ID code: '1H88' 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' --------------------------------------------------------------------------------- 11 C1' A D 2 beta 7 12 10 32 C1' T D 3 beta 28 33 31 52 C1' G D 4 beta 48 53 51 74 C1' T D 5 beta 70 75 73 94 C1' G D 6 beta 90 95 93 116 C1' G D 7 beta 112 117 115 138 C1' C D 8 beta 134 139 137 157 C1' G D 9 beta 153 158 156 179 C1' C D 10 beta 175 180 178 198 C1' A D 11 beta 194 199 197 219 C1' A D 12 beta 215 220 218 240 C1' T D 13 beta 236 241 239 260 C1' C D 14 beta 256 261 259 279 C1' C D 15 beta 275 280 278 298 C1' T D 16 beta 294 299 297 318 C1' T D 17 beta 314 319 317 338 C1' A D 18 beta 334 339 337 359 C1' A D 19 beta 355 360 358 380 C1' C D 20 beta 376 381 379 399 C1' G D 21 beta 395 400 398 421 C1' G D 22 beta 417 422 420 443 C1' A D 23 beta 439 444 442 464 C1' C D 24 beta 460 465 463 483 C1' T D 25 beta 479 484 482 503 C1' G D 26 beta 499 504 502 526 C1' C E 2 beta 522 527 525 545 C1' A E 3 beta 541 546 544 566 C1' G E 4 beta 562 567 565 588 C1' T E 5 beta 584 589 587 608 C1' C E 6 beta 604 609 607 627 C1' C E 7 beta 623 628 626 646 C1' G E 8 beta 642 647 645 668 C1' T E 9 beta 664 669 667 688 C1' T E 10 beta 684 689 687 708 C1' A E 11 beta 704 709 707 729 C1' A E 12 beta 725 730 728 750 C1' G E 13 beta 746 751 749 772 C1' G E 14 beta 768 773 771 794 C1' A E 15 beta 790 795 793 815 C1' T E 16 beta 811 816 814 835 C1' T E 17 beta 831 836 834 855 C1' G E 18 beta 851 856 854 877 C1' C E 19 beta 873 878 876 896 C1' G E 20 beta 892 897 895 918 C1' C E 21 beta 914 919 917 937 C1' C E 22 beta 933 938 936 956 C1' A E 23 beta 952 957 955 977 C1' C E 24 beta 973 978 976 996 C1' A E 25 beta 992 997 995 1017 C1' T E 26 beta 1013 1018 1016 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A D 2 11 8 31 C2' T D 3 32 29 51 C2' G D 4 52 49 73 C2' T D 5 74 71 93 C2' G D 6 94 91 115 C2' G D 7 116 113 137 C2' C D 8 138 135 156 C2' G D 9 157 154 178 C2' C D 10 179 176 197 C2' A D 11 198 195 218 C2' A D 12 219 216 239 C2' T D 13 240 237 259 C2' C D 14 260 257 278 C2' C D 15 279 276 297 C2' T D 16 298 295 317 C2' T D 17 318 315 337 C2' A D 18 338 335 358 C2' A D 19 359 356 379 C2' C D 20 380 377 398 C2' G D 21 399 396 420 C2' G D 22 421 418 442 C2' A D 23 443 440 463 C2' C D 24 464 461 482 C2' T D 25 483 480 502 C2' G D 26 503 500 525 C2' C E 2 526 523 544 C2' A E 3 545 542 565 C2' G E 4 566 563 587 C2' T E 5 588 585 607 C2' C E 6 608 605 626 C2' C E 7 627 624 645 C2' G E 8 646 643 667 C2' T E 9 668 665 687 C2' T E 10 688 685 707 C2' A E 11 708 705 728 C2' A E 12 729 726 749 C2' G E 13 750 747 771 C2' G E 14 772 769 793 C2' A E 15 794 791 814 C2' T E 16 815 812 834 C2' T E 17 835 832 854 C2' G E 18 855 852 876 C2' C E 19 877 874 895 C2' G E 20 896 893 917 C2' C E 21 918 915 936 C2' C E 22 937 934 955 C2' A E 23 956 953 976 C2' C E 24 977 974 995 C2' A E 25 996 993 1016 C2' T E 26 1017 1014 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A D 2 OK 6 9 10 29 C3' T D 3 OK 27 30 31 49 C3' G D 4 OK 47 50 51 71 C3' T D 5 OK 69 72 73 91 C3' G D 6 OK 89 92 93 113 C3' G D 7 OK 111 114 115 135 C3' C D 8 OK 133 136 137 154 C3' G D 9 OK 152 155 156 176 C3' C D 10 OK 174 177 178 195 C3' A D 11 OK 193 196 197 