ID code: '2PXT' 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 130 beta 4 10 7 32 C1' C B 131 beta 27 33 30 52 C1' U B 132 beta 47 53 50 72 C1' G B 133 beta 67 73 70 95 C1' C B 134 beta 90 96 93 115 C1' U B 135 beta 110 116 113 135 C1' G B 136 beta 130 136 133 158 C1' U B 137 beta 153 159 156 178 C1' U B 138 beta 173 179 176 198 C1' U B 139 beta 193 199 196 218 C1' A B 140 beta 213 219 216 240 C1' C B 141 beta 235 241 238 260 C1' C B 142 beta 255 261 258 280 C1' A B 143 beta 275 281 278 302 C1' G B 144 beta 297 303 300 325 C1' G B 145 beta 320 326 323 348 C1' U B 146 beta 343 349 346 368 C1' C B 147 beta 363 369 366 388 C1' A B 148 beta 383 389 386 410 C1' G B 149 beta 405 411 408 433 C1' G B 150 beta 428 434 431 456 C1' U B 151 beta 451 457 454 476 C1' C B 152 beta 471 477 474 496 C1' C B 153 beta 491 497 494 516 C1' G B 154 beta 511 517 514 539 C1' A B 155 beta 534 540 537 561 C1' A B 156 beta 556 562 559 583 C1' A B 157 beta 578 584 581 605 C1' G B 158 beta 600 606 603 628 C1' G B 159 beta 623 629 626 651 C1' A B 160 beta 646 652 649 673 C1' A B 161 beta 668 674 671 695 C1' G B 162 beta 690 696 693 718 C1' C B 163 beta 713 719 716 738 C1' A B 164 beta 733 739 736 760 C1' G B 165 beta 755 761 758 783 C1' C B 166 beta 778 784 781 803 C1' C B 167 beta 798 804 801 823 C1' A B 168 beta 818 824 821 845 C1' A B 169 beta 840 846 843 867 C1' G B 170 beta 862 868 865 890 C1' G B 171 beta 885 891 888 913 C1' C B 172 beta 908 914 911 933 C1' A B 173 beta 928 934 931 955 C1' G B 174 beta 950 956 953 978 C1' C B 175 beta 973 979 976 998 C1' G B 176 beta 993 999 996 1021 C1' G B 177 beta 1016 1022 1019 1044 C1' C B 178 beta 1039 1045 1042 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 130 OK 9 5 8 30 C2' C B 131 OK 32 28 31 50 C2' U B 132 OK 52 48 51 70 C2' G B 133 OK 72 68 71 93 C2' C B 134 OK 95 91 94 113 C2' U B 135 OK 115 111 114 133 C2' G B 136 OK 135 131 134 156 C2' U B 137 OK 158 154 157 176 C2' U B 138 OK 178 174 177 196 C2' U B 139 OK 198 194 197 216 C2' A B 140 OK 218 214 217 238 C2' C B 141 OK 240 236 239 258 C2' C B 142 OK 260 256 259 278 C2' A B 143 OK 280 276 279 300 C2' G B 144 OK 302 298 301 323 C2' G B 145 OK 325 321 324 346 C2' U B 146 OK 348 344 347 366 C2' C B 147 OK 368 364 367 386 C2' A B 148 OK 388 384 387 408 C2' G B 149 OK 410 406 409 431 C2' G B 150 OK 433 429 432 454 C2' U B 151 OK 456 452 455 474 C2' C B 152 OK 476 472 475 494 C2' C B 153 OK 496 492 495 514 C2' G B 154 OK 516 512 515 537 C2' A B 155 OK 539 535 538 559 C2' A B 156 OK 561 557 560 581 C2' A B 157 OK 583 579 582 603 C2' G B 158 OK 605 601 604 626 C2' G B 159 OK 628 624 627 649 C2' A B 160 OK 651 647 650 671 C2' A B 161 OK 673 669 672 693 C2' G B 162 OK 695 691 694 716 C2' C B 163 OK 718 714 717 736 C2' A B 164 OK 738 734 737 758 C2' G B 165 OK 760 756 759 781 C2' C B 166 OK 783 779 782 801 C2' C B 167 OK 803 799 802 821 C2' A B 168 OK 823 819 822 843 C2' A B 169 OK 845 841 844 865 C2' G B 170 OK 867 863 866 888 C2' G B 171 OK 890 886 889 911 C2' C B 172 OK 913 909 912 931 C2' A B 173 OK 933 929 932 953 C2' G B 174 OK 955 951 954 976 C2' C B 175 OK 978 974 977 996 C2' G B 176 OK 998 994 997 1019 C2' G B 177 OK 1021 1017 1020 1042 C2' C B 178 OK 1044 1040 1043 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 130 OK 3 6 7 28 C3' C B 131 OK 26 29 30 48 C3' U B 132 OK 46 49 50 68 C3' G B 