ID code: '1YLG' 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' A A 3 alpha beta 73 95 79 76 111 C1' U A 4 alpha beta 106 126 112 109 141 C1' A A 5 alpha beta 136 158 142 139 174 C1' U A 6 alpha beta 169 189 175 172 204 C1' A A 7 alpha beta 199 221 205 202 237 C1' U A 8 alpha beta 232 252 238 235 267 C1' G A 9 alpha beta 262 285 268 265 301 C1' A A 10 alpha beta 296 318 302 299 334 C1' U A 11 alpha beta 329 349 335 332 364 C1' A A 12 alpha beta 359 381 365 362 397 C1' C A 13 alpha beta 392 412 398 395 428 C1' A A 14 alpha beta 423 445 429 426 461 C1' A A 15 alpha beta 456 478 462 459 494 C1' U A 16 alpha beta 489 509 495 492 524 C1' U A 17 alpha beta 519 539 525 522 554 C1' U A 18 alpha beta 549 569 555 552 584 C1' G A 19 alpha beta 579 602 585 582 618 C1' A A 20 alpha beta 613 635 619 616 651 C1' U A 21 alpha beta 646 666 652 649 681 C1' C A 22 alpha beta 676 696 682 679 712 C1' A A 23 alpha beta 707 729 713 710 745 C1' G A 24 alpha beta 740 763 746 743 779 C1' U A 25 alpha beta 774 794 780 777 809 C1' A A 26 alpha beta 804 826 810 807 842 C1' U A 27 alpha beta 837 857 843 840 872 C1' A A 28 alpha beta 867 889 873 870 905 C1' U A 29 alpha beta 900 920 906 903 935 C1' C A 30 alpha beta 930 950 936 933 966 C1' C A 31 alpha beta 961 982 967 964 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' U A 4 OK OK 111 107 124 110 139 C2' A A 5 OK OK 141 137 156 140 172 C2' U A 6 OK OK 174 170 187 173 202 C2' A A 7 OK OK 204 200 219 203 235 C2' U A 8 OK OK 237 233 250 236 265 C2' G A 9 OK OK 267 263 283 266 299 C2' A A 10 OK OK 301 297 316 300 332 C2' U A 11 OK OK 334 330 347 333 362 C2' A A 12 OK OK 364 360 379 363 395 C2' C A 13 OK OK 397 393 410 396 426 C2' A A 14 OK OK 428 424 443 427 459 C2' A A 15 OK OK 461 457 476 460 492 C2' U A 16 OK OK 494 490 507 493 522 C2' U A 17 OK OK 524 520 537 523 552 C2' U A 18 OK OK 554 550 567 553 582 C2' G A 19 OK OK 584 580 600 583 616 C2' A A 20 OK OK 618 614 633 617 649 C2' U A 21 OK OK 651 647 664 650 679 C2' C A 22 OK OK 681 677 694 680 710 C2' A A 23 OK OK 712 708 727 711 743 C2' G A 24 OK OK 745 741 761 744 777 C2' U A 25 OK OK 779 775 792 778 807 C2' A A 26 OK OK 809 805 824 808 840 C2' U A 27 OK OK 842 838 855 841 870 C2' A A 28 OK OK 872 868 887 871 903 C2' U A 29 OK OK 905 901 918 904 933 C2' C A 30 OK OK 935 931 948 934 964 C2' C A 31 OK OK 966 962 980 965 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' U A 4 OK OK 105 123 108 109 137 C3' A A 5 OK OK 135 155 138 139 170 C3' U A 6 OK OK 168 186 171 172 200 C3' A A 7 OK OK 198 218 201 202 233 C3' U A 8 OK OK 231 249 234 235 263 C3' G A 9 OK OK 261 282 264 265 297 C3' A A 10 OK OK 295 315 298 299 330 C3' U A 11 OK OK 328 346 331 332 360 C3' A A 12 OK OK 358 378 361 362 393 C3' C A 13 OK OK 391 409 394 395 424 C3' A A 14 OK OK 422 442 425 426 457 C3' A A 15 OK OK 455 475 458 459 490 C3' U A 16 OK OK 488 506 491 492 520 C3' U A 17 OK OK 518 536 521 522 550 C3' U A 18 OK OK 548 566 551 552 580 C3' G A 19 OK OK 578 599 581 582 614 C3' A A 20 OK OK 612 632 615 616 647 C3' U A 21 OK OK 645 663 648 649 677 C3' C A 22 OK OK 675 693 678 679 708 C3' A A 23 OK OK 706 726 709 710 741 C3' G A 24 OK OK 739 760 742 743 775 C3' U A 25 OK OK 773 791 776 777 805 C3' A A 26 OK OK 803 823 806 807 838 C3' U A 27 OK OK 836 854 839 840 868 C3' A A 28 OK OK 866 886 869 870 901 C3' U A 29 OK OK 899 917 902 903 931 C3' C A 30 OK OK 929 947 932 933 962 C3' C A 31 OK OK 960 978 963 964 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' U A 4 OK OK 107 122 104 106 135 C4' A A 5 OK OK 137 154 