ID code: '2ESI' 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' U A 0 beta 4 10 7 29 C1' U A 1 beta 24 30 27 49 C1' G A 2 beta 44 50 47 72 C1' C A 3 beta 67 73 70 92 C1' G A 4 beta 87 93 90 115 C1' U A 5 beta 110 116 113 135 C1' C A 6 beta 130 136 133 155 C1' A A 7 beta 150 156 153 177 C1' C A 8 beta 172 178 175 197 C1' A A 9 beta 192 198 195 219 C1' C A 10 beta 214 220 217 239 C1' C A 11 beta 234 240 237 259 C1' G A 12 beta 254 260 257 282 C1' G A 13 beta 277 283 280 305 C1' U A 14 beta 300 306 303 325 C1' G A 15 beta 320 326 323 348 C1' A A 16 beta 343 349 346 370 C1' A A 17 beta 365 371 368 392 C1' G A 18 beta 387 393 390 415 C1' U A 19 beta 410 416 413 435 C1' C A 20 beta 430 436 433 455 C1' G A 21 beta 450 456 453 478 C1' C A 22 beta 473 479 476 496 C1' G B 25 beta 491 497 494 519 C1' C B 26 beta 514 520 517 539 C1' G B 27 beta 534 540 537 562 C1' U B 28 beta 557 563 560 582 C1' C B 29 beta 577 583 580 602 C1' A B 30 beta 597 603 600 624 C1' C B 31 beta 619 625 622 644 C1' A B 32 beta 639 645 642 666 C1' C B 33 beta 661 667 664 686 C1' C B 34 beta 681 687 684 706 C1' G B 35 beta 701 707 704 729 C1' G B 36 beta 724 730 727 752 C1' U B 37 beta 747 753 750 772 C1' G B 38 beta 767 773 770 795 C1' A B 39 beta 790 796 793 817 C1' A B 40 beta 812 818 815 839 C1' G B 41 beta 834 840 837 862 C1' U B 42 beta 857 863 860 882 C1' C B 43 beta 877 883 880 902 C1' G B 44 beta 897 903 900 925 C1' C B 45 beta 920 926 923 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 0 OK 9 5 8 27 C2' U A 1 OK 29 25 28 47 C2' G A 2 OK 49 45 48 70 C2' C A 3 OK 72 68 71 90 C2' G A 4 OK 92 88 91 113 C2' U A 5 OK 115 111 114 133 C2' C A 6 OK 135 131 134 153 C2' A A 7 OK 155 151 154 175 C2' C A 8 OK 177 173 176 195 C2' A A 9 OK 197 193 196 217 C2' C A 10 OK 219 215 218 237 C2' C A 11 OK 239 235 238 257 C2' G A 12 OK 259 255 258 280 C2' G A 13 OK 282 278 281 303 C2' U A 14 OK 305 301 304 323 C2' G A 15 OK 325 321 324 346 C2' A A 16 OK 348 344 347 368 C2' A A 17 OK 370 366 369 390 C2' G A 18 OK 392 388 391 413 C2' U A 19 OK 415 411 414 433 C2' C A 20 OK 435 431 434 453 C2' G A 21 OK 455 451 454 476 C2' C A 22 OK 478 474 477 494 C2' G B 25 OK 496 492 495 517 C2' C B 26 OK 519 515 518 537 C2' G B 27 OK 539 535 538 560 C2' U B 28 OK 562 558 561 580 C2' C B 29 OK 582 578 581 600 C2' A B 30 OK 602 598 601 622 C2' C B 31 OK 624 620 623 642 C2' A B 32 OK 644 640 643 664 C2' C B 33 OK 666 662 665 684 C2' C B 34 OK 686 682 685 704 C2' G B 35 OK 706 702 705 727 C2' G B 36 OK 729 725 728 750 C2' U B 37 OK 752 748 751 770 C2' G B 38 OK 772 768 771 793 C2' A B 39 OK 795 791 794 815 C2' A B 40 OK 817 813 816 837 C2' G B 41 OK 839 835 838 860 C2' U B 42 OK 862 858 861 880 C2' C B 43 OK 882 878 881 900 C2' G B 44 OK 902 898 901 923 C2' C B 45 OK 925 921 924 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 0 OK 3 6 7 25 C3' U A 1 OK 23 26 27 45 C3' G