ID code: '1T8E' 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' DC C1001 beta 7 12 10 30 C1' DG C1002 beta 26 31 29 52 C1' DA C1003 beta 48 53 51 73 C1' DA C1004 beta 69 74 72 94 C1' DA C1005 beta 90 95 93 115 C1' DA C1006 beta 111 116 114 136 C1' DC C1007 beta 132 137 135 155 C1' DG C1008 beta 151 156 154 177 C1' DA C1009 beta 173 178 176 198 C1' DC C1010 beta 194 199 197 217 C1' DG C1011 beta 213 218 216 239 C1' DG C1012 beta 235 240 238 261 C1' DC C1013 beta 257 262 260 280 C1' DC C1014 beta 276 281 279 299 C1' DA C1015 beta 295 300 298 320 C1' DG C1016 beta 316 321 319 342 C1' DT C1017 beta 338 343 341 362 C1' DG C1018 beta 358 363 361 384 C1' DC C1019 beta 380 385 383 403 C1' DC C1020 beta 399 404 402 422 C1' DA C1021 beta 418 423 421 450 C1' 2DT C1022 beta 449 437 446 463 C1' DT D2002 beta 459 464 462 483 C1' DG D2003 beta 479 484 482 505 C1' DG D2004 beta 501 506 504 527 C1' DA D2005 beta 523 528 526 548 C1' DT D2006 beta 544 549 547 568 C1' DG D2007 beta 564 569 567 590 C1' DG D2008 beta 586 591 589 612 C1' DC D2009 beta 608 613 611 631 C1' DA D2010 beta 627 632 630 652 C1' DC D2011 beta 648 653 651 671 C1' DT D2012 beta 667 672 670 691 C1' DG D2013 beta 687 692 690 713 C1' DG D2014 beta 709 714 712 735 C1' DC D2015 beta 731 736 734 754 C1' DC D2016 beta 750 755 753 773 C1' DG D2017 beta 769 774 772 795 C1' DT D2018 beta 791 796 794 815 C1' DC D2019 beta 811 816 814 834 C1' DG D2020 beta 830 835 833 856 C1' DT D2021 beta 852 857 855 876 C1' DT D2022 beta 872 877 875 896 C1' DT D2023 beta 892 897 895 916 C1' DT D2024 beta 912 917 915 936 C1' DC D2025 beta 932 937 935 955 C1' DG D2026 beta 951 956 954 7321 C1' DCT A1023 beta 7325 7313 7322 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' DC C1001 11 8 29 C2' DG C1002 30 27 51 C2' DA C1003 52 49 72 C2' DA C1004 73 70 93 C2' DA C1005 94 91 114 C2' DA C1006 115 112 135 C2' DC C1007 136 133 154 C2' DG C1008 155 152 176 C2' DA C1009 177 174 197 C2' DC C1010 198 195 216 C2' DG C1011 217 214 238 C2' DG C1012 239 236 260 C2' DC C1013 261 258 279 C2' DC C1014 280 277 298 C2' DA C1015 299 296 319 C2' DG C1016 320 317 341 C2' DT C1017 342 339 361 C2' DG C1018 362 359 383 C2' DC C1019 384 381 402 C2' DC C1020 403 400 421 C2' DA C1021 422 419 446 C2' 2DT C1022 450 451 462 C2' DT D2002 463 460 482 C2' DG D2003 483 480 504 C2' DG D2004 505 502 526 C2' DA D2005 527 524 547 C2' DT D2006 548 545 567 C2' DG D2007 568 565 589 C2' DG D2008 590 587 611 C2' DC D2009 612 609 630 C2' DA D2010 631 628 651 C2' DC D2011 652 649 670 C2' DT D2012 671 668 690 C2' DG D2013 691 688 712 C2' DG D2014 713 710 734 C2' DC D2015 735 732 753 C2' DC D2016 754 751 772 C2' DG D2017 773 770 794 C2' DT D2018 795 792 814 C2' DC D2019 815 812 833 C2' DG D2020 834 831 855 C2' DT D2021 856 853 875 C2' DT D2022 876 873 895 C2' DT D2023 896 893 915 C2' DT D2024 916 913 935 C2' DC D2025 936 933 954 C2' DG D2026 955 952 7322 C2' DCT A1023 7321 7323 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DC C1001 OK 6 9 10 27 C3' DG C1002 OK 25 28 29 49 C3' DA C1003 OK 47 50 51 70 C3' DA C1004 OK 68 71 72 91 C3' DA C1005 OK 89 92 93 112 C3' DA C1006 OK 110 113 114 133 C3' DC C1007 OK 131 134 135 152 C3' DG C1008 OK 150 153 154 174 C3' DA C1009 OK 172 175 176 195 C3' DC C1010 OK 193 