ID code: '2AWE' 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 25 C1' BGM A 2 beta 24 26 37 52 C1' G A 3 beta 47 53 50 75 C1' U A 4 beta 70 76 73 95 C1' G A 5 beta 90 96 93 118 C1' U A 6 beta 113 119 116 136 C1' U B 1 beta 131 137 134 152 C1' BGM B 2 beta 151 153 164 179 C1' G B 3 beta 174 180 177 202 C1' U B 4 beta 197 203 200 222 C1' G B 5 beta 217 223 220 245 C1' U B 6 beta 240 246 243 263 C1' U C 1 beta 258 264 261 279 C1' BGM C 2 beta 278 280 291 306 C1' G C 3 beta 301 307 304 329 C1' U C 4 beta 324 330 327 349 C1' G C 5 beta 344 350 347 372 C1' U C 6 beta 367 373 370 390 C1' U D 1 beta 385 391 388 406 C1' BGM D 2 beta 405 407 418 433 C1' G D 3 beta 428 434 431 456 C1' U D 4 beta 451 457 454 476 C1' G D 5 beta 471 477 474 499 C1' U D 6 beta 494 500 497 517 C1' U E 1 beta 512 518 515 533 C1' BGM E 2 beta 532 534 545 560 C1' G E 3 beta 555 561 558 583 C1' U E 4 beta 578 584 581 603 C1' G E 5 beta 598 604 601 626 C1' U E 6 beta 621 627 624 644 C1' U F 1 beta 639 645 642 660 C1' BGM F 2 beta 659 661 672 687 C1' G F 3 beta 682 688 685 710 C1' U F 4 beta 705 711 708 730 C1' G F 5 beta 725 731 728 753 C1' U F 6 beta 748 754 751 771 C1' U G 1 beta 766 772 769 787 C1' BGM G 2 beta 786 788 799 814 C1' G G 3 beta 809 815 812 841 C1' G G 5 beta 836 842 839 864 C1' U G 6 beta 859 865 862 882 C1' U H 1 beta 877 883 880 898 C1' BGM H 2 beta 897 899 910 925 C1' G H 3 beta 920 926 923 948 C1' U H 4 beta 943 949 946 968 C1' G H 5 beta 963 969 966 991 C1' U H 6 beta 986 992 989 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 37 C2' BGM A 2 25 38 50 C2' G A 3 OK 52 48 51 73 C2' U A 4 OK 75 71 74 93 C2' G A 5 OK 95 91 94 116 C2' U A 6 OK 118 114 117 134 C2' U B 1 OK 136 132 135 164 C2' BGM B 2 152 165 177 C2' G B 3 OK 179 175 178 200 C2' U B 4 OK 202 198 201 220 C2' G B 5 OK 222 218 221 243 C2' U B 6 OK 245 241 244 261 C2' U C 1 OK 263 259 262 291 C2' BGM C 2 279 292 304 C2' G C 3 OK 306 302 305 327 C2' U C 4 OK 329 325 328 347 C2' G C 5 OK 349 345 348 370 C2' U C 6 OK 372 368 371 388 C2' U D 1 OK 390 386 389 418 C2' BGM D 2 406 419 431 C2' G D 3 OK 433 429 432 454 C2' U D 4 OK 456 452 455 474 C2' G D 5 OK 476 472 475 497 C2' U D 6 OK 499 495 498 515 C2' U E 1 OK 517 513 516 545 C2' BGM E 2 533 546 558 C2' G E 3 OK 560 556 559 581 C2' U E 4 OK 583 579 582 601 C2' G E 5 OK 603 599 602 624 C2' U E 6 OK 626 622 625 642 C2' U F 1 OK 644 640 643 672 C2' BGM F 2 660 673 685 C2' G F 3 OK 687 683 686 708 C2' U F 4 OK 710 706 709 728 C2' G F 5 OK 730 726 729 751 C2' U F 6 OK 753 749 752 769 C2' U G 1 OK 771 767 770 799 C2' BGM G 2 787 800 812 C2' G G 3 OK 814 810 813 839 C2' G G 5 OK 841 837 840 862 C2' U G 6 OK 864 860 863 880 C2' U H 1 OK 882 878 881 910 C2' BGM H 2 898 911 923 C2' G H 3 OK 925 921 924 946 C2' U H 4 OK 948 944 947 966 C2' G H 5 OK 968 964 967 989 C2' U H 6 OK 991 987 990 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK 3 6 7 38 C3' BGM A 2 OK 23 