A 2 OK 43 46 47 68 C3' C A 3 OK 66 69 70 88 C3' G A 4 OK 86 89 90 111 C3' U A 5 OK 109 112 113 131 C3' C A 6 OK 129 132 133 151 C3' A A 7 OK 149 152 153 173 C3' C A 8 OK 171 174 175 193 C3' A A 9 OK 191 194 195 215 C3' C A 10 OK 213 216 217 235 C3' C A 11 OK 233 236 237 255 C3' G A 12 OK 253 256 257 278 C3' G A 13 OK 276 279 280 301 C3' U A 14 OK 299 302 303 321 C3' G A 15 OK 319 322 323 344 C3' A A 16 OK 342 345 346 366 C3' A A 17 OK 364 367 368 388 C3' G A 18 OK 386 389 390 411 C3' U A 19 OK 409 412 413 431 C3' C A 20 OK 429 432 433 451 C3' G A 21 OK 449 452 453 474 C3' C A 22 OK 472 475 476 492 C3' G B 25 OK 490 493 494 515 C3' C B 26 OK 513 516 517 535 C3' G B 27 OK 533 536 537 558 C3' U B 28 OK 556 559 560 578 C3' C B 29 OK 576 579 580 598 C3' A B 30 OK 596 599 600 620 C3' C B 31 OK 618 621 622 640 C3' A B 32 OK 638 641 642 662 C3' C B 33 OK 660 663 664 682 C3' C B 34 OK 680 683 684 702 C3' G B 35 OK 700 703 704 725 C3' G B 36 OK 723 726 727 748 C3' U B 37 OK 746 749 750 768 C3' G B 38 OK 766 769 770 791 C3' A B 39 OK 789 792 793 813 C3' A B 40 OK 811 814 815 835 C3' G B 41 OK 833 836 837 858 C3' U B 42 OK 856 859 860 878 C3' C B 43 OK 876 879 880 898 C3' G B 44 OK 896 899 900 921 C3' C B 45 OK 919 922 923 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 0 OK 5 2 4 23 C4' U A 1 OK 25 22 24 43 C4' G A 2 OK 45 42 44 66 C4' C A 3 OK 68 65 67 86 C4' G A 4 OK 88 85 87 109 C4' U A 5 OK 111 108 110 129 C4' C A 6 OK 131 128 130 149 C4' A A 7 OK 151 148 150 171 C4' C A 8 OK 173 170 172 191 C4' A A 9 OK 193 190 192 213 C4' C A 10 OK 215 212 214 233 C4' C A 11 OK 235 232 234 253 C4' G A 12 OK 255 252 254 276 C4' G A 13 OK 278 275 277 299 C4' U A 14 OK 301 298 300 319 C4' G A 15 OK 321 318 320 342 C4' A A 16 OK 344 341 343 364 C4' A A 17 OK 366 363 365 386 C4' G A 18 OK 388 385 387 409 C4' U A 19 OK 411 408 410 429 C4' C A 20 OK 431 428 430 449 C4' G A 21 OK 451 448 450 472 C4' C A 22 OK 474 471 473 490 C4' G B 25 OK 492 489 491 513 C4' C B 26 OK 515 512 514 533 C4' G B 27 OK 535 532 534 556 C4' U B 28 OK 558 555 557 576 C4' C B 29 OK 578 575 577 596 C4' A B 30 OK 598 595 597 618 C4' C B 31 OK 620 617 619 638 C4' A B 32 OK 640 637 639 660 C4' C B 33 OK 662 659 661 680 C4' C B 34 OK 682 679 681 700 C4' G B 35 OK 702 699 701 723 C4' G B 36 OK 725 722 724 746 C4' U B 37 OK 748 745 747 766 C4' G B 38 OK 768 765 767 789 C4' A B 39 OK 791 788 790 811 C4' A B 40 OK 813 810 812 833 C4' G B 41 OK 835 832 834 856 C4' U B 42 OK 858 855 857 876 C4' C B 43 OK 878 875 877 896 C4' G B 44 OK 898 895 897 919 C4' C B 45 OK 921 918 920 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 0 1 3 22 C5' U A 1 21 23 42 C5' G A 2 43 65 C5' C A 3 64 66 85 C5' G A 4 84 86 108 C5' U A 5 107 109 128 C5' C A 6 127 129 148 C5' A A 7 147 149 170 C5' C A 8 169 171 190 C5' A A 9 189 191 212 C5' C A 10 211 213 232 C5' C A 11 231 233 252 C5' G A 12 251 