ID code: '1YYO' 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' C C 1 beta 4 10 7 29 C1' G C 2 beta 24 30 27 52 C1' C C 3 beta 47 53 50 72 C1' G C 4 beta 67 73 70 95 C1' A C 5 beta 90 96 93 117 C1' A C 6 beta 112 118 115 139 C1' U C 7 beta 134 140 137 159 C1' U C 8 beta 154 160 157 179 C1' C C 9 beta 174 180 177 199 C1' G C 10 beta 194 200 197 222 C1' C C 11 beta 217 223 220 242 C1' G C 12 beta 237 243 240 263 C1' C D 13 beta 258 264 261 283 C1' G D 14 beta 278 284 281 306 C1' C D 15 beta 301 307 304 326 C1' G D 16 beta 321 327 324 349 C1' A D 17 beta 344 350 347 371 C1' A D 18 beta 366 372 369 393 C1' U D 19 beta 388 394 391 413 C1' U D 20 beta 408 414 411 433 C1' C D 21 beta 428 434 431 453 C1' G D 22 beta 448 454 451 476 C1' C D 23 beta 471 477 474 496 C1' G D 24 beta 491 497 494 517 C1' C E 1 beta 512 518 515 537 C1' G E 2 beta 532 538 535 560 C1' C E 3 beta 555 561 558 580 C1' G E 4 beta 575 581 578 603 C1' A E 5 beta 598 604 601 625 C1' A E 6 beta 620 626 623 647 C1' U E 7 beta 642 648 645 667 C1' U E 8 beta 662 668 665 687 C1' C E 9 beta 682 688 685 707 C1' G E 10 beta 702 708 705 730 C1' C E 11 beta 725 731 728 750 C1' G E 12 beta 745 751 748 771 C1' C F 13 beta 766 772 769 791 C1' G F 14 beta 786 792 789 814 C1' C F 15 beta 809 815 812 834 C1' G F 16 beta 829 835 832 857 C1' A F 17 beta 852 858 855 879 C1' A F 18 beta 874 880 877 901 C1' U F 19 beta 896 902 899 921 C1' U F 20 beta 916 922 919 941 C1' C F 21 beta 936 942 939 961 C1' G F 22 beta 956 962 959 984 C1' C F 23 beta 979 985 982 1004 C1' G F 24 beta 999 1005 1002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C C 1 OK 9 5 8 27 C2' G C 2 OK 29 25 28 50 C2' C C 3 OK 52 48 51 70 C2' G C 4 OK 72 68 71 93 C2' A C 5 OK 95 91 94 115 C2' A C 6 OK 117 113 116 137 C2' U C 7 OK 139 135 138 157 C2' U C 8 OK 159 155 158 177 C2' C C 9 OK 179 175 178 197 C2' G C 10 OK 199 195 198 220 C2' C C 11 OK 222 218 221 240 C2' G C 12 OK 242 238 241 261 C2' C D 13 OK 263 259 262 281 C2' G D 14 OK 283 279 282 304 C2' C D 15 OK 306 302 305 324 C2' G D 16 OK 326 322 325 347 C2' A D 17 OK 349 345 348 369 C2' A D 18 OK 371 367 370 391 C2' U D 19 OK 393 389 392 411 C2' U D 20 OK 413 409 412 431 C2' C D 21 OK 433 429 432 451 C2' G D 22 OK 453 449 452 474 C2' C D 23 OK 476 472 475 494 C2' G D 24 OK 496 492 495 515 C2' C E 1 OK 517 513 516 535 C2' G E 2 OK 537 533 536 558 C2' C E 3 OK 560 556 559 578 C2' G E 4 OK 580 576 579 601 C2' A E 5 OK 603 599 602 623 C2' A E 6 OK 625 621 624 645 C2' U E 7 OK 647 643 646 665 C2' U E 8 OK 667 663 666 685 C2' C E 9 OK 687 683 686 705 C2' G E 10 OK 707 703 706 728 C2' C E 11 OK 730 726 729 748 C2' G E 12 OK 750 746 749 769 C2' C F 13 OK 771 767 770 789 C2' G F 14 OK 791 787 790 812 C2' C F 15 OK 814 810 813 832 C2' G F 16 OK 834 830 833 855 C2' A F 17 OK 857 853 856 877 C2' A F 18 OK 879 875 878 899 C2' U F 19 OK 901 897 900 919 C2' U F 20 OK 921 917 920 939 C2' C F 21 OK 941 937 940 959 C2' G F 22 OK 961 957 960 982 C2' C F 23 OK 984 980 983 1002 C2' G F 24 OK 1004 1000 1003 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C C 1 OK 3 6 7 