196 197 214 C3' DG C1011 OK 212 215 216 236 C3' DG C1012 OK 234 237 238 258 C3' DC C1013 OK 256 259 260 277 C3' DC C1014 OK 275 278 279 296 C3' DA C1015 OK 294 297 298 317 C3' DG C1016 OK 315 318 319 339 C3' DT C1017 OK 337 340 341 359 C3' DG C1018 OK 357 360 361 381 C3' DC C1019 OK 379 382 383 400 C3' DC C1020 OK 398 401 402 419 C3' DA C1021 OK 417 420 421 451 C3' 2DT C1022 448 446 460 C3' DT D2002 OK 458 461 462 480 C3' DG D2003 OK 478 481 482 502 C3' DG D2004 OK 500 503 504 524 C3' DA D2005 OK 522 525 526 545 C3' DT D2006 OK 543 546 547 565 C3' DG D2007 OK 563 566 567 587 C3' DG D2008 OK 585 588 589 609 C3' DC D2009 OK 607 610 611 628 C3' DA D2010 OK 626 629 630 649 C3' DC D2011 OK 647 650 651 668 C3' DT D2012 OK 666 669 670 688 C3' DG D2013 OK 686 689 690 710 C3' DG D2014 OK 708 711 712 732 C3' DC D2015 OK 730 733 734 751 C3' DC D2016 OK 749 752 753 770 C3' DG D2017 OK 768 771 772 792 C3' DT D2018 OK 790 793 794 812 C3' DC D2019 OK 810 813 814 831 C3' DG D2020 OK 829 832 833 853 C3' DT D2021 OK 851 854 855 873 C3' DT D2022 OK 871 874 875 893 C3' DT D2023 OK 891 894 895 913 C3' DT D2024 OK 911 914 915 933 C3' DC D2025 OK 931 934 935 952 C3' DG D2026 OK 950 953 954 7323 C3' DCT A1023 7324 7322 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DC C1001 OK 8 5 7 25 C4' DG C1002 OK 27 24 26 47 C4' DA C1003 OK 49 46 48 68 C4' DA C1004 OK 70 67 69 89 C4' DA C1005 OK 91 88 90 110 C4' DA C1006 OK 112 109 111 131 C4' DC C1007 OK 133 130 132 150 C4' DG C1008 OK 152 149 151 172 C4' DA C1009 OK 174 171 173 193 C4' DC C1010 OK 195 192 194 212 C4' DG C1011 OK 214 211 213 234 C4' DG C1012 OK 236 233 235 256 C4' DC C1013 OK 258 255 257 275 C4' DC C1014 OK 277 274 276 294 C4' DA C1015 OK 296 293 295 315 C4' DG C1016 OK 317 314 316 337 C4' DT C1017 OK 339 336 338 357 C4' DG C1018 OK 359 356 358 379 C4' DC C1019 OK 381 378 380 398 C4' DC C1020 OK 400 397 399 417 C4' DA C1021 OK 419 416 418 448 C4' 2DT C1022 OK 451 447 449 458 C4' DT D2002 OK 460 457 459 478 C4' DG D2003 OK 480 477 479 500 C4' DG D2004 OK 502 499 501 522 C4' DA D2005 OK 524 521 523 543 C4' DT D2006 OK 545 542 544 563 C4' DG D2007 OK 565 562 564 585 C4' DG D2008 OK 587 584 586 607 C4' DC D2009 OK 609 606 608 626 C4' DA D2010 OK 628 625 627 647 C4' DC D2011 OK 649 646 648 666 C4' DT D2012 OK 668 665 667 686 C4' DG D2013 OK 688 685 687 708 C4' DG D2014 OK 710 707 709 730 C4' DC D2015 OK 732 729 731 749 C4' DC D2016 OK 751 748 750 768 C4' DG D2017 OK 770 767 769 790 C4' DT D2018 OK 792 789 791 810 C4' DC D2019 OK 812 809 811 829 C4' DG D2020 OK 831 828 830 851 C4' DT D2021 OK 853 850 852 871 C4' DT D2022 OK 873 870 872 891 C4' DT D2023 OK 893 890 892 911 C4' DT D2024 OK 913 910 912 931 C4' DC D2025 OK 933 930 932 950 C4' DG D2026 OK 952 949 951 7324 C4' DCT A1023 OK 7323 7326 7325 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' DC C1001 4 6 24 C5' DG C1002 23 25 46 C5' DA C1003 45 47 67 C5' DA C1004 66 68 88 C5' DA C1005 87 89 109 C5' DA C1006 108 110 130 C5' DC C1007 129 131 149 C5' DG C1008 148 150 171 C5' DA C1009 170 172 192 C5' DC C1010 191 193 211 C5' DG C1011 210 212 233 C5' DG C1012 232 234 255 C5' DC C1013 254 256 274 C5' DC C1014 273 275 293 C5' DA C1015 292 294 314 C5' DG C1016 313 315 336 C5' DT C1017 335 337 356 C5' DG C1018 