39 37 48 C3' G A 3 OK 46 49 50 71 C3' U A 4 OK 69 72 73 91 C3' G A 5 OK 89 92 93 114 C3' U A 6 OK 112 115 116 132 C3' U B 1 OK 130 133 134 165 C3' BGM B 2 OK 150 166 164 175 C3' G B 3 OK 173 176 177 198 C3' U B 4 OK 196 199 200 218 C3' G B 5 OK 216 219 220 241 C3' U B 6 OK 239 242 243 259 C3' U C 1 OK 257 260 261 292 C3' BGM C 2 OK 277 293 291 302 C3' G C 3 OK 300 303 304 325 C3' U C 4 OK 323 326 327 345 C3' G C 5 OK 343 346 347 368 C3' U C 6 OK 366 369 370 386 C3' U D 1 OK 384 387 388 419 C3' BGM D 2 OK 404 420 418 429 C3' G D 3 OK 427 430 431 452 C3' U D 4 OK 450 453 454 472 C3' G D 5 OK 470 473 474 495 C3' U D 6 OK 493 496 497 513 C3' U E 1 OK 511 514 515 546 C3' BGM E 2 OK 531 547 545 556 C3' G E 3 OK 554 557 558 579 C3' U E 4 OK 577 580 581 599 C3' G E 5 OK 597 600 601 622 C3' U E 6 OK 620 623 624 640 C3' U F 1 OK 638 641 642 673 C3' BGM F 2 OK 658 674 672 683 C3' G F 3 OK 681 684 685 706 C3' U F 4 OK 704 707 708 726 C3' G F 5 OK 724 727 728 749 C3' U F 6 OK 747 750 751 767 C3' U G 1 OK 765 768 769 800 C3' BGM G 2 OK 785 801 799 810 C3' G G 3 OK 808 811 812 837 C3' G G 5 OK 835 838 839 860 C3' U G 6 OK 858 861 862 878 C3' U H 1 OK 876 879 880 911 C3' BGM H 2 OK 896 912 910 921 C3' G H 3 OK 919 922 923 944 C3' U H 4 OK 942 945 946 964 C3' G H 5 OK 962 965 966 987 C3' U H 6 OK 985 988 989 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK 5 2 4 23 C4' BGM A 2 OK 38 22 24 46 C4' G A 3 OK 48 45 47 69 C4' U A 4 OK 71 68 70 89 C4' G A 5 OK 91 88 90 112 C4' U A 6 OK 114 111 113 130 C4' U B 1 OK 132 129 131 150 C4' BGM B 2 OK 165 149 151 173 C4' G B 3 OK 175 172 174 196 C4' U B 4 OK 198 195 197 216 C4' G B 5 OK 218 215 217 239 C4' U B 6 OK 241 238 240 257 C4' U C 1 OK 259 256 258 277 C4' BGM C 2 OK 292 276 278 300 C4' G C 3 OK 302 299 301 323 C4' U C 4 OK 325 322 324 343 C4' G C 5 OK 345 342 344 366 C4' U C 6 OK 368 365 367 384 C4' U D 1 OK 386 383 385 404 C4' BGM D 2 OK 419 403 405 427 C4' G D 3 OK 429 426 428 450 C4' U D 4 OK 452 449 451 470 C4' G D 5 OK 472 469 471 493 C4' U D 6 OK 495 492 494 511 C4' U E 1 OK 513 510 512 531 C4' BGM E 2 OK 546 530 532 554 C4' G E 3 OK 556 553 555 577 C4' U E 4 OK 579 576 578 597 C4' G E 5 OK 599 596 598 620 C4' U E 6 OK 622 619 621 638 C4' U F 1 OK 640 637 639 658 C4' BGM F 2 OK 673 657 659 681 C4' G F 3 OK 683 680 682 704 C4' U F 4 OK 706 703 705 724 C4' G F 5 OK 726 723 725 747 C4' U F 6 OK 749 746 748 765 C4' U G 1 OK 767 764 766 785 C4' BGM G 2 OK 800 784 786 808 C4' G G 3 OK 810 807 809 835 C4' G G 5 OK 837 834 836 858 C4' U G 6 OK 860 857 859 876 C4' U H 1 OK 878 875 877 896 C4' BGM H 2 OK 911 895 897 919 C4' G H 3 OK 921 918 920 942 C4' U H 4 OK 944 941 943 962 C4' G H 5 OK 964 961 963 985 C4' U H 6 OK 987 984 986 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 1 3 22 C5' BGM A 2 21 23 45 C5' G A 3 44 46 68 C5' U A 4 67 69 88 C5' G A 5 87 89 111 C5' U A 6 110 112 129 C5' U B 1 128 130 149 C5' BGM B 2 148 150 