ID code: '5UZZ' 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 22 alpha beta 4 27 10 7 44 C1' G A 23 alpha beta 39 62 45 42 78 C1' U A 24 alpha beta 73 93 79 76 108 C1' G A 25 alpha beta 103 126 109 106 142 C1' U A 26 alpha beta 137 157 143 140 172 C1' U A 27 alpha beta 167 187 173 170 202 C1' G A 28 alpha beta 197 220 203 200 236 C1' A A 29 alpha beta 231 253 237 234 269 C1' C A 30 alpha beta 264 284 270 267 300 C1' U A 31 alpha beta 295 315 301 298 330 C1' G A 32 alpha beta 325 348 331 328 364 C1' U A 33 alpha beta 359 379 365 362 394 C1' U A 34 alpha beta 389 409 395 392 424 C1' G A 35 alpha beta 419 442 425 422 458 C1' A A 36 alpha beta 453 475 459 456 491 C1' A A 37 alpha beta 486 508 492 489 524 C1' U A 38 alpha beta 519 539 525 522 554 C1' C A 39 alpha beta 549 569 555 552 585 C1' U A 40 alpha beta 580 600 586 583 615 C1' C A 41 alpha beta 610 630 616 613 646 C1' A A 42 alpha beta 641 663 647 644 679 C1' U A 43 alpha beta 674 694 680 677 709 C1' G A 44 alpha beta 704 727 710 707 743 C1' G A 45 alpha beta 738 761 744 741 777 C1' C A 46 alpha beta 772 792 778 775 808 C1' A A 47 alpha beta 803 825 809 806 841 C1' A A 48 alpha beta 836 858 842 839 874 C1' C A 49 alpha beta 869 889 875 872 905 C1' A A 50 alpha beta 900 922 906 903 938 C1' C A 51 alpha beta 933 953 939 936 969 C1' C A 52 alpha beta 964 985 970 967 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 22 OK OK 9 5 25 8 42 C2' G A 23 OK OK 44 40 60 43 76 C2' U A 24 OK OK 78 74 91 77 106 C2' G A 25 OK OK 108 104 124 107 140 C2' U A 26 OK OK 142 138 155 141 170 C2' U A 27 OK OK 172 168 185 171 200 C2' G A 28 OK OK 202 198 218 201 234 C2' A A 29 OK OK 236 232 251 235 267 C2' C A 30 OK OK 269 265 282 268 298 C2' U A 31 OK OK 300 296 313 299 328 C2' G A 32 OK OK 330 326 346 329 362 C2' U A 33 OK OK 364 360 377 363 392 C2' U A 34 OK OK 394 390 407 393 422 C2' G A 35 OK OK 424 420 440 423 456 C2' A A 36 OK OK 458 454 473 457 489 C2' A A 37 OK OK 491 487 506 490 522 C2' U A 38 OK OK 524 520 537 523 552 C2' C A 39 OK OK 554 550 567 553 583 C2' U A 40 OK OK 585 581 598 584 613 C2' C A 41 OK OK 615 611 628 614 644 C2' A A 42 OK OK 646 642 661 645 677 C2' U A 43 OK OK 679 675 692 678 707 C2' G A 44 OK OK 709 705 725 708 741 C2' G A 45 OK OK 743 739 759 742 775 C2' C A 46 OK OK 777 773 790 776 806 C2' A A 47 OK OK 808 804 823 807 839 C2' A A 48 OK OK 841 837 856 840 872 C2' C A 49 OK OK 874 870 887 873 903 C2' A A 50 OK OK 905 901 920 904 936 C2' C A 51 OK OK 938 934 951 937 967 C2' C A 52 OK OK 969 965 983 968 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 22 OK OK 3 24 6 7 40 C3' G A 23 OK OK 38 59 41 42 74 C3' U A 24 OK OK 72 90 75 76 104 C3' G A 25 OK OK 102 123 105 106 138 C3' U A 26 OK OK 136 154 139 140 168 C3' U A 27 OK OK 166 184 169 170 198 C3' G A 28 OK OK 196 217 199 200 232 C3' A A 29 OK OK 230 250 233 234 265 C3' C A 30 OK OK 263 281 266 267 296 C3' U A 31 OK OK 294 312 297 298 326 C3' G A 32 OK OK 324 345 327 328 360 C3' U A 33 OK OK 358 376 361 362 390 C3' U A 34 OK OK 388 406 391 392 420 C3' G A 35 OK OK 418 439 421 422 454 C3' A A 36 OK OK 452 472 455 456 487 C3' A A 37 OK OK 485 505 488 489 520 C3' U A 38 OK OK 518 536 521 522 550 C3' C A 39 OK OK 548 566 551 552 581 C3' U A 40 OK OK 579 597 582 583 611 C3' C A 41 OK OK 609 627 612 613 642 C3' A A 42 OK OK 640 660 643 644 675 C3' U A 43 OK OK 673 691 676 677 705 C3' G A 44 OK OK 703 724 706 707 739 C3' G A 45 OK OK 737 758 740 741 773 C3' C A 46 OK OK 771 789 774 775 804 C3' A A 47 OK OK 802 822 805 806 837 C3' A A 48 OK OK 835 855 838 839 870 C3' C A 49 OK OK 868 886 871 872 901 C3' A A 50 OK OK 899 919 902 903 934 C3' C A 51 OK OK 932 950 935 936 965 C3' C A 52 OK OK 963 981 966 967 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 22 OK OK 5 23 2 4 38 C4' G A 23 OK OK 40 58 37 39 72 C4' U A 24 