ID code: '3C44' 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' C A 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' U A 3 beta 44 50 47 69 C1' G A 4 beta 64 70 67 92 C1' C A 5 beta 87 93 90 112 C1' U A 6 beta 107 113 110 132 C1' G A 7 beta 127 133 130 155 C1' A A 8 beta 150 156 153 177 C1' A A 9 beta 172 178 175 199 C1' G A 10 beta 194 200 197 222 C1' U A 11 beta 217 223 220 242 C1' G A 12 beta 237 243 240 265 C1' C A 13 beta 260 266 263 285 C1' A A 14 beta 280 286 283 307 C1' C A 15 beta 302 308 305 327 C1' A A 16 beta 322 328 325 349 C1' C A 17 beta 344 350 347 369 C1' A A 18 beta 364 370 367 391 C1' G A 19 beta 386 392 389 414 C1' C A 20 beta 409 415 412 434 C1' A A 21 beta 429 435 432 456 C1' A A 22 beta 451 457 454 478 C1' G A 23 beta 473 479 476 499 C1' C B 1 beta 494 500 497 519 C1' U B 2 beta 514 520 517 539 C1' U B 3 beta 534 540 537 559 C1' G B 4 beta 554 560 557 582 C1' C B 5 beta 577 583 580 602 C1' U B 6 beta 597 603 600 622 C1' G B 7 beta 617 623 620 645 C1' A B 8 beta 640 646 643 667 C1' A B 9 beta 662 668 665 689 C1' G B 10 beta 684 690 687 712 C1' U B 11 beta 707 713 710 732 C1' G B 12 beta 727 733 730 755 C1' C B 13 beta 750 756 753 775 C1' A B 14 beta 770 776 773 797 C1' C B 15 beta 792 798 795 817 C1' A B 16 beta 812 818 815 839 C1' C B 17 beta 834 840 837 859 C1' A B 18 beta 854 860 857 881 C1' G B 19 beta 876 882 879 904 C1' C B 20 beta 899 905 902 924 C1' A B 21 beta 919 925 922 946 C1' A B 22 beta 941 947 944 968 C1' G B 23 beta 963 969 966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' U A 3 OK 49 45 48 67 C2' G A 4 OK 69 65 68 90 C2' C A 5 OK 92 88 91 110 C2' U A 6 OK 112 108 111 130 C2' G A 7 OK 132 128 131 153 C2' A A 8 OK 155 151 154 175 C2' A A 9 OK 177 173 176 197 C2' G A 10 OK 199 195 198 220 C2' U A 11 OK 222 218 221 240 C2' G A 12 OK 242 238 241 263 C2' C A 13 OK 265 261 264 283 C2' A A 14 OK 285 281 284 305 C2' C A 15 OK 307 303 306 325 C2' A A 16 OK 327 323 326 347 C2' C A 17 OK 349 345 348 367 C2' A A 18 OK 369 365 368 389 C2' G A 19 OK 391 387 390 412 C2' C A 20 OK 414 410 413 432 C2' A A 21 OK 434 430 433 454 C2' A A 22 OK 456 452 455 476 C2' G A 23 OK 478 474 477 497 C2' C B 1 OK 499 495 498 517 C2' U B 2 OK 519 515 518 537 C2' U B 3 OK 539 535 538 557 C2' G B 4 OK 559 555 558 580 C2' C B 5 OK 582 578 581 600 C2' U B 6 OK 602 598 601 620 C2' G B 7 OK 622 618 621 643 C2' A B 8 OK 645 641 644 665 C2' A B 9 OK 667 663 666 687 C2' G B 10 OK 689 685 688 710 C2' U B 11 OK 712 708 711 730 C2' G B 12 OK 732 728 731 753 C2' C B 13 OK 755 751 754 773 C2' A B 14 OK 775 771 774 795 C2' C B 15 OK 797 793 796 815 C2' A B 16 OK 817 813 816 837 C2' C B 17 OK 839 835 838 857 C2' A B 18 OK 859 855 858 879 C2' G B 19 OK 881 877 880 902 C2' C B 20 OK 904 900 903 922 C2' A B 21 OK 924 920 923 944 C2' A B 22 OK 946 942 945 966 C2' G B 23 OK 968 964 967 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' U A 3 OK 43 46 47 65 C3' G A 