ID code: '2PXD' 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' C B 134 beta 96 102 99 121 C1' U B 135 beta 116 122 119 141 C1' G B 136 beta 136 142 139 164 C1' U B 137 beta 159 165 162 184 C1' U B 138 beta 179 185 182 204 C1' U B 139 beta 199 205 202 224 C1' A B 140 beta 219 225 222 246 C1' C B 141 beta 241 247 244 266 C1' C B 142 beta 261 267 264 286 C1' A B 143 beta 281 287 284 308 C1' G B 144 beta 303 309 306 331 C1' G B 145 beta 326 332 329 354 C1' U B 146 beta 349 355 352 374 C1' C B 147 beta 369 375 372 394 C1' A B 148 beta 389 395 392 416 C1' G B 149 beta 411 417 414 439 C1' G B 150 beta 434 440 437 462 C1' U B 151 beta 457 463 460 482 C1' C B 152 beta 477 483 480 502 C1' C B 153 beta 497 503 500 522 C1' G B 154 beta 517 523 520 545 C1' A B 155 beta 540 546 543 567 C1' A B 156 beta 562 568 565 589 C1' A B 157 beta 584 590 587 611 C1' G B 158 beta 606 612 609 634 C1' G B 159 beta 629 635 632 657 C1' A B 160 beta 652 658 655 679 C1' A B 161 beta 674 680 677 701 C1' G B 162 beta 696 702 699 724 C1' C B 163 beta 719 725 722 744 C1' A B 164 beta 739 745 742 766 C1' G B 165 beta 761 767 764 789 C1' C B 166 beta 784 790 787 809 C1' C B 167 beta 804 810 807 829 C1' A B 168 beta 824 830 827 851 C1' A B 169 beta 846 852 849 873 C1' G B 170 beta 868 874 871 896 C1' G B 171 beta 891 897 894 919 C1' C B 172 beta 914 920 917 939 C1' A B 173 beta 934 940 937 961 C1' G B 174 beta 956 962 959 984 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' C B 134 OK 101 97 100 119 C2' U B 135 OK 121 117 120 139 C2' G B 136 OK 141 137 140 162 C2' U B 137 OK 164 160 163 182 C2' U B 138 OK 184 180 183 202 C2' U B 139 OK 204 200 203 222 C2' A B 140 OK 224 220 223 244 C2' C B 141 OK 246 242 245 264 C2' C B 142 OK 266 262 265 284 C2' A B 143 OK 286 282 285 306 C2' G B 144 OK 308 304 307 329 C2' G B 145 OK 331 327 330 352 C2' U B 146 OK 354 350 353 372 C2' C B 147 OK 374 370 373 392 C2' A B 148 OK 394 390 393 414 C2' G B 149 OK 416 412 415 437 C2' G B 150 OK 439 435 438 460 C2' U B 151 OK 462 458 461 480 C2' C B 152 OK 482 478 481 500 C2' C B 153 OK 502 498 501 520 C2' G B 154 OK 522 518 521 543 C2' A B 155 OK 545 541 544 565 C2' A B 156 OK 567 563 566 587 C2' A B 157 OK 589 585 588 609 C2' G B 158 OK 611 607 610 632 C2' G B 159 OK 634 630 633 655 C2' A B 160 OK 657 653 656 677 C2' A B 161 OK 679 675 678 699 C2' G B 162 OK 701 697 700 722 C2' C B 163 OK 724 720 723 742 C2' A B 164 OK 744 740 743 764 C2' G B 165 OK 766 762 765 787 C2' C B 166 OK 789 785 788 807 C2' C B 167 OK 809 805 808 827 C2' A B 168 OK 829 825 828 849 C2' A B 169 OK 851 847 850 871 C2' G B 170 OK 873 869 872 894 C2' G B 171 OK 896 892 895 917 C2' C B 172 OK 919 915 918 937 C2' A B 173 OK 939 935 938 959 C2' G B 174 OK 961 957 960 982 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' C B 134 OK 95 98 99 117 C3' U B 135 OK 115 118 119 137 C3' G B 136 OK 135 138 139 160 C3' U B 137 OK 158 