172 C5' G B 3 171 173 195 C5' U B 4 194 196 215 C5' G B 5 214 216 238 C5' U B 6 237 239 256 C5' U C 1 255 257 276 C5' BGM C 2 275 277 299 C5' G C 3 298 300 322 C5' U C 4 321 323 342 C5' G C 5 341 343 365 C5' U C 6 364 366 383 C5' U D 1 382 384 403 C5' BGM D 2 402 404 426 C5' G D 3 425 427 449 C5' U D 4 448 450 469 C5' G D 5 468 470 492 C5' U D 6 491 493 510 C5' U E 1 509 511 530 C5' BGM E 2 529 531 553 C5' G E 3 552 554 576 C5' U E 4 575 577 596 C5' G E 5 595 597 619 C5' U E 6 618 620 637 C5' U F 1 636 638 657 C5' BGM F 2 656 658 680 C5' G F 3 679 681 703 C5' U F 4 702 704 723 C5' G F 5 722 724 746 C5' U F 6 745 747 764 C5' U G 1 763 765 784 C5' BGM G 2 783 785 807 C5' G G 3 806 808 834 C5' G G 5 833 835 857 C5' U G 6 856 858 875 C5' U H 1 874 876 895 C5' BGM H 2 894 896 918 C5' G H 3 917 919 941 C5' U H 4 940 942 961 C5' G H 5 960 962 984 C5' U H 6 983 985 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P BGM A 2 distorted distorted 6 19 20 21 41 P G A 3 distorted distorted 39 42 43 44 64 P U A 4 distorted distorted 49 65 66 67 84 P G A 5 distorted distorted 72 85 86 87 107 P U A 6 distorted distorted 92 108 109 110 145 P BGM B 2 distorted distorted 133 146 147 148 168 P G B 3 distorted distorted 166 169 170 171 191 P U B 4 distorted distorted 176 192 193 194 211 P G B 5 distorted distorted 199 212 213 214 234 P U B 6 distorted distorted 219 235 236 237 272 P BGM C 2 distorted distorted 260 273 274 275 295 P G C 3 distorted distorted 293 296 297 298 318 P U C 4 distorted distorted 303 319 320 321 338 P G C 5 distorted distorted 326 339 340 341 361 P U C 6 distorted distorted 346 362 363 364 399 P BGM D 2 distorted distorted 387 400 401 402 422 P G D 3 distorted distorted 420 423 424 425 445 P U D 4 distorted distorted 430 446 447 448 465 P G D 5 distorted distorted 453 466 467 468 488 P U D 6 distorted distorted 473 489 490 491 526 P BGM E 2 distorted distorted 514 527 528 529 549 P G E 3 distorted distorted 547 550 551 552 572 P U E 4 distorted distorted 557 573 574 575 592 P G E 5 distorted distorted 580 593 594 595 615 P U E 6 distorted distorted 600 616 617 618 653 P BGM F 2 distorted distorted 641 654 655 656 676 P G F 3 distorted distorted 674 677 678 679 699 P U F 4 distorted distorted 684 700 701 702 719 P G F 5 distorted distorted 707 720 721 722 742 P U F 6 distorted distorted 727 743 744 745 780 P BGM G 2 distorted distorted 768 781 782 783 803 P G G 3 distorted distorted 801 804 805 806 826 P U G 4 distorted distorted 811 827 828 829 830 P G G 5 distorted distorted 831 832 833 853 P U G 6 distorted distorted 838 854 855 856 891 P BGM H 2 distorted distorted 879 892 893 894 914 P G H 3 distorted distorted 912 915 916 917 937 P U H 4 distorted distorted 922 938 939 940 957 P G H 5 distorted distorted 945 958 959 960 980 P U H 6 distorted distorted 965 981 982 983 ---------------------------------------------------------------------------------