355 357 378 C5' DC C1019 377 379 397 C5' DC C1020 396 398 416 C5' DA C1021 415 417 447 C5' 2DT C1022 436 448 457 C5' DT D2002 456 458 477 C5' DG D2003 476 478 499 C5' DG D2004 498 500 521 C5' DA D2005 520 522 542 C5' DT D2006 541 543 562 C5' DG D2007 561 563 584 C5' DG D2008 583 585 606 C5' DC D2009 605 607 625 C5' DA D2010 624 626 646 C5' DC D2011 645 647 665 C5' DT D2012 664 666 685 C5' DG D2013 684 686 707 C5' DG D2014 706 708 729 C5' DC D2015 728 730 748 C5' DC D2016 747 749 767 C5' DG D2017 766 768 789 C5' DT D2018 788 790 809 C5' DC D2019 808 810 828 C5' DG D2020 827 829 850 C5' DT D2021 849 851 870 C5' DT D2022 869 871 890 C5' DT D2023 889 891 910 C5' DT D2024 909 911 930 C5' DC D2025 929 931 949 C5' DG D2026 948 950 7326 C5' DCT A1023 7327 7324 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DC C1001 distorted distorted 2 3 4 20 P DG C1002 distorted distorted 9 21 22 23 42 P DA C1003 distorted distorted 28 43 44 45 63 P DA C1004 distorted distorted 50 64 65 66 84 P DA C1005 distorted distorted 71 85 86 87 105 P DA C1006 distorted distorted 92 106 107 108 126 P DC C1007 distorted distorted 113 127 128 129 145 P DG C1008 distorted distorted 134 146 147 148 167 P DA C1009 distorted distorted 153 168 169 170 188 P DC C1010 distorted distorted 175 189 190 191 207 P DG C1011 distorted distorted 196 208 209 210 229 P DG C1012 distorted distorted 215 230 231 232 251 P DC C1013 distorted distorted 237 252 253 254 270 P DC C1014 distorted distorted 259 271 272 273 289 P DA C1015 distorted distorted 278 290 291 292 310 P DG C1016 distorted distorted 297 311 312 313 332 P DT C1017 distorted distorted 318 333 334 335 352 P DG C1018 distorted distorted 340 353 354 355 374 P DC C1019 distorted distorted 360 375 376 377 393 P DC C1020 distorted distorted 382 394 395 396 412 P DA C1021 distorted distorted 401 413 414 415 433 P 2DT C1022 distorted distorted 420 434 435 436 453 P DT D2002 distorted distorted 454 455 456 473 P DG D2003 distorted distorted 461 474 475 476 495 P DG D2004 distorted distorted 481 496 497 498 517 P DA D2005 distorted distorted 503 518 519 520 538 P DT D2006 distorted distorted 525 539 540 541 558 P DG D2007 distorted distorted 546 559 560 561 580 P DG D2008 distorted distorted 566 581 582 583 602 P DC D2009 distorted distorted 588 603 604 605 621 P DA D2010 distorted distorted 610 622 623 624 642 P DC D2011 distorted distorted 629 643 644 645 661 P DT D2012 distorted distorted 650 662 663 664 681 P DG D2013 distorted distorted 669 682 683 684 703 P DG D2014 distorted distorted 689 704 705 706 725 P DC D2015 distorted distorted 711 726 727 728 744 P DC D2016 distorted distorted 733 745 746 747 763 P DG D2017 distorted distorted 752 764 765 766 785 P DT D2018 distorted distorted 771 786 787 788 805 P DC D2019 distorted distorted 793 806 807 808 824 P DG D2020 distorted distorted 813 825 826 827 846 P DT D2021 distorted distorted 832 847 848 849 866 P DT D2022 distorted distorted 854 867 868 869 886 P DT D2023 distorted distorted 874 887 888 889 906 P DT D2024 distorted distorted 894 907 908 909 926 P DC D2025 distorted distorted 914 927 928 929 945 P DG D2026 distorted distorted 934 946 947 948 ---------------------------------------------------------------------------------