133 OK 66 69 70 91 C3' C B 134 OK 89 92 93 111 C3' U B 135 OK 109 112 113 131 C3' G B 136 OK 129 132 133 154 C3' U B 137 OK 152 155 156 174 C3' U B 138 OK 172 175 176 194 C3' U B 139 OK 192 195 196 214 C3' A B 140 OK 212 215 216 236 C3' C B 141 OK 234 237 238 256 C3' C B 142 OK 254 257 258 276 C3' A B 143 OK 274 277 278 298 C3' G B 144 OK 296 299 300 321 C3' G B 145 OK 319 322 323 344 C3' U B 146 OK 342 345 346 364 C3' C B 147 OK 362 365 366 384 C3' A B 148 OK 382 385 386 406 C3' G B 149 OK 404 407 408 429 C3' G B 150 OK 427 430 431 452 C3' U B 151 OK 450 453 454 472 C3' C B 152 OK 470 473 474 492 C3' C B 153 OK 490 493 494 512 C3' G B 154 OK 510 513 514 535 C3' A B 155 OK 533 536 537 557 C3' A B 156 OK 555 558 559 579 C3' A B 157 OK 577 580 581 601 C3' G B 158 OK 599 602 603 624 C3' G B 159 OK 622 625 626 647 C3' A B 160 OK 645 648 649 669 C3' A B 161 OK 667 670 671 691 C3' G B 162 OK 689 692 693 714 C3' C B 163 OK 712 715 716 734 C3' A B 164 OK 732 735 736 756 C3' G B 165 OK 754 757 758 779 C3' C B 166 OK 777 780 781 799 C3' C B 167 OK 797 800 801 819 C3' A B 168 OK 817 820 821 841 C3' A B 169 OK 839 842 843 863 C3' G B 170 OK 861 864 865 886 C3' G B 171 OK 884 887 888 909 C3' C B 172 OK 907 910 911 929 C3' A B 173 OK 927 930 931 951 C3' G B 174 OK 949 952 953 974 C3' C B 175 OK 972 975 976 994 C3' G B 176 OK 992 995 996 1017 C3' G B 177 OK 1015 1018 1019 1040 C3' C B 178 OK 1038 1041 1042 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 130 OK 5 2 4 26 C4' C B 131 OK 28 25 27 46 C4' U B 132 OK 48 45 47 66 C4' G B 133 OK 68 65 67 89 C4' C B 134 OK 91 88 90 109 C4' U B 135 OK 111 108 110 129 C4' G B 136 OK 131 128 130 152 C4' U B 137 OK 154 151 153 172 C4' U B 138 OK 174 171 173 192 C4' U B 139 OK 194 191 193 212 C4' A B 140 OK 214 211 213 234 C4' C B 141 OK 236 233 235 254 C4' C B 142 OK 256 253 255 274 C4' A B 143 OK 276 273 275 296 C4' G B 144 OK 298 295 297 319 C4' G B 145 OK 321 318 320 342 C4' U B 146 OK 344 341 343 362 C4' C B 147 OK 364 361 363 382 C4' A B 148 OK 384 381 383 404 C4' G B 149 OK 406 403 405 427 C4' G B 150 OK 429 426 428 450 C4' U B 151 OK 452 449 451 470 C4' C B 152 OK 472 469 471 490 C4' C B 153 OK 492 489 491 510 C4' G B 154 OK 512 509 511 533 C4' A B 155 OK 535 532 534 555 C4' A B 156 OK 557 554 556 577 C4' A B 157 OK 579 576 578 599 C4' G B 158 OK 601 598 600 622 C4' G B 159 OK 624 621 623 645 C4' A B 160 OK 647 644 646 667 C4' A B 161 OK 669 666 668 689 C4' G B 162 OK 691 688 690 712 C4' C B 163 OK 714 711 713 732 C4' A B 164 OK 734 731 733 754 C4' G B 165 OK 756 753 755 777 C4' C B 166 OK 779 776 778 797 C4' C B 167 OK 799 796 798 817 C4' A B 168 OK 819 816 818 839 C4' A B 169 OK 841 838 840 861 C4' G B 170 OK 863 860 862 884 C4' G B 171 OK 886 883 885 907 C4' C B 172 OK 909 906 908 927 C4' A B 173 OK 929 926 928 949 C4' G B 174 OK 951 948 950 972 C4' C B 175 OK 974 971 973 992 C4' G B 176 OK 994 991 993 1015 C4' G B 177 OK 1017 1014 1016 1038 C4' C B 178 OK 1040 1037 1039 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 130 1 3 25 C5' C B 131 24 26 45 C5' U B 132 44 46 65 C5' G B 133 64 66 88 C5' C B 134 87 89 108 C5' U B 135 107 109 128 C5' G B 136 127 129 151 C5' U B 137 150 152 171 C5' U B 138 170 172 191 C5' U B 139 190 192 211 C5' A B 140 210 212 233 C5' C B 141 232 234 253 C5' C B 142 252 254 273 C5' A B 143 272 274 295 C5' G B 144 294 