ID code: '1Z7F' 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 A 1 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' A A 3 beta 47 53 50 74 C1' G A 4 beta 69 75 72 97 C1' A A 5 beta 92 98 95 119 C1' C A 6 beta 114 120 117 139 C1' U A 7 beta 134 140 137 159 C1' U A 8 beta 154 160 157 179 C1' A A 9 beta 174 180 177 201 C1' A A 10 beta 196 202 199 223 C1' A A 11 beta 218 224 221 245 C1' U A 12 beta 240 246 243 265 C1' C A 13 beta 260 266 263 285 C1' U A 14 beta 280 286 283 305 C1' G A 15 beta 300 306 303 328 C1' C A 16 beta 323 329 326 346 C1' G B 1 beta 341 347 344 369 C1' C B 2 beta 364 370 367 389 C1' A B 3 beta 384 390 387 411 C1' G B 4 beta 406 412 409 434 C1' A B 5 beta 429 435 432 456 C1' C B 6 beta 451 457 454 476 C1' U B 7 beta 471 477 474 496 C1' U B 8 beta 491 497 494 516 C1' A B 9 beta 511 517 514 538 C1' A B 10 beta 533 539 536 560 C1' A B 11 beta 555 561 558 582 C1' U B 12 beta 577 583 580 602 C1' C B 13 beta 597 603 600 622 C1' U B 14 beta 617 623 620 642 C1' G B 15 beta 637 643 640 665 C1' C B 16 beta 660 666 663 683 C1' G C 17 beta 678 684 681 706 C1' C C 18 beta 701 707 704 726 C1' A C 19 beta 721 727 724 748 C1' G C 20 beta 743 749 746 771 C1' A C 21 beta 766 772 769 793 C1' C C 22 beta 788 794 791 813 C1' U C 23 beta 808 814 811 833 C1' U C 24 beta 828 834 831 853 C1' A C 25 beta 848 854 851 875 C1' A C 26 beta 870 876 873 897 C1' A C 27 beta 892 898 895 919 C1' U C 28 beta 914 920 917 939 C1' C C 29 beta 934 940 937 959 C1' U C 30 beta 954 960 957 979 C1' G C 31 beta 974 980 977 1002 C1' C C 32 beta 997 1003 1000 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' A A 3 OK 52 48 51 72 C2' G A 4 OK 74 70 73 95 C2' A A 5 OK 97 93 96 117 C2' C A 6 OK 119 115 118 137 C2' U A 7 OK 139 135 138 157 C2' U A 8 OK 159 155 158 177 C2' A A 9 OK 179 175 178 199 C2' A A 10 OK 201 197 200 221 C2' A A 11 OK 223 219 222 243 C2' U A 12 OK 245 241 244 263 C2' C A 13 OK 265 261 264 283 C2' U A 14 OK 285 281 284 303 C2' G A 15 OK 305 301 304 326 C2' C A 16 OK 328 324 327 344 C2' G B 1 OK 346 342 345 367 C2' C B 2 OK 369 365 368 387 C2' A B 3 OK 389 385 388 409 C2' G B 4 OK 411 407 410 432 C2' A B 5 OK 434 430 433 454 C2' C B 6 OK 456 452 455 474 C2' U B 7 OK 476 472 475 494 C2' U B 8 OK 496 492 495 514 C2' A B 9 OK 516 512 515 536 C2' A B 10 OK 538 534 537 558 C2' A B 11 OK 560 556 559 580 C2' U B 12 OK 582 578 581 600 C2' C B 13 OK 602 598 601 620 C2' U B 14 OK 622 618 621 640 C2' G B 15 OK 642 638 641 663 C2' C B 16 OK 665 661 664 681 C2' G C 17 OK 683 679 682 704 C2' C C 18 OK 706 702 705 724 C2' A C 19 OK 726 722 725 746 C2' G C 20 OK 748 744 747 769 C2' A C 21 OK 771 767 770 791 C2' C C 22 OK 793 789 792 811 C2' U C 23 OK 813 809 812 831 C2' U C 24 OK 833 829 832 851 C2' A C 25 OK 853 849 852 873 C2' A C 26 OK 875 871 874 895 C2' A C 27 OK 897 893 896 917 C2' U C 28 OK 919 915 918 937 C2' C C 29 OK 939 935 938 957 C2' U C 30 OK 959 955 958 977 C2' G C 31 OK 979 975 978 1000 C2' C C 32 OK 1002 998 1001 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' A