134 136 168 C4' U A 6 OK OK 170 185 167 169 198 C4' A A 7 OK OK 200 217 197 199 231 C4' U A 8 OK OK 233 248 230 232 261 C4' G A 9 OK OK 263 281 260 262 295 C4' A A 10 OK OK 297 314 294 296 328 C4' U A 11 OK OK 330 345 327 329 358 C4' A A 12 OK OK 360 377 357 359 391 C4' C A 13 OK OK 393 408 390 392 422 C4' A A 14 OK OK 424 441 421 423 455 C4' A A 15 OK OK 457 474 454 456 488 C4' U A 16 OK OK 490 505 487 489 518 C4' U A 17 OK OK 520 535 517 519 548 C4' U A 18 OK OK 550 565 547 549 578 C4' G A 19 OK OK 580 598 577 579 612 C4' A A 20 OK OK 614 631 611 613 645 C4' U A 21 OK OK 647 662 644 646 675 C4' C A 22 OK OK 677 692 674 676 706 C4' A A 23 OK OK 708 725 705 707 739 C4' G A 24 OK OK 741 759 738 740 773 C4' U A 25 OK OK 775 790 772 774 803 C4' A A 26 OK OK 805 822 802 804 836 C4' U A 27 OK OK 838 853 835 837 866 C4' A A 28 OK OK 868 885 865 867 899 C4' U A 29 OK OK 901 916 898 900 929 C4' C A 30 OK OK 931 946 928 930 960 C4' C A 31 OK OK 962 977 959 961 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' U A 4 OK OK 103 120 121 105 134 C5' A A 5 OK OK 133 152 153 135 167 C5' U A 6 OK OK 166 183 184 168 197 C5' A A 7 OK OK 196 215 216 198 230 C5' U A 8 OK OK 229 246 247 231 260 C5' G A 9 OK OK 259 279 280 261 294 C5' A A 10 OK OK 293 312 313 295 327 C5' U A 11 OK OK 326 343 344 328 357 C5' A A 12 OK OK 356 375 376 358 390 C5' C A 13 OK OK 389 406 407 391 421 C5' A A 14 OK OK 420 439 440 422 454 C5' A A 15 OK OK 453 472 473 455 487 C5' U A 16 OK OK 486 503 504 488 517 C5' U A 17 OK OK 516 533 534 518 547 C5' U A 18 OK OK 546 563 564 548 577 C5' G A 19 OK OK 576 596 597 578 611 C5' A A 20 OK OK 610 629 630 612 644 C5' U A 21 OK OK 643 660 661 645 674 C5' C A 22 OK OK 673 690 691 675 705 C5' A A 23 OK OK 704 723 724 706 738 C5' G A 24 OK OK 737 757 758 739 772 C5' U A 25 OK OK 771 788 789 773 802 C5' A A 26 OK OK 801 820 821 803 835 C5' U A 27 OK OK 834 851 852 836 865 C5' A A 28 OK OK 864 883 884 866 898 C5' U A 29 OK OK 897 914 915 899 928 C5' C A 30 OK OK 927 944 945 929 959 C5' C A 31 OK OK 958 975 976 960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P U A 4 distorted distorted 75 101 102 103 130 P A A 5 distorted distorted 108 131 132 133 163 P U A 6 distorted distorted 138 164 165 166 193 P A A 7 distorted distorted 171 194 195 196 226 P U A 8 distorted distorted 201 227 228 229 256 P G A 9 distorted distorted 234 257 258 259 290 P A A 10 distorted distorted 264 291 292 293 323 P U A 11 distorted distorted 298 324 325 326 353 P A A 12 distorted distorted 331 354 355 356 386 P C A 13 distorted distorted 361 387 388 389 417 P A A 14 distorted distorted 394 418 419 420 450 P A A 15 distorted distorted 425 451 452 453 483 P U A 16 distorted distorted 458 484 485 486 513 P U A 17 distorted distorted 491 514 515 516 543 P U A 18 distorted distorted 521 544 545 546 573 P G A 19 distorted distorted 551 574 575 576 607 P A A 20 distorted distorted 581 608 609 610 640 P U A 21 distorted distorted 615 641 642 643 670 P C A 22 distorted distorted 648 671 672 673 701 P A A 23 distorted distorted 678 702 703 704 734 P G A 24 distorted distorted 709 735 736 737 768 P U A 25 distorted distorted 742 769 770 771 798 P A A 26 distorted distorted 776 799 800 801 831 P U A 27 distorted distorted 806 832 833 834 861 P A A 28 distorted distorted 839 862 863 864 894 P U A 29 distorted distorted 869 895 896 897 924 P C A 30 distorted distorted 902 925 926 927 955 P C A 31 distorted distorted 932 956 957 958 ---------------------------------------------------------------------------------