4 OK 63 66 67 88 C3' C A 5 OK 86 89 90 108 C3' U A 6 OK 106 109 110 128 C3' G A 7 OK 126 129 130 151 C3' A A 8 OK 149 152 153 173 C3' A A 9 OK 171 174 175 195 C3' G A 10 OK 193 196 197 218 C3' U A 11 OK 216 219 220 238 C3' G A 12 OK 236 239 240 261 C3' C A 13 OK 259 262 263 281 C3' A A 14 OK 279 282 283 303 C3' C A 15 OK 301 304 305 323 C3' A A 16 OK 321 324 325 345 C3' C A 17 OK 343 346 347 365 C3' A A 18 OK 363 366 367 387 C3' G A 19 OK 385 388 389 410 C3' C A 20 OK 408 411 412 430 C3' A A 21 OK 428 431 432 452 C3' A A 22 OK 450 453 454 474 C3' G A 23 OK 472 475 476 495 C3' C B 1 OK 493 496 497 515 C3' U B 2 OK 513 516 517 535 C3' U B 3 OK 533 536 537 555 C3' G B 4 OK 553 556 557 578 C3' C B 5 OK 576 579 580 598 C3' U B 6 OK 596 599 600 618 C3' G B 7 OK 616 619 620 641 C3' A B 8 OK 639 642 643 663 C3' A B 9 OK 661 664 665 685 C3' G B 10 OK 683 686 687 708 C3' U B 11 OK 706 709 710 728 C3' G B 12 OK 726 729 730 751 C3' C B 13 OK 749 752 753 771 C3' A B 14 OK 769 772 773 793 C3' C B 15 OK 791 794 795 813 C3' A B 16 OK 811 814 815 835 C3' C B 17 OK 833 836 837 855 C3' A B 18 OK 853 856 857 877 C3' G B 19 OK 875 878 879 900 C3' C B 20 OK 898 901 902 920 C3' A B 21 OK 918 921 922 942 C3' A B 22 OK 940 943 944 964 C3' G B 23 OK 962 965 966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' U A 3 OK 45 42 44 63 C4' G A 4 OK 65 62 64 86 C4' C A 5 OK 88 85 87 106 C4' U A 6 OK 108 105 107 126 C4' G A 7 OK 128 125 127 149 C4' A A 8 OK 151 148 150 171 C4' A A 9 OK 173 170 172 193 C4' G A 10 OK 195 192 194 216 C4' U A 11 OK 218 215 217 236 C4' G A 12 OK 238 235 237 259 C4' C A 13 OK 261 258 260 279 C4' A A 14 OK 281 278 280 301 C4' C A 15 OK 303 300 302 321 C4' A A 16 OK 323 320 322 343 C4' C A 17 OK 345 342 344 363 C4' A A 18 OK 365 362 364 385 C4' G A 19 OK 387 384 386 408 C4' C A 20 OK 410 407 409 428 C4' A A 21 OK 430 427 429 450 C4' A A 22 OK 452 449 451 472 C4' G A 23 OK 474 471 473 493 C4' C B 1 OK 495 492 494 513 C4' U B 2 OK 515 512 514 533 C4' U B 3 OK 535 532 534 553 C4' G B 4 OK 555 552 554 576 C4' C B 5 OK 578 575 577 596 C4' U B 6 OK 598 595 597 616 C4' G B 7 OK 618 615 617 639 C4' A B 8 OK 641 638 640 661 C4' A B 9 OK 663 660 662 683 C4' G B 10 OK 685 682 684 706 C4' U B 11 OK 708 705 707 726 C4' G B 12 OK 728 725 727 749 C4' C B 13 OK 751 748 750 769 C4' A B 14 OK 771 768 770 791 C4' C B 15 OK 793 790 792 811 C4' A B 16 OK 813 810 812 833 C4' C B 17 OK 835 832 834 853 C4' A B 18 OK 855 852 854 875 C4' G B 19 OK 877 874 876 898 C4' C B 20 OK 900 897 899 918 C4' A B 21 OK 920 917 919 940 C4' A B 22 OK 942 939 941 962 C4' G B 23 OK 964 961 963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' U A 2 21 23 42 C5' U A 3 41 43 62 C5' G A 4 61 63 85 C5' C A 5 84 86 105 C5' U A 6 104 106 125 C5' G A 7 124 126 148 C5' A A 8 147 149 170 C5' A A 9 169 171 192 C5' G A 10 191 193 215 C5' U A 11 214 216 235 C5' G A 12 234 236 258 C5' C A 13 257 259 278 C5' A A 14 277 279 300 