296 318 C5' G B 145 317 319 341 C5' U B 146 340 342 361 C5' C B 147 360 362 381 C5' A B 148 380 382 403 C5' G B 149 402 404 426 C5' G B 150 425 427 449 C5' U B 151 448 450 469 C5' C B 152 468 470 489 C5' C B 153 488 490 509 C5' G B 154 508 510 532 C5' A B 155 531 533 554 C5' A B 156 553 555 576 C5' A B 157 575 577 598 C5' G B 158 597 599 621 C5' G B 159 620 622 644 C5' A B 160 643 645 666 C5' A B 161 665 667 688 C5' G B 162 687 689 711 C5' C B 163 710 712 731 C5' A B 164 730 732 753 C5' G B 165 752 754 776 C5' C B 166 775 777 796 C5' C B 167 795 797 816 C5' A B 168 815 817 838 C5' A B 169 837 839 860 C5' G B 170 859 861 883 C5' G B 171 882 884 906 C5' C B 172 905 907 926 C5' A B 173 925 927 948 C5' G B 174 947 949 971 C5' C B 175 970 972 991 C5' G B 176 990 992 1014 C5' G B 177 1013 1015 1037 C5' C B 178 1036 1038 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C B 131 distorted distorted 6 22 23 24 41 P U B 132 distorted distorted 29 42 43 44 61 P G B 133 distorted distorted 49 62 63 64 84 P C B 134 distorted distorted 69 85 86 87 104 P U B 135 distorted distorted 92 105 106 107 124 P G B 136 distorted distorted 112 125 126 127 147 P U B 137 distorted distorted 132 148 149 150 167 P U B 138 distorted distorted 155 168 169 170 187 P U B 139 distorted distorted 175 188 189 190 207 P A B 140 distorted distorted 195 208 209 210 229 P C B 141 distorted distorted 215 230 231 232 249 P C B 142 distorted distorted 237 250 251 252 269 P A B 143 distorted distorted 257 270 271 272 291 P G B 144 distorted distorted 277 292 293 294 314 P G B 145 distorted distorted 299 315 316 317 337 P U B 146 distorted distorted 322 338 339 340 357 P C B 147 distorted distorted 345 358 359 360 377 P A B 148 distorted distorted 365 378 379 380 399 P G B 149 distorted distorted 385 400 401 402 422 P G B 150 distorted distorted 407 423 424 425 445 P U B 151 distorted distorted 430 446 447 448 465 P C B 152 distorted distorted 453 466 467 468 485 P C B 153 distorted distorted 473 486 487 488 505 P G B 154 distorted distorted 493 506 507 508 528 P A B 155 distorted distorted 513 529 530 531 550 P A B 156 distorted distorted 536 551 552 553 572 P A B 157 distorted distorted 558 573 574 575 594 P G B 158 distorted distorted 580 595 596 597 617 P G B 159 distorted distorted 602 618 619 620 640 P A B 160 distorted distorted 625 641 642 643 662 P A B 161 distorted distorted 648 663 664 665 684 P G B 162 distorted distorted 670 685 686 687 707 P C B 163 distorted distorted 692 708 709 710 727 P A B 164 distorted distorted 715 728 729 730 749 P G B 165 distorted distorted 735 750 751 752 772 P C B 166 distorted distorted 757 773 774 775 792 P C B 167 distorted distorted 780 793 794 795 812 P A B 168 distorted distorted 800 813 814 815 834 P A B 169 distorted distorted 820 835 836 837 856 P G B 170 distorted distorted 842 857 858 859 879 P G B 171 distorted distorted 864 880 881 882 902 P C B 172 distorted distorted 887 903 904 905 922 P A B 173 distorted distorted 910 923 924 925 944 P G B 174 distorted distorted 930 945 946 947 967 P C B 175 distorted distorted 952 968 969 970 987 P G B 176 distorted distorted 975 988 989 990 1010 P G B 177 distorted distorted 995 1011 1012 1013 1033 P C B 178 distorted distorted 1018 1034 1035 1036 ---------------------------------------------------------------------------------