161 162 180 C3' U B 138 OK 178 181 182 200 C3' U B 139 OK 198 201 202 220 C3' A B 140 OK 218 221 222 242 C3' C B 141 OK 240 243 244 262 C3' C B 142 OK 260 263 264 282 C3' A B 143 OK 280 283 284 304 C3' G B 144 OK 302 305 306 327 C3' G B 145 OK 325 328 329 350 C3' U B 146 OK 348 351 352 370 C3' C B 147 OK 368 371 372 390 C3' A B 148 OK 388 391 392 412 C3' G B 149 OK 410 413 414 435 C3' G B 150 OK 433 436 437 458 C3' U B 151 OK 456 459 460 478 C3' C B 152 OK 476 479 480 498 C3' C B 153 OK 496 499 500 518 C3' G B 154 OK 516 519 520 541 C3' A B 155 OK 539 542 543 563 C3' A B 156 OK 561 564 565 585 C3' A B 157 OK 583 586 587 607 C3' G B 158 OK 605 608 609 630 C3' G B 159 OK 628 631 632 653 C3' A B 160 OK 651 654 655 675 C3' A B 161 OK 673 676 677 697 C3' G B 162 OK 695 698 699 720 C3' C B 163 OK 718 721 722 740 C3' A B 164 OK 738 741 742 762 C3' G B 165 OK 760 763 764 785 C3' C B 166 OK 783 786 787 805 C3' C B 167 OK 803 806 807 825 C3' A B 168 OK 823 826 827 847 C3' A B 169 OK 845 848 849 869 C3' G B 170 OK 867 870 871 892 C3' G B 171 OK 890 893 894 915 C3' C B 172 OK 913 916 917 935 C3' A B 173 OK 933 936 937 957 C3' G B 174 OK 955 958 959 980 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' C B 134 OK 97 94 96 115 C4' U B 135 OK 117 114 116 135 C4' G B 136 OK 137 134 136 158 C4' U B 137 OK 160 157 159 178 C4' U B 138 OK 180 177 179 198 C4' U B 139 OK 200 197 199 218 C4' A B 140 OK 220 217 219 240 C4' C B 141 OK 242 239 241 260 C4' C B 142 OK 262 259 261 280 C4' A B 143 OK 282 279 281 302 C4' G B 144 OK 304 301 303 325 C4' G B 145 OK 327 324 326 348 C4' U B 146 OK 350 347 349 368 C4' C B 147 OK 370 367 369 388 C4' A B 148 OK 390 387 389 410 C4' G B 149 OK 412 409 411 433 C4' G B 150 OK 435 432 434 456 C4' U B 151 OK 458 455 457 476 C4' C B 152 OK 478 475 477 496 C4' C B 153 OK 498 495 497 516 C4' G B 154 OK 518 515 517 539 C4' A B 155 OK 541 538 540 561 C4' A B 156 OK 563 560 562 583 C4' A B 157 OK 585 582 584 605 C4' G B 158 OK 607 604 606 628 C4' G B 159 OK 630 627 629 651 C4' A B 160 OK 653 650 652 673 C4' A B 161 OK 675 672 674 695 C4' G B 162 OK 697 694 696 718 C4' C B 163 OK 720 717 719 738 C4' A B 164 OK 740 737 739 760 C4' G B 165 OK 762 759 761 783 C4' C B 166 OK 785 782 784 803 C4' C B 167 OK 805 802 804 823 C4' A B 168 OK 825 822 824 845 C4' A B 169 OK 847 844 846 867 C4' G B 170 OK 869 866 868 890 C4' G B 171 OK 892 889 891 913 C4' C B 172 OK 915 912 914 933 C4' A B 173 OK 935 932 934 955 C4' G B 174 OK 957 954 956 978 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' C B 134 93 95 114 C5' U B 135 113 115 134 C5' G B 136 133 135 157 C5' U B 137 156 158 177 C5' U B 138 176 178 197 C5' U B 139 196 198 217 C5' A B 140 216 218 239 C5' C B 141 238 240 259 C5' C B 142 258 260 279 C5' A B 143 278 280 301 C5' G B 144 300 302 324 C5' G B 145 323 325 347 C5' U B 146 346 348 367 C5' C B 147 366 368 387 C5' A B 148 386 388 409 C5' G B 