ID code: '1L1W' 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' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' C A 7 alpha beta 201 221 207 204 237 C1' U A 8 alpha beta 232 252 238 235 267 C1' C A 9 alpha beta 262 282 268 265 298 C1' C A 10 alpha beta 293 313 299 296 329 C1' C A 11 alpha beta 324 344 330 327 360 C1' G A 12 alpha beta 355 378 361 358 394 C1' G A 13 alpha beta 389 412 395 392 428 C1' G A 14 alpha beta 423 446 429 426 462 C1' A A 15 alpha beta 457 479 463 460 495 C1' G A 16 alpha beta 490 513 496 493 529 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' G A 20 alpha beta 623 646 629 626 662 C1' G A 21 alpha beta 657 680 663 660 696 C1' G A 22 alpha beta 691 714 697 694 730 C1' A A 23 alpha beta 725 747 731 728 763 C1' C A 24 alpha beta 758 778 764 761 794 C1' C A 25 alpha beta 789 809 795 792 825 C1' A A 26 alpha beta 820 842 826 823 858 C1' C A 27 alpha beta 853 873 859 856 889 C1' C A 28 alpha beta 884 904 890 887 920 C1' A A 29 alpha beta 915 937 921 918 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' A A 5 OK OK 142 138 157 141 173 C2' C A 6 OK OK 175 171 188 174 204 C2' C A 7 OK OK 206 202 219 205 235 C2' U A 8 OK OK 237 233 250 236 265 C2' C A 9 OK OK 267 263 280 266 296 C2' C A 10 OK OK 298 294 311 297 327 C2' C A 11 OK OK 329 325 342 328 358 C2' G A 12 OK OK 360 356 376 359 392 C2' G A 13 OK OK 394 390 410 393 426 C2' G A 14 OK OK 428 424 444 427 460 C2' A A 15 OK OK 462 458 477 461 493 C2' G A 16 OK OK 495 491 511 494 527 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' G A 20 OK OK 628 624 644 627 660 C2' G A 21 OK OK 662 658 678 661 694 C2' G A 22 OK OK 696 692 712 695 728 C2' A A 23 OK OK 730 726 745 729 761 C2' C A 24 OK OK 763 759 776 762 792 C2' C A 25 OK OK 794 790 807 793 823 C2' A A 26 OK OK 825 821 840 824 856 C2' C A 27 OK OK 858 854 871 857 887 C2' C A 28 OK OK 889 885 902 888 918 C2' A A 29 OK OK 920 916 935 919 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' A A 5 OK OK 136 156 139 140 171 C3' C A 6 OK OK 169 187 172 173 202 C3' C A 7 OK OK 200 218 203 204 233 C3' U A 8 OK OK 231 249 234 235 263 C3' C A 9 OK OK 261 279 264 265 294 C3' C A 10 OK OK 292 310 295 296 325 C3' C A 11 OK OK 323 341 326 327 356 C3' G A 12 OK OK 354 375 357 358 390 C3' G A 13 OK OK 388 409 391 392 424 C3' G A 14 OK OK 422 443 425 426 458 C3' A A 15 OK OK 456 476 459 460 491 C3' G A 16 OK OK 489 510 492 493 525 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' G A 20 OK OK 622 643 625 626 658 C3' G A 21 OK OK 656 677 659 660 692 C3' G A 22 OK OK 690 711 693 694 726 C3' A A 23 OK OK 724 744 727 728 759 C3' C A 24 OK OK 757 775 760 761 790 C3' C A 25 OK OK 788 806 791 792 821 C3' A A 26 OK OK 819 839 822 823 854 C3' C A 27 OK OK 852 870 855 856 885 C3' C A 28 OK OK 883 901 886 887 916 C3' A A 29 OK OK 914 934 917 918 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' A A 5 OK OK 138 155 135 137 169 C4' C A 6 OK OK 171 186 168 170 200 C4' C A 7 OK OK 202 217 199 201 231 C4' U A 8 OK