ID code: '1UTS' 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 B 17 alpha beta 4 27 10 7 44 C1' G B 18 alpha beta 39 62 45 42 78 C1' C B 19 alpha beta 73 93 79 76 109 C1' A B 20 alpha beta 104 126 110 107 142 C1' G B 21 alpha beta 137 160 143 140 176 C1' A B 22 alpha beta 171 193 177 174 209 C1' U B 23 alpha beta 204 224 210 207 239 C1' C B 24 alpha beta 234 254 240 237 270 C1' U B 25 alpha beta 265 285 271 268 300 C1' G B 26 alpha beta 295 318 301 298 334 C1' A B 27 alpha beta 329 351 335 332 367 C1' G B 28 alpha beta 362 385 368 365 401 C1' C B 29 alpha beta 396 416 402 399 432 C1' C B 30 alpha beta 427 447 433 430 463 C1' U B 31 alpha beta 458 478 464 461 493 C1' G B 32 alpha beta 488 511 494 491 527 C1' G B 33 alpha beta 522 545 528 525 561 C1' G B 34 alpha beta 556 579 562 559 595 C1' A B 35 alpha beta 590 612 596 593 628 C1' G B 36 alpha beta 623 646 629 626 662 C1' C B 37 alpha beta 657 677 663 660 693 C1' U B 38 alpha beta 688 708 694 691 723 C1' C B 39 alpha beta 718 738 724 721 754 C1' U B 40 alpha beta 749 769 755 752 784 C1' C B 41 alpha beta 779 799 785 782 815 C1' U B 42 alpha beta 810 830 816 813 845 C1' G B 43 alpha beta 840 863 846 843 879 C1' C B 44 alpha beta 874 894 880 877 910 C1' C B 45 alpha beta 905 926 911 908 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 17 OK OK 9 5 25 8 42 C2' G B 18 OK OK 44 40 60 43 76 C2' C B 19 OK OK 78 74 91 77 107 C2' A B 20 OK OK 109 105 124 108 140 C2' G B 21 OK OK 142 138 158 141 174 C2' A B 22 OK OK 176 172 191 175 207 C2' U B 23 OK OK 209 205 222 208 237 C2' C B 24 OK OK 239 235 252 238 268 C2' U B 25 OK OK 270 266 283 269 298 C2' G B 26 OK OK 300 296 316 299 332 C2' A B 27 OK OK 334 330 349 333 365 C2' G B 28 OK OK 367 363 383 366 399 C2' C B 29 OK OK 401 397 414 400 430 C2' C B 30 OK OK 432 428 445 431 461 C2' U B 31 OK OK 463 459 476 462 491 C2' G B 32 OK OK 493 489 509 492 525 C2' G B 33 OK OK 527 523 543 526 559 C2' G B 34 OK OK 561 557 577 560 593 C2' A B 35 OK OK 595 591 610 594 626 C2' G B 36 OK OK 628 624 644 627 660 C2' C B 37 OK OK 662 658 675 661 691 C2' U B 38 OK OK 693 689 706 692 721 C2' C B 39 OK OK 723 719 736 722 752 C2' U B 40 OK OK 754 750 767 753 782 C2' C B 41 OK OK 784 780 797 783 813 C2' U B 42 OK OK 815 811 828 814 843 C2' G B 43 OK OK 845 841 861 844 877 C2' C B 44 OK OK 879 875 892 878 908 C2' C B 45 OK OK 910 906 924 909 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 17 OK OK 3 24 6 7 40 C3' G B 18 OK OK 38 59 41 42 74 C3' C B 19 OK OK 72 90 75 76 105 C3' A B 20 OK OK 103 123 106 107 138 C3' G B 21 OK OK 136 157 139 140 172 C3' A B 22 OK OK 170 190 173 174 205 C3' U B 23 OK OK 203 221 206 207 235 C3' C B 24 OK OK 233 251 236 237 266 C3' U B 25 OK OK 264 282 267 268 296 C3' G B 26 OK OK 294 315 297 298 330 C3' A B 27 OK OK 328 348 331 332 363 C3' G B 28 OK OK 361 382 364 365 397 C3' C B 29 OK OK 395 413 398 399 428 C3' C B 30 OK OK 426 444 429 430 459 C3' U B 31 OK OK 457 475 460 461 489 C3' G B 32 OK OK 487 508 490 491 523 C3' G B 33 OK OK 521 542 524 525 557 C3' G B 34 OK OK 555 576 558 559 591 C3' A B 35 OK OK 589 609 592 593 624 C3' G B 36 OK OK 622 643 625 626 658 C3' C B 37 OK OK 656 674 659 660 689 C3' U B 38 OK OK 687 705 690 691 719 C3' C B 39 OK OK 717 735 720 721 750 C3' U B 40 OK OK 748 766 751 752 780 C3' C B 41 OK OK 778 796 781 782 811 C3' U B 42 OK OK 809 827 812 813 841 C3' G B 43 OK OK 839 860 842 843 875 C3' C B 44 OK OK 873 891 876 877 906 C3' C B 45 OK OK 904 922 907 908 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 17 OK OK 5 23 2 4 38 C4' G B 18 OK OK 40 58 37 39 72 C4' C