253 275 C5' G A 13 274 276 298 C5' U A 14 297 299 318 C5' G A 15 317 319 341 C5' A A 16 340 342 363 C5' A A 17 362 364 385 C5' G A 18 384 386 408 C5' U A 19 407 409 428 C5' C A 20 427 429 448 C5' G A 21 447 449 471 C5' C A 22 470 472 489 C5' G B 25 488 490 512 C5' C B 26 511 513 532 C5' G B 27 531 533 555 C5' U B 28 554 556 575 C5' C B 29 574 576 595 C5' A B 30 594 596 617 C5' C B 31 616 618 637 C5' A B 32 636 638 659 C5' C B 33 658 660 679 C5' C B 34 678 680 699 C5' G B 35 698 700 722 C5' G B 36 721 723 745 C5' U B 37 744 746 765 C5' G B 38 764 766 788 C5' A B 39 787 789 810 C5' A B 40 809 811 832 C5' G B 41 831 833 855 C5' U B 42 854 856 875 C5' C B 43 874 876 895 C5' G B 44 894 896 918 C5' C B 45 917 919 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 1 distorted distorted 6 19 20 21 38 P G A 2 distorted distorted 26 39 40 41 61 P C A 3 distorted distorted 46 62 63 64 81 P G A 4 distorted distorted 69 82 83 84 104 P U A 5 distorted distorted 89 105 106 107 124 P C A 6 distorted distorted 112 125 126 127 144 P A A 7 distorted distorted 132 145 146 147 166 P C A 8 distorted distorted 152 167 168 169 186 P A A 9 distorted distorted 174 187 188 189 208 P C A 10 distorted distorted 194 209 210 211 228 P C A 11 distorted distorted 216 229 230 231 248 P G A 12 distorted distorted 236 249 250 251 271 P G A 13 distorted distorted 256 272 273 274 294 P U A 14 distorted distorted 279 295 296 297 314 P G A 15 distorted distorted 302 315 316 317 337 P A A 16 distorted distorted 322 338 339 340 359 P A A 17 distorted distorted 345 360 361 362 381 P G A 18 distorted distorted 367 382 383 384 404 P U A 19 distorted distorted 389 405 406 407 424 P C A 20 distorted distorted 412 425 426 427 444 P G A 21 distorted distorted 432 445 446 447 467 P C A 22 distorted distorted 452 468 469 470 508 P C B 26 distorted distorted 493 509 510 511 528 P G B 27 distorted distorted 516 529 530 531 551 P U B 28 distorted distorted 536 552 553 554 571 P C B 29 distorted distorted 559 572 573 574 591 P A B 30 distorted distorted 579 592 593 594 613 P C B 31 distorted distorted 599 614 615 616 633 P A B 32 distorted distorted 621 634 635 636 655 P C B 33 distorted distorted 641 656 657 658 675 P C B 34 distorted distorted 663 676 677 678 695 P G B 35 distorted distorted 683 696 697 698 718 P G B 36 distorted distorted 703 719 720 721 741 P U B 37 distorted distorted 726 742 743 744 761 P G B 38 distorted distorted 749 762 763 764 784 P A B 39 distorted distorted 769 785 786 787 806 P A B 40 distorted distorted 792 807 808 809 828 P G B 41 distorted distorted 814 829 830 831 851 P U B 42 distorted distorted 836 852 853 854 871 P C B 43 distorted distorted 859 872 873 874 891 P G B 44 distorted distorted 879 892 893 894 914 P C B 45 distorted distorted 899 915 916 917 ---------------------------------------------------------------------------------