ID code: '4PDQ' 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 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' G A 3 beta 44 50 47 72 C1' C A 4 beta 67 73 70 92 C1' G A 5 beta 87 93 90 115 C1' U A 6 beta 110 116 113 135 C1' C A 7 beta 130 136 133 155 C1' A A 8 beta 150 156 153 177 C1' C A 9 beta 172 178 175 197 C1' G A 10 beta 192 198 195 220 C1' C A 11 beta 215 221 218 240 C1' C A 12 beta 235 241 238 260 C1' G A 13 beta 255 261 258 283 C1' G A 14 beta 278 284 281 306 C1' C A 15 beta 301 307 304 326 C1' G A 16 beta 321 327 324 349 C1' A A 17 beta 344 350 347 371 C1' A A 18 beta 366 372 369 393 C1' G A 19 beta 388 394 391 416 C1' U A 20 beta 411 417 414 436 C1' C A 21 beta 431 437 434 456 C1' G A 22 beta 451 457 454 479 C1' C A 23 beta 474 480 477 497 C1' U B 24 beta 492 498 495 517 C1' U B 25 beta 512 518 515 537 C1' G B 26 beta 532 538 535 560 C1' C B 27 beta 555 561 558 580 C1' G B 28 beta 575 581 578 603 C1' U B 29 beta 598 604 601 623 C1' C B 30 beta 618 624 621 643 C1' A B 31 beta 638 644 641 665 C1' C B 32 beta 660 666 663 685 C1' G B 33 beta 680 686 683 708 C1' C B 34 beta 703 709 706 728 C1' C B 35 beta 723 729 726 748 C1' G B 36 beta 743 749 746 771 C1' G B 37 beta 766 772 769 794 C1' C B 38 beta 789 795 792 814 C1' G B 39 beta 809 815 812 837 C1' A B 40 beta 832 838 835 859 C1' A B 41 beta 854 860 857 881 C1' G B 42 beta 876 882 879 904 C1' U B 43 beta 899 905 902 924 C1' C B 44 beta 919 925 922 944 C1' G B 45 beta 939 945 942 967 C1' C B 46 beta 962 968 965 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' G A 3 OK 49 45 48 70 C2' C A 4 OK 72 68 71 90 C2' G A 5 OK 92 88 91 113 C2' U A 6 OK 115 111 114 133 C2' C A 7 OK 135 131 134 153 C2' A A 8 OK 155 151 154 175 C2' C A 9 OK 177 173 176 195 C2' G A 10 OK 197 193 196 218 C2' C A 11 OK 220 216 219 238 C2' C A 12 OK 240 236 239 258 C2' G A 13 OK 260 256 259 281 C2' G A 14 OK 283 279 282 304 C2' C A 15 OK 306 302 305 324 C2' G A 16 OK 326 322 325 347 C2' A A 17 OK 349 345 348 369 C2' A A 18 OK 371 367 370 391 C2' G A 19 OK 393 389 392 414 C2' U A 20 OK 416 412 415 434 C2' C A 21 OK 436 432 435 454 C2' G A 22 OK 456 452 455 477 C2' C A 23 OK 479 475 478 495 C2' U B 24 OK 497 493 496 515 C2' U B 25 OK 517 513 516 535 C2' G B 26 OK 537 533 536 558 C2' C B 27 OK 560 556 559 578 C2' G B 28 OK 580 576 579 601 C2' U B 29 OK 603 599 602 621 C2' C B 30 OK 623 619 622 641 C2' A B 31 OK 643 639 642 663 C2' C B 32 OK 665 661 664 683 C2' G B 33 OK 685 681 684 706 C2' C B 34 OK 708 704 707 726 C2' C B 35 OK 728 724 727 746 C2' G B 36 OK 748 744 747 769 C2' G B 37 OK 771 767 770 792 C2' C B 38 OK 794 790 793 812 C2' G B 39 OK 814 810 813 835 C2' A B 40 OK 837 833 836 857 C2' A B 41 OK 859 855 858 879 C2' G B 42 OK 881 877 880 902 C2' U B 43 OK 904 900 903 922 C2' C B 44 OK 924 920 923 942 C2' G B 45 OK 944 940 943 965 C2' C B 46 OK 967 963 966 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' G A 3 OK 43 46 47 68 C3' C A 4 OK 66 