25 C3' G C 2 OK 23 26 27 48 C3' C C 3 OK 46 49 50 68 C3' G C 4 OK 66 69 70 91 C3' A C 5 OK 89 92 93 113 C3' A C 6 OK 111 114 115 135 C3' U C 7 OK 133 136 137 155 C3' U C 8 OK 153 156 157 175 C3' C C 9 OK 173 176 177 195 C3' G C 10 OK 193 196 197 218 C3' C C 11 OK 216 219 220 238 C3' G C 12 OK 236 239 240 259 C3' C D 13 OK 257 260 261 279 C3' G D 14 OK 277 280 281 302 C3' C D 15 OK 300 303 304 322 C3' G D 16 OK 320 323 324 345 C3' A D 17 OK 343 346 347 367 C3' A D 18 OK 365 368 369 389 C3' U D 19 OK 387 390 391 409 C3' U D 20 OK 407 410 411 429 C3' C D 21 OK 427 430 431 449 C3' G D 22 OK 447 450 451 472 C3' C D 23 OK 470 473 474 492 C3' G D 24 OK 490 493 494 513 C3' C E 1 OK 511 514 515 533 C3' G E 2 OK 531 534 535 556 C3' C E 3 OK 554 557 558 576 C3' G E 4 OK 574 577 578 599 C3' A E 5 OK 597 600 601 621 C3' A E 6 OK 619 622 623 643 C3' U E 7 OK 641 644 645 663 C3' U E 8 OK 661 664 665 683 C3' C E 9 OK 681 684 685 703 C3' G E 10 OK 701 704 705 726 C3' C E 11 OK 724 727 728 746 C3' G E 12 OK 744 747 748 767 C3' C F 13 OK 765 768 769 787 C3' G F 14 OK 785 788 789 810 C3' C F 15 OK 808 811 812 830 C3' G F 16 OK 828 831 832 853 C3' A F 17 OK 851 854 855 875 C3' A F 18 OK 873 876 877 897 C3' U F 19 OK 895 898 899 917 C3' U F 20 OK 915 918 919 937 C3' C F 21 OK 935 938 939 957 C3' G F 22 OK 955 958 959 980 C3' C F 23 OK 978 981 982 1000 C3' G F 24 OK 998 1001 1002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C C 1 OK 5 2 4 23 C4' G C 2 OK 25 22 24 46 C4' C C 3 OK 48 45 47 66 C4' G C 4 OK 68 65 67 89 C4' A C 5 OK 91 88 90 111 C4' A C 6 OK 113 110 112 133 C4' U C 7 OK 135 132 134 153 C4' U C 8 OK 155 152 154 173 C4' C C 9 OK 175 172 174 193 C4' G C 10 OK 195 192 194 216 C4' C C 11 OK 218 215 217 236 C4' G C 12 OK 238 235 237 257 C4' C D 13 OK 259 256 258 277 C4' G D 14 OK 279 276 278 300 C4' C D 15 OK 302 299 301 320 C4' G D 16 OK 322 319 321 343 C4' A D 17 OK 345 342 344 365 C4' A D 18 OK 367 364 366 387 C4' U D 19 OK 389 386 388 407 C4' U D 20 OK 409 406 408 427 C4' C D 21 OK 429 426 428 447 C4' G D 22 OK 449 446 448 470 C4' C D 23 OK 472 469 471 490 C4' G D 24 OK 492 489 491 511 C4' C E 1 OK 513 510 512 531 C4' G E 2 OK 533 530 532 554 C4' C E 3 OK 556 553 555 574 C4' G E 4 OK 576 573 575 597 C4' A E 5 OK 599 596 598 619 C4' A E 6 OK 621 618 620 641 C4' U E 7 OK 643 640 642 661 C4' U E 8 OK 663 660 662 681 C4' C E 9 OK 683 680 682 701 C4' G E 10 OK 703 700 702 724 C4' C E 11 OK 726 723 725 744 C4' G E 12 OK 746 743 745 765 C4' C F 13 OK 767 764 766 785 C4' G F 14 OK 787 784 786 808 C4' C F 15 OK 810 807 809 828 C4' G F 16 OK 830 827 829 851 C4' A F 17 OK 853 850 852 873 C4' A F 18 OK 875 872 874 895 C4' U F 19 OK 897 894 896 915 C4' U F 20 OK 917 914 916 935 C4' C F 21 OK 937 934 936 955 C4' G F 22 OK 957 954 956 978 C4' C F 23 OK 980 977 979 998 C4' G F 24 OK 1000 997 999 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C C 1 1 3 22 C5' G C 2 21 23 45 C5' C C 3 44 46 65 C5' G C 4 64 66 88 C5' A C 5 87 89 110 C5' A C 6 109 111 132 C5' U C 7 131 133 152 C5' U C 8 151 153 172 C5' C C 9 171 173 192 C5' G C 10 191 193 215 