ID code: '1NA2' 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' G A 3 alpha beta 73 96 79 76 112 C1' C A 4 alpha beta 107 127 113 110 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' U A 8 alpha beta 232 252 238 235 267 C1' U A 9 alpha beta 262 282 268 265 297 C1' U A 10 alpha beta 292 312 298 295 327 C1' U A 11 alpha beta 322 342 328 325 357 C1' C A 12 alpha beta 352 372 358 355 388 C1' U A 13 alpha beta 383 403 389 386 418 C1' C A 14 alpha beta 413 433 419 416 449 C1' G A 15 alpha beta 444 467 450 447 483 C1' C A 16 alpha beta 478 498 484 481 514 C1' U A 17 alpha beta 509 529 515 512 544 C1' G A 18 alpha beta 539 562 545 542 578 C1' A A 19 alpha beta 573 595 579 576 611 C1' C A 20 alpha beta 606 626 612 609 642 C1' U A 21 alpha beta 637 657 643 640 672 C1' U A 22 alpha beta 667 687 673 670 702 C1' U A 23 alpha beta 697 717 703 700 732 C1' C A 24 alpha beta 727 747 733 730 763 C1' A A 25 alpha beta 758 780 764 761 796 C1' G A 26 alpha beta 791 814 797 794 830 C1' C A 27 alpha beta 825 845 831 828 861 C1' C A 28 alpha beta 856 876 862 859 892 C1' C A 29 alpha beta 887 907 893 890 923 C1' C A 30 alpha beta 918 939 924 921 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' C A 4 OK OK 112 108 125 111 141 C2' U A 5 OK OK 143 139 156 142 171 C2' G A 6 OK OK 173 169 189 172 205 C2' U A 7 OK OK 207 203 220 206 235 C2' U A 8 OK OK 237 233 250 236 265 C2' U A 9 OK OK 267 263 280 266 295 C2' U A 10 OK OK 297 293 310 296 325 C2' U A 11 OK OK 327 323 340 326 355 C2' C A 12 OK OK 357 353 370 356 386 C2' U A 13 OK OK 388 384 401 387 416 C2' C A 14 OK OK 418 414 431 417 447 C2' G A 15 OK OK 449 445 465 448 481 C2' C A 16 OK OK 483 479 496 482 512 C2' U A 17 OK OK 514 510 527 513 542 C2' G A 18 OK OK 544 540 560 543 576 C2' A A 19 OK OK 578 574 593 577 609 C2' C A 20 OK OK 611 607 624 610 640 C2' U A 21 OK OK 642 638 655 641 670 C2' U A 22 OK OK 672 668 685 671 700 C2' U A 23 OK OK 702 698 715 701 730 C2' C A 24 OK OK 732 728 745 731 761 C2' A A 25 OK OK 763 759 778 762 794 C2' G A 26 OK OK 796 792 812 795 828 C2' C A 27 OK OK 830 826 843 829 859 C2' C A 28 OK OK 861 857 874 860 890 C2' C A 29 OK OK 892 888 905 891 921 C2' C A 30 OK OK 923 919 937 922 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' C A 4 OK OK 106 124 109 110 139 C3' U A 5 OK OK 137 155 140 141 169 C3' G A 6 OK OK 167 188 170 171 203 C3' U A 7 OK OK 201 219 204 205 233 C3' U A 8 OK OK 231 249 234 235 263 C3' U A 9 OK OK 261 279 264 265 293 C3' U A 10 OK OK 291 309 294 295 323 C3' U A 11 OK OK 321 339 324 325 353 C3' C A 12 OK OK 351 369 354 355 384 C3' U A 13 OK OK 382 400 385 386 414 C3' C A 14 OK OK 412 430 415 416 445 C3' G A 15 OK OK 443 464 446 447 479 C3' C A 16 OK OK 477 495 480 481 510 C3' U A 17 OK OK 508 526 511 512 540 C3' G A 18 OK OK 538 559 541 542 574 C3' A A 19 OK OK 572 592 575 576 607 C3' C A 20 OK OK 605 623 608 609 638 C3' U A 21 OK OK 636 654 639 640 668 C3' U A 22 OK OK 666 684 669 670 698 C3' U A 23 OK OK 696 714 699 700 728 C3' C A 24 OK OK 726 744 729 730 759 C3' A A 25 OK OK 757 777 760 761 792 C3' G A 26 OK OK 790 811 793 794 826 C3' C A 27 OK OK 824 842 827 828 857 C3' C A 28 OK OK 855 873 858 859 888 C3' C A 29 OK OK 886 904 889 890 919 C3' C A 30 OK OK 917 935 920 921 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' C A 4 OK OK 108 123 105 107 137 C4' U A 5 OK OK 139 154 136 138 167 C4' G A 6 OK OK 169 187 