ID code: '2PXF' 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' G B 131 beta 27 33 30 55 C1' G B 132 beta 50 56 53 78 C1' G B 133 beta 73 79 76 101 C1' G B 134 beta 96 102 99 124 C1' U B 135 beta 119 125 122 144 C1' G B 136 beta 139 145 142 167 C1' U B 137 beta 162 168 165 187 C1' U B 138 beta 182 188 185 207 C1' U B 139 beta 202 208 205 227 C1' A B 140 beta 222 228 225 249 C1' C B 141 beta 244 250 247 269 C1' C B 142 beta 264 270 267 289 C1' A B 143 beta 284 290 287 311 C1' G B 144 beta 306 312 309 334 C1' G B 145 beta 329 335 332 357 C1' U B 146 beta 352 358 355 377 C1' C B 147 beta 372 378 375 397 C1' A B 148 beta 392 398 395 419 C1' G B 149 beta 414 420 417 442 C1' G B 150 beta 437 443 440 465 C1' U B 151 beta 460 466 463 485 C1' C B 152 beta 480 486 483 505 C1' C B 153 beta 500 506 503 525 C1' G B 154 beta 520 526 523 548 C1' A B 155 beta 543 549 546 570 C1' A B 156 beta 565 571 568 592 C1' A B 157 beta 587 593 590 614 C1' G B 158 beta 609 615 612 637 C1' G B 159 beta 632 638 635 660 C1' A B 160 beta 655 661 658 682 C1' A B 161 beta 677 683 680 704 C1' G B 162 beta 699 705 702 727 C1' C B 163 beta 722 728 725 747 C1' A B 164 beta 742 748 745 769 C1' G B 165 beta 764 770 767 792 C1' C B 166 beta 787 793 790 812 C1' C B 167 beta 807 813 810 832 C1' A B 168 beta 827 833 830 854 C1' A B 169 beta 849 855 852 876 C1' G B 170 beta 871 877 874 899 C1' G B 171 beta 894 900 897 922 C1' C B 172 beta 917 923 920 942 C1' A B 173 beta 937 943 940 964 C1' C B 174 beta 959 965 962 984 C1' U B 175 beta 979 985 982 1004 C1' U B 176 beta 999 1005 1002 1024 C1' C B 177 beta 1019 1025 1022 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' G B 131 OK 32 28 31 53 C2' G B 132 OK 55 51 54 76 C2' G B 133 OK 78 74 77 99 C2' G B 134 OK 101 97 100 122 C2' U B 135 OK 124 120 123 142 C2' G B 136 OK 144 140 143 165 C2' U B 137 OK 167 163 166 185 C2' U B 138 OK 187 183 186 205 C2' U B 139 OK 207 203 206 225 C2' A B 140 OK 227 223 226 247 C2' C B 141 OK 249 245 248 267 C2' C B 142 OK 269 265 268 287 C2' A B 143 OK 289 285 288 309 C2' G B 144 OK 311 307 310 332 C2' G B 145 OK 334 330 333 355 C2' U B 146 OK 357 353 356 375 C2' C B 147 OK 377 373 376 395 C2' A B 148 OK 397 393 396 417 C2' G B 149 OK 419 415 418 440 C2' G B 150 OK 442 438 441 463 C2' U B 151 OK 465 461 464 483 C2' C B 152 OK 485 481 484 503 C2' C B 153 OK 505 501 504 523 C2' G B 154 OK 525 521 524 546 C2' A B 155 OK 548 544 547 568 C2' A B 156 OK 570 566 569 590 C2' A B 157 OK 592 588 591 612 C2' G B 158 OK 614 610 613 635 C2' G B 159 OK 637 633 636 658 C2' A B 160 OK 660 656 659 680 C2' A B 161 OK 682 678 681 702 C2' G B 162 OK 704 700 703 725 C2' C B 163 OK 727 723 726 745 C2' A B 164 OK 747 743 746 767 C2' G B 165 OK 769 765 768 790 C2' C B 166 OK 792 788 791 810 C2' C B 167 OK 812 808 811 830 C2' A B 168 OK 832 828 831 852 C2' A B 169 OK 854 850 853 874 C2' G B 170 OK 876 872 875 897 C2' G B 171 OK 899 895 898 920 C2' C B 172 OK 922 918 921 940 C2' A B 173 OK 942 938 941 962 C2' C B 174 OK 964 960 963 982 C2' U B 175 OK 984 980 983 1002 C2' U B 176 OK 1004 1000 1003 1022 C2' C B 177 OK 1024 1020 1023 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' G B 131 OK 26 29 30 51 C3' G B 132 OK 49 52 53 74 C3' G B 133 OK 72 75 76 97 C3' G B 134 OK 95 98 99 120 