A 3 OK 46 49 50 70 C3' G A 4 OK 68 71 72 93 C3' A A 5 OK 91 94 95 115 C3' C A 6 OK 113 116 117 135 C3' U A 7 OK 133 136 137 155 C3' U A 8 OK 153 156 157 175 C3' A A 9 OK 173 176 177 197 C3' A A 10 OK 195 198 199 219 C3' A A 11 OK 217 220 221 241 C3' U A 12 OK 239 242 243 261 C3' C A 13 OK 259 262 263 281 C3' U A 14 OK 279 282 283 301 C3' G A 15 OK 299 302 303 324 C3' C A 16 OK 322 325 326 342 C3' G B 1 OK 340 343 344 365 C3' C B 2 OK 363 366 367 385 C3' A B 3 OK 383 386 387 407 C3' G B 4 OK 405 408 409 430 C3' A B 5 OK 428 431 432 452 C3' C B 6 OK 450 453 454 472 C3' U B 7 OK 470 473 474 492 C3' U B 8 OK 490 493 494 512 C3' A B 9 OK 510 513 514 534 C3' A B 10 OK 532 535 536 556 C3' A B 11 OK 554 557 558 578 C3' U B 12 OK 576 579 580 598 C3' C B 13 OK 596 599 600 618 C3' U B 14 OK 616 619 620 638 C3' G B 15 OK 636 639 640 661 C3' C B 16 OK 659 662 663 679 C3' G C 17 OK 677 680 681 702 C3' C C 18 OK 700 703 704 722 C3' A C 19 OK 720 723 724 744 C3' G C 20 OK 742 745 746 767 C3' A C 21 OK 765 768 769 789 C3' C C 22 OK 787 790 791 809 C3' U C 23 OK 807 810 811 829 C3' U C 24 OK 827 830 831 849 C3' A C 25 OK 847 850 851 871 C3' A C 26 OK 869 872 873 893 C3' A C 27 OK 891 894 895 915 C3' U C 28 OK 913 916 917 935 C3' C C 29 OK 933 936 937 955 C3' U C 30 OK 953 956 957 975 C3' G C 31 OK 973 976 977 998 C3' C C 32 OK 996 999 1000 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' A A 3 OK 48 45 47 68 C4' G A 4 OK 70 67 69 91 C4' A A 5 OK 93 90 92 113 C4' C A 6 OK 115 112 114 133 C4' U A 7 OK 135 132 134 153 C4' U A 8 OK 155 152 154 173 C4' A A 9 OK 175 172 174 195 C4' A A 10 OK 197 194 196 217 C4' A A 11 OK 219 216 218 239 C4' U A 12 OK 241 238 240 259 C4' C A 13 OK 261 258 260 279 C4' U A 14 OK 281 278 280 299 C4' G A 15 OK 301 298 300 322 C4' C A 16 OK 324 321 323 340 C4' G B 1 OK 342 339 341 363 C4' C B 2 OK 365 362 364 383 C4' A B 3 OK 385 382 384 405 C4' G B 4 OK 407 404 406 428 C4' A B 5 OK 430 427 429 450 C4' C B 6 OK 452 449 451 470 C4' U B 7 OK 472 469 471 490 C4' U B 8 OK 492 489 491 510 C4' A B 9 OK 512 509 511 532 C4' A B 10 OK 534 531 533 554 C4' A B 11 OK 556 553 555 576 C4' U B 12 OK 578 575 577 596 C4' C B 13 OK 598 595 597 616 C4' U B 14 OK 618 615 617 636 C4' G B 15 OK 638 635 637 659 C4' C B 16 OK 661 658 660 677 C4' G C 17 OK 679 676 678 700 C4' C C 18 OK 702 699 701 720 C4' A C 19 OK 722 719 721 742 C4' G C 20 OK 744 741 743 765 C4' A C 21 OK 767 764 766 787 C4' C C 22 OK 789 786 788 807 C4' U C 23 OK 809 806 808 827 C4' U C 24 OK 829 826 828 847 C4' A C 25 OK 849 846 848 869 C4' A C 26 OK 871 868 870 891 C4' A C 27 OK 893 890 892 913 C4' U C 28 OK 915 912 914 933 C4' C C 29 OK 935 932 934 953 C4' U C 30 OK 955 952 954 973 C4' G C 31 OK 975 972 974 996 C4' C C 32 OK 998 995 997 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' A A 3 44 46 67 C5' G A 4 66 68 90 C5' A A 5 89 91 112 C5' C A 6 111 113 132 C5' U A 7 131 133 152 C5' U A 8 151 153 172 C5' A A 9 171 173 194 C5' A A 10 193 195 216 C5' A A 11 215 217 238 C5' U A 12 237 239 258 C5' C A 13 257 