B 19 OK OK 74 89 71 73 103 C4' A B 20 OK OK 105 122 102 104 136 C4' G B 21 OK OK 138 156 135 137 170 C4' A B 22 OK OK 172 189 169 171 203 C4' U B 23 OK OK 205 220 202 204 233 C4' C B 24 OK OK 235 250 232 234 264 C4' U B 25 OK OK 266 281 263 265 294 C4' G B 26 OK OK 296 314 293 295 328 C4' A B 27 OK OK 330 347 327 329 361 C4' G B 28 OK OK 363 381 360 362 395 C4' C B 29 OK OK 397 412 394 396 426 C4' C B 30 OK OK 428 443 425 427 457 C4' U B 31 OK OK 459 474 456 458 487 C4' G B 32 OK OK 489 507 486 488 521 C4' G B 33 OK OK 523 541 520 522 555 C4' G B 34 OK OK 557 575 554 556 589 C4' A B 35 OK OK 591 608 588 590 622 C4' G B 36 OK OK 624 642 621 623 656 C4' C B 37 OK OK 658 673 655 657 687 C4' U B 38 OK OK 689 704 686 688 717 C4' C B 39 OK OK 719 734 716 718 748 C4' U B 40 OK OK 750 765 747 749 778 C4' C B 41 OK OK 780 795 777 779 809 C4' U B 42 OK OK 811 826 808 810 839 C4' G B 43 OK OK 841 859 838 840 873 C4' C B 44 OK OK 875 890 872 874 904 C4' C B 45 OK OK 906 921 903 905 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 17 OK OK 1 21 22 3 37 C5' G B 18 OK OK 36 56 57 38 71 C5' C B 19 OK OK 70 87 88 72 102 C5' A B 20 OK OK 101 120 121 103 135 C5' G B 21 OK OK 134 154 155 136 169 C5' A B 22 OK OK 168 187 188 170 202 C5' U B 23 OK OK 201 218 219 203 232 C5' C B 24 OK OK 231 248 249 233 263 C5' U B 25 OK OK 262 279 280 264 293 C5' G B 26 OK OK 292 312 313 294 327 C5' A B 27 OK OK 326 345 346 328 360 C5' G B 28 OK OK 359 379 380 361 394 C5' C B 29 OK OK 393 410 411 395 425 C5' C B 30 OK OK 424 441 442 426 456 C5' U B 31 OK OK 455 472 473 457 486 C5' G B 32 OK OK 485 505 506 487 520 C5' G B 33 OK OK 519 539 540 521 554 C5' G B 34 OK OK 553 573 574 555 588 C5' A B 35 OK OK 587 606 607 589 621 C5' G B 36 OK OK 620 640 641 622 655 C5' C B 37 OK OK 654 671 672 656 686 C5' U B 38 OK OK 685 702 703 687 716 C5' C B 39 OK OK 715 732 733 717 747 C5' U B 40 OK OK 746 763 764 748 777 C5' C B 41 OK OK 776 793 794 778 808 C5' U B 42 OK OK 807 824 825 809 838 C5' G B 43 OK OK 837 857 858 839 872 C5' C B 44 OK OK 871 888 889 873 903 C5' C B 45 OK OK 902 919 920 904 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G B 18 distorted distorted 6 34 35 36 67 P C B 19 distorted distorted 41 68 69 70 98 P A B 20 distorted distorted 75 99 100 101 131 P G B 21 distorted distorted 106 132 133 134 165 P A B 22 distorted distorted 139 166 167 168 198 P U B 23 distorted distorted 173 199 200 201 228 P C B 24 distorted distorted 206 229 230 231 259 P U B 25 distorted distorted 236 260 261 262 289 P G B 26 distorted distorted 267 290 291 292 323 P A B 27 distorted distorted 297 324 325 326 356 P G B 28 distorted distorted 331 357 358 359 390 P C B 29 distorted distorted 364 391 392 393 421 P C B 30 distorted distorted 398 422 423 424 452 P U B 31 distorted distorted 429 453 454 455 482 P G B 32 distorted distorted 460 483 484 485 516 P G B 33 distorted distorted 490 517 518 519 550 P G B 34 distorted distorted 524 551 552 553 584 P A B 35 distorted distorted 558 585 586 587 617 P G B 36 distorted distorted 592 618 619 620 651 P C B 37 distorted distorted 625 652 653 654 682 P U B 38 distorted distorted 659 683 684 685 712 P C B 39 distorted distorted 690 713 714 715 743 P U B 40 distorted distorted 720 744 745 746 773 P C B 41 distorted distorted 751 774 775 776 804 P U B 42 distorted distorted 781 805 806 807 834 P G B 43 distorted distorted 812 835 836 837 868 P C B 44 distorted distorted 842 869 870 871 899 P C B 45 distorted distorted 876 900 901 902 ---------------------------------------------------------------------------------