C3' U B 135 OK 118 121 122 140 C3' G B 136 OK 138 141 142 163 C3' U B 137 OK 161 164 165 183 C3' U B 138 OK 181 184 185 203 C3' U B 139 OK 201 204 205 223 C3' A B 140 OK 221 224 225 245 C3' C B 141 OK 243 246 247 265 C3' C B 142 OK 263 266 267 285 C3' A B 143 OK 283 286 287 307 C3' G B 144 OK 305 308 309 330 C3' G B 145 OK 328 331 332 353 C3' U B 146 OK 351 354 355 373 C3' C B 147 OK 371 374 375 393 C3' A B 148 OK 391 394 395 415 C3' G B 149 OK 413 416 417 438 C3' G B 150 OK 436 439 440 461 C3' U B 151 OK 459 462 463 481 C3' C B 152 OK 479 482 483 501 C3' C B 153 OK 499 502 503 521 C3' G B 154 OK 519 522 523 544 C3' A B 155 OK 542 545 546 566 C3' A B 156 OK 564 567 568 588 C3' A B 157 OK 586 589 590 610 C3' G B 158 OK 608 611 612 633 C3' G B 159 OK 631 634 635 656 C3' A B 160 OK 654 657 658 678 C3' A B 161 OK 676 679 680 700 C3' G B 162 OK 698 701 702 723 C3' C B 163 OK 721 724 725 743 C3' A B 164 OK 741 744 745 765 C3' G B 165 OK 763 766 767 788 C3' C B 166 OK 786 789 790 808 C3' C B 167 OK 806 809 810 828 C3' A B 168 OK 826 829 830 850 C3' A B 169 OK 848 851 852 872 C3' G B 170 OK 870 873 874 895 C3' G B 171 OK 893 896 897 918 C3' C B 172 OK 916 919 920 938 C3' A B 173 OK 936 939 940 960 C3' C B 174 OK 958 961 962 980 C3' U B 175 OK 978 981 982 1000 C3' U B 176 OK 998 1001 1002 1020 C3' C B 177 OK 1018 1021 1022 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' G B 131 OK 28 25 27 49 C4' G B 132 OK 51 48 50 72 C4' G B 133 OK 74 71 73 95 C4' G B 134 OK 97 94 96 118 C4' U B 135 OK 120 117 119 138 C4' G B 136 OK 140 137 139 161 C4' U B 137 OK 163 160 162 181 C4' U B 138 OK 183 180 182 201 C4' U B 139 OK 203 200 202 221 C4' A B 140 OK 223 220 222 243 C4' C B 141 OK 245 242 244 263 C4' C B 142 OK 265 262 264 283 C4' A B 143 OK 285 282 284 305 C4' G B 144 OK 307 304 306 328 C4' G B 145 OK 330 327 329 351 C4' U B 146 OK 353 350 352 371 C4' C B 147 OK 373 370 372 391 C4' A B 148 OK 393 390 392 413 C4' G B 149 OK 415 412 414 436 C4' G B 150 OK 438 435 437 459 C4' U B 151 OK 461 458 460 479 C4' C B 152 OK 481 478 480 499 C4' C B 153 OK 501 498 500 519 C4' G B 154 OK 521 518 520 542 C4' A B 155 OK 544 541 543 564 C4' A B 156 OK 566 563 565 586 C4' A B 157 OK 588 585 587 608 C4' G B 158 OK 610 607 609 631 C4' G B 159 OK 633 630 632 654 C4' A B 160 OK 656 653 655 676 C4' A B 161 OK 678 675 677 698 C4' G B 162 OK 700 697 699 721 C4' C B 163 OK 723 720 722 741 C4' A B 164 OK 743 740 742 763 C4' G B 165 OK 765 762 764 786 C4' C B 166 OK 788 785 787 806 C4' C B 167 OK 808 805 807 826 C4' A B 168 OK 828 825 827 848 C4' A B 169 OK 850 847 849 870 C4' G B 170 OK 872 869 871 893 C4' G B 171 OK 895 892 894 916 C4' C B 172 OK 918 915 917 936 C4' A B 173 OK 938 935 937 958 C4' C B 174 OK 960 957 959 978 C4' U B 175 OK 980 977 979 998 C4' U B 176 OK 1000 997 999 1018 C4' C B 177 OK 1020 1017 1019 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' G B 131 24 26 48 C5' G B 132 47 49 71 C5' G B 133 70 72 94 C5' G B 134 93 95 117 C5' U B 135 116 118 137 C5' G B 136 136 138 160 C5' U B 137 159 161 180 C5' U B 138 179 181 200 C5' U B 139 199 201 220 C5' A B 140 219 221 242 C5' C B 141 241 243 262 C5' C B 142 261 263 282 C5' A B 143 281 283 304 C5' G B 144 303 305 327 C5' G B 145 326 328 350 C5' U B 146 349 351 370 C5' C B 147 369 