216 C3' A D 12 OK 214 217 218 237 C3' T D 13 OK 235 238 239 257 C3' C D 14 OK 255 258 259 276 C3' C D 15 OK 274 277 278 295 C3' T D 16 OK 293 296 297 315 C3' T D 17 OK 313 316 317 335 C3' A D 18 OK 333 336 337 356 C3' A D 19 OK 354 357 358 377 C3' C D 20 OK 375 378 379 396 C3' G D 21 OK 394 397 398 418 C3' G D 22 OK 416 419 420 440 C3' A D 23 OK 438 441 442 461 C3' C D 24 OK 459 462 463 480 C3' T D 25 OK 478 481 482 500 C3' G D 26 OK 498 501 502 523 C3' C E 2 OK 521 524 525 542 C3' A E 3 OK 540 543 544 563 C3' G E 4 OK 561 564 565 585 C3' T E 5 OK 583 586 587 605 C3' C E 6 OK 603 606 607 624 C3' C E 7 OK 622 625 626 643 C3' G E 8 OK 641 644 645 665 C3' T E 9 OK 663 666 667 685 C3' T E 10 OK 683 686 687 705 C3' A E 11 OK 703 706 707 726 C3' A E 12 OK 724 727 728 747 C3' G E 13 OK 745 748 749 769 C3' G E 14 OK 767 770 771 791 C3' A E 15 OK 789 792 793 812 C3' T E 16 OK 810 813 814 832 C3' T E 17 OK 830 833 834 852 C3' G E 18 OK 850 853 854 874 C3' C E 19 OK 872 875 876 893 C3' G E 20 OK 891 894 895 915 C3' C E 21 OK 913 916 917 934 C3' C E 22 OK 932 935 936 953 C3' A E 23 OK 951 954 955 974 C3' C E 24 OK 972 975 976 993 C3' A E 25 OK 991 994 995 1014 C3' T E 26 OK 1012 1015 1016 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A D 2 OK 8 5 7 27 C4' T D 3 OK 29 26 28 47 C4' G D 4 OK 49 46 48 69 C4' T D 5 OK 71 68 70 89 C4' G D 6 OK 91 88 90 111 C4' G D 7 OK 113 110 112 133 C4' C D 8 OK 135 132 134 152 C4' G D 9 OK 154 151 153 174 C4' C D 10 OK 176 173 175 193 C4' A D 11 OK 195 192 194 214 C4' A D 12 OK 216 213 215 235 C4' T D 13 OK 237 234 236 255 C4' C D 14 OK 257 254 256 274 C4' C D 15 OK 276 273 275 293 C4' T D 16 OK 295 292 294 313 C4' T D 17 OK 315 312 314 333 C4' A D 18 OK 335 332 334 354 C4' A D 19 OK 356 353 355 375 C4' C D 20 OK 377 374 376 394 C4' G D 21 OK 396 393 395 416 C4' G D 22 OK 418 415 417 438 C4' A D 23 OK 440 437 439 459 C4' C D 24 OK 461 458 460 478 C4' T D 25 OK 480 477 479 498 C4' G D 26 OK 500 497 499 521 C4' C E 2 OK 523 520 522 540 C4' A E 3 OK 542 539 541 561 C4' G E 4 OK 563 560 562 583 C4' T E 5 OK 585 582 584 603 C4' C E 6 OK 605 602 604 622 C4' C E 7 OK 624 621 623 641 C4' G E 8 OK 643 640 642 663 C4' T E 9 OK 665 662 664 683 C4' T E 10 OK 685 682 684 703 C4' A E 11 OK 705 702 704 724 C4' A E 12 OK 726 723 725 745 C4' G E 13 OK 747 744 746 767 C4' G E 14 OK 769 766 768 789 C4' A E 15 OK 791 788 790 810 C4' T E 16 OK 812 809 811 830 C4' T E 17 OK 832 829 831 850 C4' G E 18 OK 852 849 851 872 C4' C E 19 OK 874 871 873 891 C4' G E 20 OK 893 890 892 913 C4' C E 21 OK 915 912 914 932 C4' C E 22 OK 934 931 933 951 C4' A E 23 OK 953 950 952 972 C4' C E 24 OK 974 971 973 991 C4' A E 25 OK 993 990 992 1012 C4' T E 26 OK 1014 1011 1013 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A D 2 4 6 26 C5' T D 3 25 27 46 C5' G D 4 45 47 68 C5' T D 5 67 69 88 C5' G D 6 87 89 110 C5' G D 7 109 111 132 C5' C D 8 131 133 151 C5' G D 9 150 152 173 C5' C D 10 172 174 192 C5' A D 11 191 193 213 C5' A D 12 212 214 234 C5' T D 13 233 235 254 C5' C D 14 253 255 273 C5' C D 15 272 274 292 C5' T D 16 291 293 312 C5' T D 17 311 313 332 C5' A D 18 331 333 353 C5' A D 19 352 354 374 C5' C D 20 373 375 393 C5' G D 21 392 394 415 C5' G D 