OK OK 74 89 71 73 102 C4' G A 25 OK OK 104 122 101 103 136 C4' U A 26 OK OK 138 153 135 137 166 C4' U A 27 OK OK 168 183 165 167 196 C4' G A 28 OK OK 198 216 195 197 230 C4' A A 29 OK OK 232 249 229 231 263 C4' C A 30 OK OK 265 280 262 264 294 C4' U A 31 OK OK 296 311 293 295 324 C4' G A 32 OK OK 326 344 323 325 358 C4' U A 33 OK OK 360 375 357 359 388 C4' U A 34 OK OK 390 405 387 389 418 C4' G A 35 OK OK 420 438 417 419 452 C4' A A 36 OK OK 454 471 451 453 485 C4' A A 37 OK OK 487 504 484 486 518 C4' U A 38 OK OK 520 535 517 519 548 C4' C A 39 OK OK 550 565 547 549 579 C4' U A 40 OK OK 581 596 578 580 609 C4' C A 41 OK OK 611 626 608 610 640 C4' A A 42 OK OK 642 659 639 641 673 C4' U A 43 OK OK 675 690 672 674 703 C4' G A 44 OK OK 705 723 702 704 737 C4' G A 45 OK OK 739 757 736 738 771 C4' C A 46 OK OK 773 788 770 772 802 C4' A A 47 OK OK 804 821 801 803 835 C4' A A 48 OK OK 837 854 834 836 868 C4' C A 49 OK OK 870 885 867 869 899 C4' A A 50 OK OK 901 918 898 900 932 C4' C A 51 OK OK 934 949 931 933 963 C4' C A 52 OK OK 965 980 962 964 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 22 OK OK 1 21 22 3 37 C5' G A 23 OK OK 36 56 57 38 71 C5' U A 24 OK OK 70 87 88 72 101 C5' G A 25 OK OK 100 120 121 102 135 C5' U A 26 OK OK 134 151 152 136 165 C5' U A 27 OK OK 164 181 182 166 195 C5' G A 28 OK OK 194 214 215 196 229 C5' A A 29 OK OK 228 247 248 230 262 C5' C A 30 OK OK 261 278 279 263 293 C5' U A 31 OK OK 292 309 310 294 323 C5' G A 32 OK OK 322 342 343 324 357 C5' U A 33 OK OK 356 373 374 358 387 C5' U A 34 OK OK 386 403 404 388 417 C5' G A 35 OK OK 416 436 437 418 451 C5' A A 36 OK OK 450 469 470 452 484 C5' A A 37 OK OK 483 502 503 485 517 C5' U A 38 OK OK 516 533 534 518 547 C5' C A 39 OK OK 546 563 564 548 578 C5' U A 40 OK OK 577 594 595 579 608 C5' C A 41 OK OK 607 624 625 609 639 C5' A A 42 OK OK 638 657 658 640 672 C5' U A 43 OK OK 671 688 689 673 702 C5' G A 44 OK OK 701 721 722 703 736 C5' G A 45 OK OK 735 755 756 737 770 C5' C A 46 OK OK 769 786 787 771 801 C5' A A 47 OK OK 800 819 820 802 834 C5' A A 48 OK OK 833 852 853 835 867 C5' C A 49 OK OK 866 883 884 868 898 C5' A A 50 OK OK 897 916 917 899 931 C5' C A 51 OK OK 930 947 948 932 962 C5' C A 52 OK OK 961 978 979 963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 23 distorted distorted 6 34 35 36 67 P U A 24 distorted distorted 41 68 69 70 97 P G A 25 distorted distorted 75 98 99 100 131 P U A 26 distorted distorted 105 132 133 134 161 P U A 27 distorted distorted 139 162 163 164 191 P G A 28 distorted distorted 169 192 193 194 225 P A A 29 distorted distorted 199 226 227 228 258 P C A 30 distorted distorted 233 259 260 261 289 P U A 31 distorted distorted 266 290 291 292 319 P G A 32 distorted distorted 297 320 321 322 353 P U A 33 distorted distorted 327 354 355 356 383 P U A 34 distorted distorted 361 384 385 386 413 P G A 35 distorted distorted 391 414 415 416 447 P A A 36 distorted distorted 421 448 449 450 480 P A A 37 distorted distorted 455 481 482 483 513 P U A 38 distorted distorted 488 514 515 516 543 P C A 39 distorted distorted 521 544 545 546 574 P U A 40 distorted distorted 551 575 576 577 604 P C A 41 distorted distorted 582 605 606 607 635 P A A 42 distorted distorted 612 636 637 638 668 P U A 43 distorted distorted 643 669 670 671 698 P G A 44 distorted distorted 676 699 700 701 732 P G A 45 distorted distorted 706 733 734 735 766 P C A 46 distorted distorted 740 767 768 769 797 P A A 47 distorted distorted 774 798 799 800 830 P A A 48 distorted distorted 805 831 832 833 863 P C A 49 distorted distorted 838 864 865 866 894 P A A 50 distorted distorted 871 895 896 897 927 P C A 51 distorted distorted 902 928 929 930 958 P C A 52 distorted distorted 935 959 960 961 ---------------------------------------------------------------------------------