C5' C A 15 299 301 320 C5' A A 16 319 321 342 C5' C A 17 341 343 362 C5' A A 18 361 363 384 C5' G A 19 383 385 407 C5' C A 20 406 408 427 C5' A A 21 426 428 449 C5' A A 22 448 450 471 C5' G A 23 470 472 492 C5' C B 1 491 493 512 C5' U B 2 511 513 532 C5' U B 3 531 533 552 C5' G B 4 551 553 575 C5' C B 5 574 576 595 C5' U B 6 594 596 615 C5' G B 7 614 616 638 C5' A B 8 637 639 660 C5' A B 9 659 661 682 C5' G B 10 681 683 705 C5' U B 11 704 706 725 C5' G B 12 724 726 748 C5' C B 13 747 749 768 C5' A B 14 767 769 790 C5' C B 15 789 791 810 C5' A B 16 809 811 832 C5' C B 17 831 833 852 C5' A B 18 851 853 874 C5' G B 19 873 875 897 C5' C B 20 896 898 917 C5' A B 21 916 918 939 C5' A B 22 938 940 961 C5' G B 23 960 962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P U A 3 distorted distorted 26 39 40 41 58 P G A 4 distorted distorted 46 59 60 61 81 P C A 5 distorted distorted 66 82 83 84 101 P U A 6 distorted distorted 89 102 103 104 121 P G A 7 distorted distorted 109 122 123 124 144 P A A 8 distorted distorted 129 145 146 147 166 P A A 9 distorted distorted 152 167 168 169 188 P G A 10 distorted distorted 174 189 190 191 211 P U A 11 distorted distorted 196 212 213 214 231 P G A 12 distorted distorted 219 232 233 234 254 P C A 13 distorted distorted 239 255 256 257 274 P A A 14 distorted distorted 262 275 276 277 296 P C A 15 distorted distorted 282 297 298 299 316 P A A 16 distorted distorted 304 317 318 319 338 P C A 17 distorted distorted 324 339 340 341 358 P A A 18 distorted distorted 346 359 360 361 380 P G A 19 distorted distorted 366 381 382 383 403 P C A 20 distorted distorted 388 404 405 406 423 P A A 21 distorted distorted 411 424 425 426 445 P A A 22 distorted distorted 431 446 447 448 467 P G A 23 distorted distorted 453 468 469 470 508 P U B 2 distorted distorted 496 509 510 511 528 P U B 3 distorted distorted 516 529 530 531 548 P G B 4 distorted distorted 536 549 550 551 571 P C B 5 distorted distorted 556 572 573 574 591 P U B 6 distorted distorted 579 592 593 594 611 P G B 7 distorted distorted 599 612 613 614 634 P A B 8 distorted distorted 619 635 636 637 656 P A B 9 distorted distorted 642 657 658 659 678 P G B 10 distorted distorted 664 679 680 681 701 P U B 11 distorted distorted 686 702 703 704 721 P G B 12 distorted distorted 709 722 723 724 744 P C B 13 distorted distorted 729 745 746 747 764 P A B 14 distorted distorted 752 765 766 767 786 P C B 15 distorted distorted 772 787 788 789 806 P A B 16 distorted distorted 794 807 808 809 828 P C B 17 distorted distorted 814 829 830 831 848 P A B 18 distorted distorted 836 849 850 851 870 P G B 19 distorted distorted 856 871 872 873 893 P C B 20 distorted distorted 878 894 895 896 913 P A B 21 distorted distorted 901 914 915 916 935 P A B 22 distorted distorted 921 936 937 938 957 P G B 23 distorted distorted 943 958 959 960 ---------------------------------------------------------------------------------