149 408 410 432 C5' G B 150 431 433 455 C5' U B 151 454 456 475 C5' C B 152 474 476 495 C5' C B 153 494 496 515 C5' G B 154 514 516 538 C5' A B 155 537 539 560 C5' A B 156 559 561 582 C5' A B 157 581 583 604 C5' G B 158 603 605 627 C5' G B 159 626 628 650 C5' A B 160 649 651 672 C5' A B 161 671 673 694 C5' G B 162 693 695 717 C5' C B 163 716 718 737 C5' A B 164 736 738 759 C5' G B 165 758 760 782 C5' C B 166 781 783 802 C5' C B 167 801 803 822 C5' A B 168 821 823 844 C5' A B 169 843 845 866 C5' G B 170 865 867 889 C5' G B 171 888 890 912 C5' C B 172 911 913 932 C5' A B 173 931 933 954 C5' G B 174 953 955 977 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 C B 134 distorted distorted 75 91 92 93 110 P U B 135 distorted distorted 98 111 112 113 130 P G B 136 distorted distorted 118 131 132 133 153 P U B 137 distorted distorted 138 154 155 156 173 P U B 138 distorted distorted 161 174 175 176 193 P U B 139 distorted distorted 181 194 195 196 213 P A B 140 distorted distorted 201 214 215 216 235 P C B 141 distorted distorted 221 236 237 238 255 P C B 142 distorted distorted 243 256 257 258 275 P A B 143 distorted distorted 263 276 277 278 297 P G B 144 distorted distorted 283 298 299 300 320 P G B 145 distorted distorted 305 321 322 323 343 P U B 146 distorted distorted 328 344 345 346 363 P C B 147 distorted distorted 351 364 365 366 383 P A B 148 distorted distorted 371 384 385 386 405 P G B 149 distorted distorted 391 406 407 408 428 P G B 150 distorted distorted 413 429 430 431 451 P U B 151 distorted distorted 436 452 453 454 471 P C B 152 distorted distorted 459 472 473 474 491 P C B 153 distorted distorted 479 492 493 494 511 P G B 154 distorted distorted 499 512 513 514 534 P A B 155 distorted distorted 519 535 536 537 556 P A B 156 distorted distorted 542 557 558 559 578 P A B 157 distorted distorted 564 579 580 581 600 P G B 158 distorted distorted 586 601 602 603 623 P G B 159 distorted distorted 608 624 625 626 646 P A B 160 distorted distorted 631 647 648 649 668 P A B 161 distorted distorted 654 669 670 671 690 P G B 162 distorted distorted 676 691 692 693 713 P C B 163 distorted distorted 698 714 715 716 733 P A B 164 distorted distorted 721 734 735 736 755 P G B 165 distorted distorted 741 756 757 758 778 P C B 166 distorted distorted 763 779 780 781 798 P C B 167 distorted distorted 786 799 800 801 818 P A B 168 distorted distorted 806 819 820 821 840 P A B 169 distorted distorted 826 841 842 843 862 P G B 170 distorted distorted 848 863 864 865 885 P G B 171 distorted distorted 870 886 887 888 908 P C B 172 distorted distorted 893 909 910 911 928 P A B 173 distorted distorted 916 929 930 931 950 P G B 174 distorted distorted 936 951 952 953 973 P U B 175 distorted distorted 958 974 975 976 993 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 ---------------------------------------------------------------------------------