ID code: '4JAH' 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' U A 2 beta 27 33 30 52 C1' G A 3 beta 47 53 50 75 C1' U A 4 beta 70 76 73 95 C1' A A 5 beta 90 96 93 115 C1' RUS A 6 beta 123 107 116 137 C1' A A 7 beta 132 138 135 159 C1' C A 8 beta 154 160 157 177 C1' G B 9 beta 172 178 175 200 C1' U B 10 beta 195 201 198 220 C1' G B 11 beta 215 221 218 243 C1' U B 12 beta 238 244 241 263 C1' A B 13 beta 258 264 261 283 C1' RUS B 14 beta 291 275 284 305 C1' A B 15 beta 300 306 303 327 C1' C B 16 beta 322 328 325 345 C1' G D 9 beta 340 346 343 368 C1' U D 10 beta 363 369 366 388 C1' G D 11 beta 383 389 386 411 C1' U D 12 beta 406 412 409 431 C1' A D 13 beta 426 432 429 451 C1' RUS D 14 beta 459 443 452 473 C1' A D 15 beta 468 474 471 495 C1' C D 16 beta 490 496 493 513 C1' G E 1 beta 508 514 511 536 C1' U E 2 beta 531 537 534 556 C1' G E 3 beta 551 557 554 579 C1' U E 4 beta 574 580 577 599 C1' A E 5 beta 594 600 597 619 C1' RUS E 6 beta 627 611 620 641 C1' A E 7 beta 636 642 639 663 C1' C E 8 beta 658 664 661 681 C1' G C 1 beta 676 682 679 704 C1' U C 2 beta 699 705 702 724 C1' G C 3 beta 719 725 722 747 C1' U C 4 beta 742 748 745 767 C1' A C 5 beta 762 768 765 787 C1' RUS C 6 beta 795 779 788 809 C1' A C 7 beta 804 810 807 831 C1' C C 8 beta 826 832 829 849 C1' G F 9 beta 844 850 847 872 C1' U F 10 beta 867 873 870 892 C1' G F 11 beta 887 893 890 915 C1' U F 12 beta 910 916 913 935 C1' A F 13 beta 930 936 933 955 C1' RUS F 14 beta 963 947 956 977 C1' A F 15 beta 972 978 975 999 C1' C F 16 beta 994 1000 997 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 2 OK 32 28 31 50 C2' G A 3 OK 52 48 51 73 C2' U A 4 OK 75 71 74 93 C2' A A 5 OK 95 91 94 116 C2' RUS A 6 OK 115 119 117 135 C2' A A 7 OK 137 133 136 157 C2' C A 8 OK 159 155 158 175 C2' G B 9 OK 177 173 176 198 C2' U B 10 OK 200 196 199 218 C2' G B 11 OK 220 216 219 241 C2' U B 12 OK 243 239 242 261 C2' A B 13 OK 263 259 262 284 C2' RUS B 14 OK 283 287 285 303 C2' A B 15 OK 305 301 304 325 C2' C B 16 OK 327 323 326 343 C2' G D 9 OK 345 341 344 366 C2' U D 10 OK 368 364 367 386 C2' G D 11 OK 388 384 387 409 C2' U D 12 OK 411 407 410 429 C2' A D 13 OK 431 427 430 452 C2' RUS D 14 OK 451 455 453 471 C2' A D 15 OK 473 469 472 493 C2' C D 16 OK 495 491 494 511 C2' G E 1 OK 513 509 512 534 C2' U E 2 OK 536 532 535 554 C2' G E 3 OK 556 552 555 577 C2' U E 4 OK 579 575 578 597 C2' A E 5 OK 599 595 598 620 C2' RUS E 6 OK 619 623 621 639 C2' A E 7 OK 641 637 640 661 C2' C E 8 OK 663 659 662 679 C2' G C 1 OK 681 677 680 702 C2' U C 2 OK 704 700 703 722 C2' G C 3 OK 724 720 723 745 C2' U C 4 OK 747 743 746 765 C2' A C 5 OK 767 763 766 788 C2' RUS C 6 OK 787 791 789 807 C2' A C 7 OK 809 805 808 829 C2' C C 8 OK 831 827 830 847 C2' G F 9 OK 849 845 848 870 C2' U F 10 OK 872 868 871 890 C2' G F 11 OK 892 888 891 913 C2' U F 12 OK 915 911 914 933 C2' A F 13 OK 935 931 934 956 C2' RUS F 14 OK 955 959 957 975 C2' A F 15 OK 977 973 976 997 C2' C F 16 OK 999 995 998 