371 390 C5' A B 148 389 391 412 C5' G B 149 411 413 435 C5' G B 150 434 436 458 C5' U B 151 457 459 478 C5' C B 152 477 479 498 C5' C B 153 497 499 518 C5' G B 154 517 519 541 C5' A B 155 540 542 563 C5' A B 156 562 564 585 C5' A B 157 584 586 607 C5' G B 158 606 608 630 C5' G B 159 629 631 653 C5' A B 160 652 654 675 C5' A B 161 674 676 697 C5' G B 162 696 698 720 C5' C B 163 719 721 740 C5' A B 164 739 741 762 C5' G B 165 761 763 785 C5' C B 166 784 786 805 C5' C B 167 804 806 825 C5' A B 168 824 826 847 C5' A B 169 846 848 869 C5' G B 170 868 870 892 C5' G B 171 891 893 915 C5' C B 172 914 916 935 C5' A B 173 934 936 957 C5' C B 174 956 958 977 C5' U B 175 976 978 997 C5' U B 176 996 998 1017 C5' C B 177 1016 1018 1037 C5' C B 178 1036 1038 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G B 131 distorted distorted 6 22 23 24 44 P G B 132 distorted distorted 29 45 46 47 67 P G B 133 distorted distorted 52 68 69 70 90 P G B 134 distorted distorted 75 91 92 93 113 P U B 135 distorted distorted 98 114 115 116 133 P G B 136 distorted distorted 121 134 135 136 156 P U B 137 distorted distorted 141 157 158 159 176 P U B 138 distorted distorted 164 177 178 179 196 P U B 139 distorted distorted 184 197 198 199 216 P A B 140 distorted distorted 204 217 218 219 238 P C B 141 distorted distorted 224 239 240 241 258 P C B 142 distorted distorted 246 259 260 261 278 P A B 143 distorted distorted 266 279 280 281 300 P G B 144 distorted distorted 286 301 302 303 323 P G B 145 distorted distorted 308 324 325 326 346 P U B 146 distorted distorted 331 347 348 349 366 P C B 147 distorted distorted 354 367 368 369 386 P A B 148 distorted distorted 374 387 388 389 408 P G B 149 distorted distorted 394 409 410 411 431 P G B 150 distorted distorted 416 432 433 434 454 P U B 151 distorted distorted 439 455 456 457 474 P C B 152 distorted distorted 462 475 476 477 494 P C B 153 distorted distorted 482 495 496 497 514 P G B 154 distorted distorted 502 515 516 517 537 P A B 155 distorted distorted 522 538 539 540 559 P A B 156 distorted distorted 545 560 561 562 581 P A B 157 distorted distorted 567 582 583 584 603 P G B 158 distorted distorted 589 604 605 606 626 P G B 159 distorted distorted 611 627 628 629 649 P A B 160 distorted distorted 634 650 651 652 671 P A B 161 distorted distorted 657 672 673 674 693 P G B 162 distorted distorted 679 694 695 696 716 P C B 163 distorted distorted 701 717 718 719 736 P A B 164 distorted distorted 724 737 738 739 758 P G B 165 distorted distorted 744 759 760 761 781 P C B 166 distorted distorted 766 782 783 784 801 P C B 167 distorted distorted 789 802 803 804 821 P A B 168 distorted distorted 809 822 823 824 843 P A B 169 distorted distorted 829 844 845 846 865 P G B 170 distorted distorted 851 866 867 868 888 P G B 171 distorted distorted 873 889 890 891 911 P C B 172 distorted distorted 896 912 913 914 931 P A B 173 distorted distorted 919 932 933 934 953 P C B 174 distorted distorted 939 954 955 956 973 P U B 175 distorted distorted 961 974 975 976 993 P U B 176 distorted distorted 981 994 995 996 1013 P C B 177 distorted distorted 1001 1014 1015 1016 1033 P C B 178 distorted distorted 1021 1034 1035 1036 ---------------------------------------------------------------------------------