166 168 201 C4' U A 7 OK OK 203 218 200 202 231 C4' U A 8 OK OK 233 248 230 232 261 C4' U A 9 OK OK 263 278 260 262 291 C4' U A 10 OK OK 293 308 290 292 321 C4' U A 11 OK OK 323 338 320 322 351 C4' C A 12 OK OK 353 368 350 352 382 C4' U A 13 OK OK 384 399 381 383 412 C4' C A 14 OK OK 414 429 411 413 443 C4' G A 15 OK OK 445 463 442 444 477 C4' C A 16 OK OK 479 494 476 478 508 C4' U A 17 OK OK 510 525 507 509 538 C4' G A 18 OK OK 540 558 537 539 572 C4' A A 19 OK OK 574 591 571 573 605 C4' C A 20 OK OK 607 622 604 606 636 C4' U A 21 OK OK 638 653 635 637 666 C4' U A 22 OK OK 668 683 665 667 696 C4' U A 23 OK OK 698 713 695 697 726 C4' C A 24 OK OK 728 743 725 727 757 C4' A A 25 OK OK 759 776 756 758 790 C4' G A 26 OK OK 792 810 789 791 824 C4' C A 27 OK OK 826 841 823 825 855 C4' C A 28 OK OK 857 872 854 856 886 C4' C A 29 OK OK 888 903 885 887 917 C4' C A 30 OK OK 919 934 916 918 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' C A 4 OK OK 104 121 122 106 136 C5' U A 5 OK OK 135 152 153 137 166 C5' G A 6 OK OK 165 185 186 167 200 C5' U A 7 OK OK 199 216 217 201 230 C5' U A 8 OK OK 229 246 247 231 260 C5' U A 9 OK OK 259 276 277 261 290 C5' U A 10 OK OK 289 306 307 291 320 C5' U A 11 OK OK 319 336 337 321 350 C5' C A 12 OK OK 349 366 367 351 381 C5' U A 13 OK OK 380 397 398 382 411 C5' C A 14 OK OK 410 427 428 412 442 C5' G A 15 OK OK 441 461 462 443 476 C5' C A 16 OK OK 475 492 493 477 507 C5' U A 17 OK OK 506 523 524 508 537 C5' G A 18 OK OK 536 556 557 538 571 C5' A A 19 OK OK 570 589 590 572 604 C5' C A 20 OK OK 603 620 621 605 635 C5' U A 21 OK OK 634 651 652 636 665 C5' U A 22 OK OK 664 681 682 666 695 C5' U A 23 OK OK 694 711 712 696 725 C5' C A 24 OK OK 724 741 742 726 756 C5' A A 25 OK OK 755 774 775 757 789 C5' G A 26 OK OK 788 808 809 790 823 C5' C A 27 OK OK 822 839 840 824 854 C5' C A 28 OK OK 853 870 871 855 885 C5' C A 29 OK OK 884 901 902 886 916 C5' C A 30 OK OK 915 932 933 917 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P C A 4 distorted distorted 75 102 103 104 132 P U A 5 distorted distorted 109 133 134 135 162 P G A 6 distorted distorted 140 163 164 165 196 P U A 7 distorted distorted 170 197 198 199 226 P U A 8 distorted distorted 204 227 228 229 256 P U A 9 distorted distorted 234 257 258 259 286 P U A 10 distorted distorted 264 287 288 289 316 P U A 11 distorted distorted 294 317 318 319 346 P C A 12 distorted distorted 324 347 348 349 377 P U A 13 distorted distorted 354 378 379 380 407 P C A 14 distorted distorted 385 408 409 410 438 P G A 15 distorted distorted 415 439 440 441 472 P C A 16 distorted distorted 446 473 474 475 503 P U A 17 distorted distorted 480 504 505 506 533 P G A 18 distorted distorted 511 534 535 536 567 P A A 19 distorted distorted 541 568 569 570 600 P C A 20 distorted distorted 575 601 602 603 631 P U A 21 distorted distorted 608 632 633 634 661 P U A 22 distorted distorted 639 662 663 664 691 P U A 23 distorted distorted 669 692 693 694 721 P C A 24 distorted distorted 699 722 723 724 752 P A A 25 distorted distorted 729 753 754 755 785 P G A 26 distorted distorted 760 786 787 788 819 P C A 27 distorted distorted 793 820 821 822 850 P C A 28 distorted distorted 827 851 852 853 881 P C A 29 distorted distorted 858 882 883 884 912 P C A 30 distorted distorted 889 913 914 915 ---------------------------------------------------------------------------------