OK 233 248 230 232 261 C4' C A 9 OK OK 263 278 260 262 292 C4' C A 10 OK OK 294 309 291 293 323 C4' C A 11 OK OK 325 340 322 324 354 C4' G A 12 OK OK 356 374 353 355 388 C4' G A 13 OK OK 390 408 387 389 422 C4' G A 14 OK OK 424 442 421 423 456 C4' A A 15 OK OK 458 475 455 457 489 C4' G A 16 OK OK 491 509 488 490 523 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' G A 20 OK OK 624 642 621 623 656 C4' G A 21 OK OK 658 676 655 657 690 C4' G A 22 OK OK 692 710 689 691 724 C4' A A 23 OK OK 726 743 723 725 757 C4' C A 24 OK OK 759 774 756 758 788 C4' C A 25 OK OK 790 805 787 789 819 C4' A A 26 OK OK 821 838 818 820 852 C4' C A 27 OK OK 854 869 851 853 883 C4' C A 28 OK OK 885 900 882 884 914 C4' A A 29 OK OK 916 933 913 915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' A A 5 OK OK 134 153 154 136 168 C5' C A 6 OK OK 167 184 185 169 199 C5' C A 7 OK OK 198 215 216 200 230 C5' U A 8 OK OK 229 246 247 231 260 C5' C A 9 OK OK 259 276 277 261 291 C5' C A 10 OK OK 290 307 308 292 322 C5' C A 11 OK OK 321 338 339 323 353 C5' G A 12 OK OK 352 372 373 354 387 C5' G A 13 OK OK 386 406 407 388 421 C5' G A 14 OK OK 420 440 441 422 455 C5' A A 15 OK OK 454 473 474 456 488 C5' G A 16 OK OK 487 507 508 489 522 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' G A 20 OK OK 620 640 641 622 655 C5' G A 21 OK OK 654 674 675 656 689 C5' G A 22 OK OK 688 708 709 690 723 C5' A A 23 OK OK 722 741 742 724 756 C5' C A 24 OK OK 755 772 773 757 787 C5' C A 25 OK OK 786 803 804 788 818 C5' A A 26 OK OK 817 836 837 819 851 C5' C A 27 OK OK 850 867 868 852 882 C5' C A 28 OK OK 881 898 899 883 913 C5' A A 29 OK OK 912 931 932 914 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P A A 5 distorted distorted 105 132 133 134 164 P C A 6 distorted distorted 139 165 166 167 195 P C A 7 distorted distorted 172 196 197 198 226 P U A 8 distorted distorted 203 227 228 229 256 P C A 9 distorted distorted 234 257 258 259 287 P C A 10 distorted distorted 264 288 289 290 318 P C A 11 distorted distorted 295 319 320 321 349 P G A 12 distorted distorted 326 350 351 352 383 P G A 13 distorted distorted 357 384 385 386 417 P G A 14 distorted distorted 391 418 419 420 451 P A A 15 distorted distorted 425 452 453 454 484 P G A 16 distorted distorted 459 485 486 487 518 P C A 17 distorted distorted 492 519 520 521 549 P G A 18 distorted distorted 526 550 551 552 583 P G A 19 distorted distorted 557 584 585 586 617 P G A 20 distorted distorted 591 618 619 620 651 P G A 21 distorted distorted 625 652 653 654 685 P G A 22 distorted distorted 659 686 687 688 719 P A A 23 distorted distorted 693 720 721 722 752 P C A 24 distorted distorted 727 753 754 755 783 P C A 25 distorted distorted 760 784 785 786 814 P A A 26 distorted distorted 791 815 816 817 847 P C A 27 distorted distorted 822 848 849 850 878 P C A 28 distorted distorted 855 879 880 881 909 P A A 29 distorted distorted 886 910 911 912 ---------------------------------------------------------------------------------