 C2' U A 3 OK OK 77 73 90 76 105 C2' A A 4 OK OK 107 103 122 106 138 C2' G A 5 OK OK 140 136 156 139 172 C2' A A 6 OK OK 174 170 189 173 205 C2' A A 7 OK OK 207 203 222 206 238 C2' A A 8 OK OK 240 236 255 239 271 C2' C A 9 OK OK 273 269 286 272 302 C2' A A 10 OK OK 304 300 319 303 335 C2' A A 11 OK OK 337 333 352 336 368 C2' G A 12 OK OK 370 366 386 369 402 C2' G A 13 OK OK 404 400 420 403 436 C2' C A 14 OK OK 438 434 451 437 467 C2' U A 15 OK OK 469 465 482 468 497 C2' U A 16 OK OK 499 495 512 498 527 C2' C A 17 OK OK 529 525 542 528 558 C2' G A 18 OK OK 560 556 576 559 592 C2' G A 19 OK OK 594 590 610 593 626 C2' C A 20 OK OK 628 624 641 627 657 C2' C A 21 OK OK 659 655 672 658 688 C2' U A 22 OK OK 690 686 703 689 718 C2' G A 23 OK OK 720 716 736 719 752 C2' C A 24 OK OK 754 750 767 753 783 C2' U A 25 OK OK 785 781 798 784 813 C2' U A 26 OK OK 815 811 828 814 843 C2' U A 27 OK OK 845 841 858 844 873 C2' C A 28 OK OK 875 871 888 874 904 C2' G A 29 OK OK 906 902 922 905 938 C2' C A 30 OK OK 940 936 953 939 969 C2' U A 31 OK OK 971 967 985 970 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A A 1 OK OK 3 23 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' U A 3 OK OK 71 89 74 75 103 C3' A A 4 OK OK 101 121 104 105 136 C3' G A 5 OK OK 134 155 137 138 170 C3' A A 6 OK OK 168 188 171 172 203 C3' A A 7 OK OK 201 221 204 205 236 C3' A A 8 OK OK 234 254 237 238 269 C3' C A 9 OK OK 267 285 270 271 300 C3' A A 10 OK OK 298 318 301 302 333 C3' A A 11 OK OK 331 351 334 335 366 C3' G A 12 OK OK 364 385 367 368 400 C3' G A 13 OK OK 398 419 401 402 434 C3' C A 14 OK OK 432 450 435 436 465 C3' U A 15 OK OK 463 481 466 467 495 C3' U A 16 OK OK 493 511 496 497 525 C3' C A 17 OK OK 523 541 526 527 556 C3' G A 18 OK OK 554 575 557 558 590 C3' G A 19 OK OK 588 609 591 592 624 C3' C A 20 OK OK 622 640 625 626 655 C3' C A 21 OK OK 653 671 656 657 686 C3' U A 22 OK OK 684 702 687 688 716 C3' G A 23 OK OK 714 735 717 718 750 C3' C A 24 OK OK 748 766 751 752 781 C3' U A 25 OK OK 779 797 782 783 811 C3' U A 26 OK OK 809 827 812 813 841 C3' U A 27 OK OK 839 857 842 843 871 C3' C A 28 OK OK 869 887 872 873 902 C3' G A 29 OK OK 900 921 903 904 936 C3' C A 30 OK OK 934 952 937 938 967 C3' U A 31 OK OK 965 983 968 969 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A A 1 OK OK 5 22 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' U A 3 OK OK 73 88 70 72 101 C4' A A 4 OK OK 103 120 100 102 134 C4' G A 5 OK OK 136 154 133 135 168 C4' A A 6 OK OK 170 187 167 169 201 C4' A A 7 OK OK 203 220 200 202 234 C4' A A 8 OK OK 236 253 233 235 267 C4' C A 9 OK OK 269 284 266 268 298 C4' A A 10 OK OK 300 317 297 299 331 C4' A A 11 OK OK 333 350 330 332 364 C4' G A 12 OK OK 366 384 363 365 398 C4' G A 13 OK OK 400 418 397 399 432 C4' C A 14 OK OK 434 449 431 433 463 C4' U A 15 OK OK 465 480 462 464 493 C4' U A 16 OK OK 495 510 492 494 523 C4' C A 17 OK OK 525 540 522 524 554 C4' G A 18 OK OK 556 574 553 555 588 C4' G A 19 OK OK 590 608 587 589 622 C4' C A 20 OK OK 624 639 621 623 653 C4' C A 21 OK OK 655 670 652 654 684 C4' U A 