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' U A 2 OK 26 29 30 48 C3' G A 3 OK 46 49 50 71 C3' U A 4 OK 69 72 73 91 C3' A A 5 OK 89 92 93 119 C3' RUS A 6 OK 122 120 116 133 C3' A A 7 OK 131 134 135 155 C3' C A 8 OK 153 156 157 173 C3' G B 9 OK 171 174 175 196 C3' U B 10 OK 194 197 198 216 C3' G B 11 OK 214 217 218 239 C3' U B 12 OK 237 240 241 259 C3' A B 13 OK 257 260 261 287 C3' RUS B 14 OK 290 288 284 301 C3' A B 15 OK 299 302 303 323 C3' C B 16 OK 321 324 325 341 C3' G D 9 OK 339 342 343 364 C3' U D 10 OK 362 365 366 384 C3' G D 11 OK 382 385 386 407 C3' U D 12 OK 405 408 409 427 C3' A D 13 OK 425 428 429 455 C3' RUS D 14 OK 458 456 452 469 C3' A D 15 OK 467 470 471 491 C3' C D 16 OK 489 492 493 509 C3' G E 1 OK 507 510 511 532 C3' U E 2 OK 530 533 534 552 C3' G E 3 OK 550 553 554 575 C3' U E 4 OK 573 576 577 595 C3' A E 5 OK 593 596 597 623 C3' RUS E 6 OK 626 624 620 637 C3' A E 7 OK 635 638 639 659 C3' C E 8 OK 657 660 661 677 C3' G C 1 OK 675 678 679 700 C3' U C 2 OK 698 701 702 720 C3' G C 3 OK 718 721 722 743 C3' U C 4 OK 741 744 745 763 C3' A C 5 OK 761 764 765 791 C3' RUS C 6 OK 794 792 788 805 C3' A C 7 OK 803 806 807 827 C3' C C 8 OK 825 828 829 845 C3' G F 9 OK 843 846 847 868 C3' U F 10 OK 866 869 870 888 C3' G F 11 OK 886 889 890 911 C3' U F 12 OK 909 912 913 931 C3' A F 13 OK 929 932 933 959 C3' RUS F 14 OK 962 960 956 973 C3' A F 15 OK 971 974 975 995 C3' C F 16 OK 993 996 997 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' U A 2 OK 28 25 27 46 C4' G A 3 OK 48 45 47 69 C4' U A 4 OK 71 68 70 89 C4' A A 5 OK 91 88 90 122 C4' RUS A 6 OK 119 124 123 131 C4' A A 7 OK 133 130 132 153 C4' C A 8 OK 155 152 154 171 C4' G B 9 OK 173 170 172 194 C4' U B 10 OK 196 193 195 214 C4' G B 11 OK 216 213 215 237 C4' U B 12 OK 239 236 238 257 C4' A B 13 OK 259 256 258 290 C4' RUS B 14 OK 287 292 291 299 C4' A B 15 OK 301 298 300 321 C4' C B 16 OK 323 320 322 339 C4' G D 9 OK 341 338 340 362 C4' U D 10 OK 364 361 363 382 C4' G D 11 OK 384 381 383 405 C4' U D 12 OK 407 404 406 425 C4' A D 13 OK 427 424 426 458 C4' RUS D 14 OK 455 460 459 467 C4' A D 15 OK 469 466 468 489 C4' C D 16 OK 491 488 490 507 C4' G E 1 OK 509 506 508 530 C4' U E 2 OK 532 529 531 550 C4' G E 3 OK 552 549 551 573 C4' U E 4 OK 575 572 574 593 C4' A E 5 OK 595 592 594 626 C4' RUS E 6 OK 623 628 627 635 C4' A E 7 OK 637 634 636 657 C4' C E 8 OK 659 656 658 675 C4' G C 1 OK 677 674 676 698 C4' U C 2 OK 700 697 699 718 C4' G C 3 OK 720 717 719 741 C4' U C 4 OK 743 740 742 761 C4' A C 5 OK 763 760 762 794 C4' RUS C 6 OK 791 796 795 803 C4' A C 7 OK 805 802 804 825 C4' C C 8 OK 827 824 826 843 C4' G F 9 OK 845 842 844 866 C4' U F 10 OK 868 865 867 886 C4' G F 11 OK 888 885 887 909 C4' U F 12 OK 911 908 910 929 C4' A F 13 OK 931 928 930 962 C4' RUS F 14 OK 959 964 963 971 C4' A F 15 OK 973 970 972 993 C4' C F 16 OK 995 992 994 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' U A 2 24 26 45 C5' G A 3 44 46 68 C5' U A 4 67 69 88 C5' A A 5 87 89 124 C5' RUS A 