C5' C C 11 214 216 235 C5' G C 12 234 236 256 C5' C D 13 255 257 276 C5' G D 14 275 277 299 C5' C D 15 298 300 319 C5' G D 16 318 320 342 C5' A D 17 341 343 364 C5' A D 18 363 365 386 C5' U D 19 385 387 406 C5' U D 20 405 407 426 C5' C D 21 425 427 446 C5' G D 22 445 447 469 C5' C D 23 468 470 489 C5' G D 24 488 490 510 C5' C E 1 509 511 530 C5' G E 2 529 531 553 C5' C E 3 552 554 573 C5' G E 4 572 574 596 C5' A E 5 595 597 618 C5' A E 6 617 619 640 C5' U E 7 639 641 660 C5' U E 8 659 661 680 C5' C E 9 679 681 700 C5' G E 10 699 701 723 C5' C E 11 722 724 743 C5' G E 12 742 744 764 C5' C F 13 763 765 784 C5' G F 14 783 785 807 C5' C F 15 806 808 827 C5' G F 16 826 828 850 C5' A F 17 849 851 872 C5' A F 18 871 873 894 C5' U F 19 893 895 914 C5' U F 20 913 915 934 C5' C F 21 933 935 954 C5' G F 22 953 955 977 C5' C F 23 976 978 997 C5' G F 24 996 998 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G C 2 distorted distorted 6 19 20 21 41 P C C 3 distorted distorted 26 42 43 44 61 P G C 4 distorted distorted 49 62 63 64 84 P A C 5 distorted distorted 69 85 86 87 106 P A C 6 distorted distorted 92 107 108 109 128 P U C 7 distorted distorted 114 129 130 131 148 P U C 8 distorted distorted 136 149 150 151 168 P C C 9 distorted distorted 156 169 170 171 188 P G C 10 distorted distorted 176 189 190 191 211 P C C 11 distorted distorted 196 212 213 214 231 P G C 12 distorted distorted 219 232 233 234 272 P G D 14 distorted distorted 260 273 274 275 295 P C D 15 distorted distorted 280 296 297 298 315 P G D 16 distorted distorted 303 316 317 318 338 P A D 17 distorted distorted 323 339 340 341 360 P A D 18 distorted distorted 346 361 362 363 382 P U D 19 distorted distorted 368 383 384 385 402 P U D 20 distorted distorted 390 403 404 405 422 P C D 21 distorted distorted 410 423 424 425 442 P G D 22 distorted distorted 430 443 444 445 465 P C D 23 distorted distorted 450 466 467 468 485 P G D 24 distorted distorted 473 486 487 488 526 P G E 2 distorted distorted 514 527 528 529 549 P C E 3 distorted distorted 534 550 551 552 569 P G E 4 distorted distorted 557 570 571 572 592 P A E 5 distorted distorted 577 593 594 595 614 P A E 6 distorted distorted 600 615 616 617 636 P U E 7 distorted distorted 622 637 638 639 656 P U E 8 distorted distorted 644 657 658 659 676 P C E 9 distorted distorted 664 677 678 679 696 P G E 10 distorted distorted 684 697 698 699 719 P C E 11 distorted distorted 704 720 721 722 739 P G E 12 distorted distorted 727 740 741 742 780 P G F 14 distorted distorted 768 781 782 783 803 P C F 15 distorted distorted 788 804 805 806 823 P G F 16 distorted distorted 811 824 825 826 846 P A F 17 distorted distorted 831 847 848 849 868 P A F 18 distorted distorted 854 869 870 871 890 P U F 19 distorted distorted 876 891 892 893 910 P U F 20 distorted distorted 898 911 912 913 930 P C F 21 distorted distorted 918 931 932 933 950 P G F 22 distorted distorted 938 951 952 953 973 P C F 23 distorted distorted 958 974 975 976 993 P G F 24 distorted distorted 981 994 995 996 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