22 OK OK 686 701 683 685 714 C4' G A 23 OK OK 716 734 713 715 748 C4' C A 24 OK OK 750 765 747 749 779 C4' U A 25 OK OK 781 796 778 780 809 C4' U A 26 OK OK 811 826 808 810 839 C4' U A 27 OK OK 841 856 838 840 869 C4' C A 28 OK OK 871 886 868 870 900 C4' G A 29 OK OK 902 920 899 901 934 C4' C A 30 OK OK 936 951 933 935 965 C4' U A 31 OK OK 967 982 964 966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A A 1 OK OK 1 20 21 3 36 C5' G A 2 OK OK 35 55 56 37 70 C5' U A 3 OK OK 69 86 87 71 100 C5' A A 4 OK OK 99 118 119 101 133 C5' G A 5 OK OK 132 152 153 134 167 C5' A A 6 OK OK 166 185 186 168 200 C5' A A 7 OK OK 199 218 219 201 233 C5' A A 8 OK OK 232 251 252 234 266 C5' C A 9 OK OK 265 282 283 267 297 C5' A A 10 OK OK 296 315 316 298 330 C5' A A 11 OK OK 329 348 349 331 363 C5' G A 12 OK OK 362 382 383 364 397 C5' G A 13 OK OK 396 416 417 398 431 C5' C A 14 OK OK 430 447 448 432 462 C5' U A 15 OK OK 461 478 479 463 492 C5' U A 16 OK OK 491 508 509 493 522 C5' C A 17 OK OK 521 538 539 523 553 C5' G A 18 OK OK 552 572 573 554 587 C5' G A 19 OK OK 586 606 607 588 621 C5' C A 20 OK OK 620 637 638 622 652 C5' C A 21 OK OK 651 668 669 653 683 C5' U A 22 OK OK 682 699 700 684 713 C5' G A 23 OK OK 712 732 733 714 747 C5' C A 24 OK OK 746 763 764 748 778 C5' U A 25 OK OK 777 794 795 779 808 C5' U A 26 OK OK 807 824 825 809 838 C5' U A 27 OK OK 837 854 855 839 868 C5' C A 28 OK OK 867 884 885 869 899 C5' G A 29 OK OK 898 918 919 900 933 C5' C A 30 OK OK 932 949 950 934 964 C5' U A 31 OK OK 963 980 981 965 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P U A 3 distorted distorted 40 67 68 69 96 P A A 4 distorted distorted 74 97 98 99 129 P G A 5 distorted distorted 104 130 131 132 163 P A A 6 distorted distorted 137 164 165 166 196 P A A 7 distorted distorted 171 197 198 199 229 P A A 8 distorted distorted 204 230 231 232 262 P C A 9 distorted distorted 237 263 264 265 293 P A A 10 distorted distorted 270 294 295 296 326 P A A 11 distorted distorted 301 327 328 329 359 P G A 12 distorted distorted 334 360 361 362 393 P G A 13 distorted distorted 367 394 395 396 427 P C A 14 distorted distorted 401 428 429 430 458 P U A 15 distorted distorted 435 459 460 461 488 P U A 16 distorted distorted 466 489 490 491 518 P C A 17 distorted distorted 496 519 520 521 549 P G A 18 distorted distorted 526 550 551 552 583 P G A 19 distorted distorted 557 584 585 586 617 P C A 20 distorted distorted 591 618 619 620 648 P C A 21 distorted distorted 625 649 650 651 679 P U A 22 distorted distorted 656 680 681 682 709 P G A 23 distorted distorted 687 710 711 712 743 P C A 24 distorted distorted 717 744 745 746 774 P U A 25 distorted distorted 751 775 776 777 804 P U A 26 distorted distorted 782 805 806 807 834 P U A 27 distorted distorted 812 835 836 837 864 P C A 28 distorted distorted 842 865 866 867 895 P G A 29 distorted distorted 872 896 897 898 929 P C A 30 distorted distorted 903 930 931 932 960 P U A 31 distorted distorted 937 961 962 963 ---------------------------------------------------------------------------------