259 278 C5' U A 14 277 279 298 C5' G A 15 297 299 321 C5' C A 16 320 322 339 C5' G B 1 338 340 362 C5' C B 2 361 363 382 C5' A B 3 381 383 404 C5' G B 4 403 405 427 C5' A B 5 426 428 449 C5' C B 6 448 450 469 C5' U B 7 468 470 489 C5' U B 8 488 490 509 C5' A B 9 508 510 531 C5' A B 10 530 532 553 C5' A B 11 552 554 575 C5' U B 12 574 576 595 C5' C B 13 594 596 615 C5' U B 14 614 616 635 C5' G B 15 634 636 658 C5' C B 16 657 659 676 C5' G C 17 675 677 699 C5' C C 18 698 700 719 C5' A C 19 718 720 741 C5' G C 20 740 742 764 C5' A C 21 763 765 786 C5' C C 22 785 787 806 C5' U C 23 805 807 826 C5' U C 24 825 827 846 C5' A C 25 845 847 868 C5' A C 26 867 869 890 C5' A C 27 889 891 912 C5' U C 28 911 913 932 C5' C C 29 931 933 952 C5' U C 30 951 953 972 C5' G C 31 971 973 995 C5' C C 32 994 996 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P A A 3 distorted distorted 29 42 43 44 63 P G A 4 distorted distorted 49 64 65 66 86 P A A 5 distorted distorted 71 87 88 89 108 P C A 6 distorted distorted 94 109 110 111 128 P U A 7 distorted distorted 116 129 130 131 148 P U A 8 distorted distorted 136 149 150 151 168 P A A 9 distorted distorted 156 169 170 171 190 P A A 10 distorted distorted 176 191 192 193 212 P A A 11 distorted distorted 198 213 214 215 234 P U A 12 distorted distorted 220 235 236 237 254 P C A 13 distorted distorted 242 255 256 257 274 P U A 14 distorted distorted 262 275 276 277 294 P G A 15 distorted distorted 282 295 296 297 317 P C A 16 distorted distorted 302 318 319 320 358 P C B 2 distorted distorted 343 359 360 361 378 P A B 3 distorted distorted 366 379 380 381 400 P G B 4 distorted distorted 386 401 402 403 423 P A B 5 distorted distorted 408 424 425 426 445 P C B 6 distorted distorted 431 446 447 448 465 P U B 7 distorted distorted 453 466 467 468 485 P U B 8 distorted distorted 473 486 487 488 505 P A B 9 distorted distorted 493 506 507 508 527 P A B 10 distorted distorted 513 528 529 530 549 P A B 11 distorted distorted 535 550 551 552 571 P U B 12 distorted distorted 557 572 573 574 591 P C B 13 distorted distorted 579 592 593 594 611 P U B 14 distorted distorted 599 612 613 614 631 P G B 15 distorted distorted 619 632 633 634 654 P C B 16 distorted distorted 639 655 656 657 695 P C C 18 distorted distorted 680 696 697 698 715 P A C 19 distorted distorted 703 716 717 718 737 P G C 20 distorted distorted 723 738 739 740 760 P A C 21 distorted distorted 745 761 762 763 782 P C C 22 distorted distorted 768 783 784 785 802 P U C 23 distorted distorted 790 803 804 805 822 P U C 24 distorted distorted 810 823 824 825 842 P A C 25 distorted distorted 830 843 844 845 864 P A C 26 distorted distorted 850 865 866 867 886 P A C 27 distorted distorted 872 887 888 889 908 P U C 28 distorted distorted 894 909 910 911 928 P C C 29 distorted distorted 916 929 930 931 948 P U C 30 distorted distorted 936 949 950 951 968 P G C 31 distorted distorted 956 969 970 971 991 P C C 32 distorted distorted 976 992 993 994 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