22 414 416 437 C5' A D 23 436 438 458 C5' C D 24 457 459 477 C5' T D 25 476 478 497 C5' G D 26 496 498 520 C5' C E 2 519 521 539 C5' A E 3 538 540 560 C5' G E 4 559 561 582 C5' T E 5 581 583 602 C5' C E 6 601 603 621 C5' C E 7 620 622 640 C5' G E 8 639 641 662 C5' T E 9 661 663 682 C5' T E 10 681 683 702 C5' A E 11 701 703 723 C5' A E 12 722 724 744 C5' G E 13 743 745 766 C5' G E 14 765 767 788 C5' A E 15 787 789 809 C5' T E 16 808 810 829 C5' T E 17 828 830 849 C5' G E 18 848 850 871 C5' C E 19 870 872 890 C5' G E 20 889 891 912 C5' C E 21 911 913 931 C5' C E 22 930 932 950 C5' A E 23 949 951 971 C5' C E 24 970 972 990 C5' A E 25 989 991 1011 C5' T E 26 1010 1012 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A D 2 distorted distorted 2 3 4 22 P T D 3 distorted distorted 9 23 24 25 42 P G D 4 distorted distorted 30 43 44 45 64 P T D 5 distorted distorted 50 65 66 67 84 P G D 6 distorted distorted 72 85 86 87 106 P G D 7 distorted distorted 92 107 108 109 128 P C D 8 distorted distorted 114 129 130 131 147 P G D 9 distorted distorted 136 148 149 150 169 P C D 10 distorted distorted 155 170 171 172 188 P A D 11 distorted distorted 177 189 190 191 209 P A D 12 distorted distorted 196 210 211 212 230 P T D 13 distorted distorted 217 231 232 233 250 P C D 14 distorted distorted 238 251 252 253 269 P C D 15 distorted distorted 258 270 271 272 288 P T D 16 distorted distorted 277 289 290 291 308 P T D 17 distorted distorted 296 309 310 311 328 P A D 18 distorted distorted 316 329 330 331 349 P A D 19 distorted distorted 336 350 351 352 370 P C D 20 distorted distorted 357 371 372 373 389 P G D 21 distorted distorted 378 390 391 392 411 P G D 22 distorted distorted 397 412 413 414 433 P A D 23 distorted distorted 419 434 435 436 454 P C D 24 distorted distorted 441 455 456 457 473 P T D 25 distorted distorted 462 474 475 476 493 P G D 26 distorted distorted 481 494 495 496 516 P C E 2 distorted distorted 517 518 519 535 P A E 3 distorted distorted 524 536 537 538 556 P G E 4 distorted distorted 543 557 558 559 578 P T E 5 distorted distorted 564 579 580 581 598 P C E 6 distorted distorted 586 599 600 601 617 P C E 7 distorted distorted 606 618 619 620 636 P G E 8 distorted distorted 625 637 638 639 658 P T E 9 distorted distorted 644 659 660 661 678 P T E 10 distorted distorted 666 679 680 681 698 P A E 11 distorted distorted 686 699 700 701 719 P A E 12 distorted distorted 706 720 721 722 740 P G E 13 distorted distorted 727 741 742 743 762 P G E 14 distorted distorted 748 763 764 765 784 P A E 15 distorted distorted 770 785 786 787 805 P T E 16 distorted distorted 792 806 807 808 825 P T E 17 distorted distorted 813 826 827 828 845 P G E 18 distorted distorted 833 846 847 848 867 P C E 19 distorted distorted 853 868 869 870 886 P G E 20 distorted distorted 875 887 888 889 908 P C E 21 distorted distorted 894 909 910 911 927 P C E 22 distorted distorted 916 928 929 930 946 P A E 23 distorted distorted 935 947 948 949 967 P C E 24 distorted distorted 954 968 969 970 986 P A E 25 distorted distorted 975 987 988 989 1007 P T E 26 distorted distorted 994 1008 1009 1010 ---------------------------------------------------------------------------------