ID code: '1YNE' 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' U A 13 alpha beta 392 412 398 395 427 C1' A A 14 alpha beta 422 444 428 425 460 C1' A A 15 alpha beta 455 477 461 458 493 C1' U A 16 alpha beta 488 508 494 491 523 C1' U A 17 alpha beta 518 538 524 521 553 C1' U A 18 alpha beta 548 568 554 551 583 C1' G A 19 alpha beta 578 601 584 581 617 C1' A A 20 alpha beta 612 634 618 615 650 C1' U A 21 alpha beta 645 665 651 648 680 C1' C A 22 alpha beta 675 695 681 678 711 C1' A A 23 alpha beta 706 728 712 709 744 C1' G A 24 alpha beta 739 762 745 742 778 C1' U A 25 alpha beta 773 793 779 776 808 C1' A A 26 alpha beta 803 825 809 806 841 C1' U A 27 alpha beta 836 856 842 839 871 C1' A A 28 alpha beta 866 888 872 869 904 C1' U A 29 alpha beta 899 919 905 902 934 C1' C A 30 alpha beta 929 949 935 932 965 C1' C A 31 alpha beta 960 981 966 963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 13 OK OK 397 393 410 396 425 C2' A A 14 OK OK 427 423 442 426 458 C2' A A 15 OK OK 460 456 475 459 491 C2' U A 16 OK OK 493 489 506 492 521 C2' U A 17 OK OK 523 519 536 522 551 C2' U A 18 OK OK 553 549 566 552 581 C2' G A 19 OK OK 583 579 599 582 615 C2' A A 20 OK OK 617 613 632 616 648 C2' U A 21 OK OK 650 646 663 649 678 C2' C A 22 OK OK 680 676 693 679 709 C2' A A 23 OK OK 711 707 726 710 742 C2' G A 24 OK OK 744 740 760 743 776 C2' U A 25 OK OK 778 774 791 777 806 C2' A A 26 OK OK 808 804 823 807 839 C2' U A 27 OK OK 841 837 854 840 869 C2' A A 28 OK OK 871 867 886 870 902 C2' U A 29 OK OK 904 900 917 903 932 C2' C A 30 OK OK 934 930 947 933 963 C2' C A 31 OK OK 965 961 979 964 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 13 OK OK 391 409 394 395 423 C3' A A 14 OK OK 421 441 424 425 456 C3' A A 15 OK OK 454 474 457 458 489 C3' U A 16 OK OK 487 505 490 491 519 C3' U A 17 OK OK 517 535 520 521 549 C3' U A 18 OK OK 547 565 550 551 579 C3' G A 19 OK OK 577 598 580 581 613 C3' A A 20 OK OK 611 631 614 615 646 C3' U A 21 OK OK 644 662 647 648 676 C3' C A 22 OK OK 674 692 677 678 707 C3' A A 23 OK OK 705 725 708 709 740 C3' G A 24 OK OK 738 759 741 742 774 C3' U A 25 OK OK 772 790 775 776 804 C3' A A 26 OK OK 802 822 805 806 837 C3' U A 27 OK OK 835 853 838 839 867 C3' A A 28 OK OK 865 885 868 869 900 C3' U A 29 OK OK 898 916 901 902 930 C3' C A 30 OK OK 928 946 931 932 961 C3' C A 31 OK OK 959 977 962 963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 13 OK OK 393 408 390 392 421 C4' A A 14 OK OK 423 440 420 422 454 C4' A A 15 OK OK 456 473 453 455 487 C4' U A 16 OK OK 489 504 486 488 517 C4' U A 17 OK OK 519 534 516 518 547 C4' U A 18 OK OK 549 564 546 548 577 C4' G A 19 OK OK 579 597 576 578 611 C4' A A 20 OK OK 613 630 610 612 644 C4' U A 21 OK OK 646 661 643 645 674 C4' C A 22 OK OK 676 691 673 675 705 C4' A A 23 OK OK 707 724 704 706 738 C4' G A 24 OK OK 740 758 737 739 772 C4' U A 25 OK OK 774 789 771 773 802 C4' A A 26 OK OK 804 821 801 803 835 C4' U A 27 OK OK 837 852 834 836 865 C4' A A 28 OK OK 867 884 864 866 898 C4' U A 29 OK OK 900 915 897 899 928 C4' C A 30 OK OK 930 945 927 929 959 C4' C A 31 OK OK 961 976 958 960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 13 OK OK 389 406 407 391 420 C5' A A 14 OK OK 419 438 439 421 453 C5' A A 15 OK OK 452 471 472 454 486 C5' U A 16 OK OK 485 502 503 487 516 C5' U A 17 OK OK 515 532 533 517 546 C5' U A 18 OK OK 545 562 563 547 576 C5' G A 19 OK OK 575 595 596 577 610 C5' A A 20 OK OK 609 628 629 611 643 C5' U A 21 OK OK 642 659 660 644 673 C5' C A 22 OK OK 672 689 690 674 704 C5' A A 23 OK OK 703 722 723 705 737 C5' G A 24 OK OK 736 756 757 738 771 C5' U A 25 OK OK 770 787 788 772 801 C5' A A 26 OK OK 800 819 820 802 834 C5' U A 27 OK OK 833 850 851 835 864 C5' A A 28 OK OK 863 882 883 865 897 C5' U A 29 OK OK 896 913 914 898 927 C5' C A 30 OK OK 926 943 944 928 958 C5' C A 31 OK OK 957 974 975 959 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 13 distorted distorted 361 387 388 389 416 P A A 14 distorted distorted 394 417 418 419 449 P A A 15 distorted distorted 424 450 451 452 482 P U A 16 distorted distorted 457 483 484 485 512 P U A 17 distorted distorted 490 513 514 515 542 P U A 18 distorted distorted 520 543 544 545 572 P G A 19 distorted distorted 550 573 574 575 606 P A A 20 distorted distorted 580 607 608 609 639 P U A 21 distorted distorted 614 640 641 642 669 P C A 22 distorted distorted 647 670 671 672 700 P A A 23 distorted distorted 677 701 702 703 733 P G A 24 distorted distorted 708 734 735 736 767 P U A 25 distorted distorted 741 768 769 770 797 P A A 26 distorted distorted 775 798 799 800 830 P U A 27 distorted distorted 805 831 832 833 860 P A A 28 distorted distorted 838 861 862 863 893 P U A 29 distorted distorted 868 894 895 896 923 P C A 30 distorted distorted 901 924 925 926 954 P C A 31 distorted distorted 931 955 956 957 ---------------------------------------------------------------------------------