6 125 122 130 C5' A A 7 129 131 152 C5' C A 8 151 153 170 C5' G B 9 169 171 193 C5' U B 10 192 194 213 C5' G B 11 212 214 236 C5' U B 12 235 237 256 C5' A B 13 255 257 292 C5' RUS B 14 293 290 298 C5' A B 15 297 299 320 C5' C B 16 319 321 338 C5' G D 9 337 339 361 C5' U D 10 360 362 381 C5' G D 11 380 382 404 C5' U D 12 403 405 424 C5' A D 13 423 425 460 C5' RUS D 14 461 458 466 C5' A D 15 465 467 488 C5' C D 16 487 489 506 C5' G E 1 505 507 529 C5' U E 2 528 530 549 C5' G E 3 548 550 572 C5' U E 4 571 573 592 C5' A E 5 591 593 628 C5' RUS E 6 629 626 634 C5' A E 7 633 635 656 C5' C E 8 655 657 674 C5' G C 1 673 675 697 C5' U C 2 696 698 717 C5' G C 3 716 718 740 C5' U C 4 739 741 760 C5' A C 5 759 761 796 C5' RUS C 6 797 794 802 C5' A C 7 801 803 824 C5' C C 8 823 825 842 C5' G F 9 841 843 865 C5' U F 10 864 866 885 C5' G F 11 884 886 908 C5' U F 12 907 909 928 C5' A F 13 927 929 964 C5' RUS F 14 965 962 970 C5' A F 15 969 971 992 C5' C F 16 991 993 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P U A 2 distorted distorted 6 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P U A 4 distorted distorted 49 65 66 67 84 P A A 5 distorted distorted 72 85 86 87 106 P RUS A 6 92 118 125 126 P A A 7 distorted distorted 120 127 128 129 148 P C A 8 distorted distorted 134 149 150 151 189 P U B 10 distorted distorted 174 190 191 192 209 P G B 11 distorted distorted 197 210 211 212 232 P U B 12 distorted distorted 217 233 234 235 252 P A B 13 distorted distorted 240 253 254 255 274 P RUS B 14 260 286 293 294 P A B 15 distorted distorted 288 295 296 297 316 P C B 16 distorted distorted 302 317 318 319 357 P U D 10 distorted distorted 342 358 359 360 377 P G D 11 distorted distorted 365 378 379 380 400 P U D 12 distorted distorted 385 401 402 403 420 P A D 13 distorted distorted 408 421 422 423 442 P RUS D 14 428 454 461 462 P A D 15 distorted distorted 456 463 464 465 484 P C D 16 distorted distorted 470 485 486 487 525 P U E 2 distorted distorted 510 526 527 528 545 P G E 3 distorted distorted 533 546 547 548 568 P U E 4 distorted distorted 553 569 570 571 588 P A E 5 distorted distorted 576 589 590 591 610 P RUS E 6 596 622 629 630 P A E 7 distorted distorted 624 631 632 633 652 P C E 8 distorted distorted 638 653 654 655 693 P U C 2 distorted distorted 678 694 695 696 713 P G C 3 distorted distorted 701 714 715 716 736 P U C 4 distorted distorted 721 737 738 739 756 P A C 5 distorted distorted 744 757 758 759 778 P RUS C 6 764 790 797 798 P A C 7 distorted distorted 792 799 800 801 820 P C C 8 distorted distorted 806 821 822 823 861 P U F 10 distorted distorted 846 862 863 864 881 P G F 11 distorted distorted 869 882 883 884 904 P U F 12 distorted distorted 889 905 906 907 924 P A F 13 distorted distorted 912 925 926 927 946 P RUS F 14 932 958 965 966 P A F 15 distorted distorted 960 967 968 969 988 P C F 16 distorted distorted 974 989 990 991 ---------------------------------------------------------------------------------