69 70 88 C3' G A 5 OK 86 89 90 111 C3' U A 6 OK 109 112 113 131 C3' C A 7 OK 129 132 133 151 C3' A A 8 OK 149 152 153 173 C3' C A 9 OK 171 174 175 193 C3' G A 10 OK 191 194 195 216 C3' C A 11 OK 214 217 218 236 C3' C A 12 OK 234 237 238 256 C3' G A 13 OK 254 257 258 279 C3' G A 14 OK 277 280 281 302 C3' C A 15 OK 300 303 304 322 C3' G A 16 OK 320 323 324 345 C3' A A 17 OK 343 346 347 367 C3' A A 18 OK 365 368 369 389 C3' G A 19 OK 387 390 391 412 C3' U A 20 OK 410 413 414 432 C3' C A 21 OK 430 433 434 452 C3' G A 22 OK 450 453 454 475 C3' C A 23 OK 473 476 477 493 C3' U B 24 OK 491 494 495 513 C3' U B 25 OK 511 514 515 533 C3' G B 26 OK 531 534 535 556 C3' C B 27 OK 554 557 558 576 C3' G B 28 OK 574 577 578 599 C3' U B 29 OK 597 600 601 619 C3' C B 30 OK 617 620 621 639 C3' A B 31 OK 637 640 641 661 C3' C B 32 OK 659 662 663 681 C3' G B 33 OK 679 682 683 704 C3' C B 34 OK 702 705 706 724 C3' C B 35 OK 722 725 726 744 C3' G B 36 OK 742 745 746 767 C3' G B 37 OK 765 768 769 790 C3' C B 38 OK 788 791 792 810 C3' G B 39 OK 808 811 812 833 C3' A B 40 OK 831 834 835 855 C3' A B 41 OK 853 856 857 877 C3' G B 42 OK 875 878 879 900 C3' U B 43 OK 898 901 902 920 C3' C B 44 OK 918 921 922 940 C3' G B 45 OK 938 941 942 963 C3' C B 46 OK 961 964 965 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' G A 3 OK 45 42 44 66 C4' C A 4 OK 68 65 67 86 C4' G A 5 OK 88 85 87 109 C4' U A 6 OK 111 108 110 129 C4' C A 7 OK 131 128 130 149 C4' A A 8 OK 151 148 150 171 C4' C A 9 OK 173 170 172 191 C4' G A 10 OK 193 190 192 214 C4' C A 11 OK 216 213 215 234 C4' C A 12 OK 236 233 235 254 C4' G A 13 OK 256 253 255 277 C4' G A 14 OK 279 276 278 300 C4' C A 15 OK 302 299 301 320 C4' G A 16 OK 322 319 321 343 C4' A A 17 OK 345 342 344 365 C4' A A 18 OK 367 364 366 387 C4' G A 19 OK 389 386 388 410 C4' U A 20 OK 412 409 411 430 C4' C A 21 OK 432 429 431 450 C4' G A 22 OK 452 449 451 473 C4' C A 23 OK 475 472 474 491 C4' U B 24 OK 493 490 492 511 C4' U B 25 OK 513 510 512 531 C4' G B 26 OK 533 530 532 554 C4' C B 27 OK 556 553 555 574 C4' G B 28 OK 576 573 575 597 C4' U B 29 OK 599 596 598 617 C4' C B 30 OK 619 616 618 637 C4' A B 31 OK 639 636 638 659 C4' C B 32 OK 661 658 660 679 C4' G B 33 OK 681 678 680 702 C4' C B 34 OK 704 701 703 722 C4' C B 35 OK 724 721 723 742 C4' G B 36 OK 744 741 743 765 C4' G B 37 OK 767 764 766 788 C4' C B 38 OK 790 787 789 808 C4' G B 39 OK 810 807 809 831 C4' A B 40 OK 833 830 832 853 C4' A B 41 OK 855 852 854 875 C4' G B 42 OK 877 874 876 898 C4' U B 43 OK 900 897 899 918 C4' C B 44 OK 920 917 919 938 C4' G B 45 OK 940 937 939 961 C4' C B 46 OK 963 960 962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 1 3 22 C5' U A 2 21 23 42 C5' G A 3 41 43 65 C5' C A 4 64 66 85 C5' G A 5 84 86 108 C5' U A 6 107 109 128 C5' C A 7 127 129 148 C5' A A 8 147 149 170 C5' C A 9 169 171 190 C5' G A 10 189 191 213 C5' C A 11 212 214 233 C5' C A 12 232 234 253 C5' G A 13 252 254 276 C5' G A 14 275 277 299 C5' C A 15 298 300 319 C5' G A 16 318 320 342 C5' A A 17 341 343 364 C5' A A 18 363 365 386 C5' G A 19 385 387 409 C5' U A 20 408 410 429 C5' C A 21 428 430 449 C5' G A 22 448 450 472 C5' C A 23 471 473 490 C5' U B 24 489 491 510 C5' U B 25 509 511 530 C5' G B 26 529 531 553 C5' C B 27 552 554 573 C5' G B 28 572 574 596 C5' U B 29 595 597 616 C5' C B 30 615 617 636 C5' A B 31 635 637 658 C5' C B 32 657 659 678 C5' G B 33 677 679 701 C5' C B 34 700 702 721 C5' C B 35 720 722 741 C5' G B 36 740 742 764 C5' G B 37 763 765 787 C5' C B 38 786 788 807 C5' G B 39 806 808 830 C5' A B 40 829 831 852 C5' A B 41 851 853 874 C5' G B 42 873 875 897 C5' U B 43 896 898 917 C5' C B 44 916 918 937 C5' G B 45 936 938 960 C5' C B 46 959 961 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P G A 3 distorted distorted 26 39 40 41 61 P C A 4 distorted distorted 46 62 63 64 81 P G A 5 distorted distorted 69 82 83 84 104 P U A 6 distorted distorted 89 105 106 107 124 P C A 7 distorted distorted 112 125 126 127 144 P A A 8 distorted distorted 132 145 146 147 166 P C A 9 distorted distorted 152 167 168 169 186 P G A 10 distorted distorted 174 187 188 189 209 P C A 11 distorted distorted 194 210 211 212 229 P C A 12 distorted distorted 217 230 231 232 249 P G A 13 distorted distorted 237 250 251 252 272 P G A 14 distorted distorted 257 273 274 275 295 P C A 15 distorted distorted 280 296 297 298 315 P G A 16 distorted distorted 303 316 317 318 338 P A A 17 distorted distorted 323 339 340 341 360 P A A 18 distorted distorted 346 361 362 363 382 P G A 19 distorted distorted 368 383 384 385 405 P U A 20 distorted distorted 390 406 407 408 425 P C A 21 distorted distorted 413 426 427 428 445 P G A 22 distorted distorted 433 446 447 448 468 P C A 23 distorted distorted 453 469 470 471 506 P U B 25 distorted distorted 494 507 508 509 526 P G B 26 distorted distorted 514 527 528 529 549 P C B 27 distorted distorted 534 550 551 552 569 P G B 28 distorted distorted 557 570 571 572 592 P U B 29 distorted distorted 577 593 594 595 612 P C B 30 distorted distorted 600 613 614 615 632 P A B 31 distorted distorted 620 633 634 635 654 P C B 32 distorted distorted 640 655 656 657 674 P G B 33 distorted distorted 662 675 676 677 697 P C B 34 distorted distorted 682 698 699 700 717 P C B 35 distorted distorted 705 718 719 720 737 P G B 36 distorted distorted 725 738 739 740 760 P G B 37 distorted distorted 745 761 762 763 783 P C B 38 distorted distorted 768 784 785 786 803 P G B 39 distorted distorted 791 804 805 806 826 P A B 40 distorted distorted 811 827 828 829 848 P A B 41 distorted distorted 834 849 850 851 870 P G B 42 distorted distorted 856 871 872 873 893 P U B 43 distorted distorted 878 894 895 896 913 P C B 44 distorted distorted 901 914 915 916 933 P G B 45 distorted distorted 921 934 935 936 956 P C B 46 distorted distorted 941 957 958 959 ---------------------------------------------------------------------------------