ID code: '2LDT' 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 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' G A 4 alpha beta 107 130 113 110 146 C1' A A 5 alpha beta 141 163 147 144 179 C1' G A 6 alpha beta 174 197 180 177 213 C1' U A 7 alpha beta 208 228 214 211 243 C1' A A 8 alpha beta 238 260 244 241 276 C1' C A 9 alpha beta 271 291 277 274 307 C1' G A 10 alpha beta 302 325 308 305 341 C1' G A 11 alpha beta 336 359 342 339 375 C1' C A 12 alpha beta 370 390 376 373 406 C1' C A 13 alpha beta 401 421 407 404 437 C1' G A 14 alpha beta 432 455 438 435 471 C1' C A 15 alpha beta 466 486 472 469 502 C1' A A 16 alpha beta 497 519 503 500 535 C1' A A 17 alpha beta 530 552 536 533 568 C1' G A 18 alpha beta 563 586 569 566 602 C1' G A 19 alpha beta 597 620 603 600 636 C1' U A 20 alpha beta 631 651 637 634 666 C1' U A 21 alpha beta 661 681 667 664 696 C1' A A 22 alpha beta 691 713 697 694 729 C1' A A 23 alpha beta 724 746 730 727 762 C1' A A 24 alpha beta 757 779 763 760 795 C1' A A 25 alpha beta 790 812 796 793 828 C1' C A 26 alpha beta 823 843 829 826 859 C1' U A 27 alpha beta 854 874 860 857 889 C1' C A 28 alpha beta 884 904 890 887 920 C1' C A 29 alpha beta 915 935 921 918 951 C1' C A 30 alpha beta 946 966 952 949 982 C1' C A 31 alpha beta 977 998 983 980 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' G A 4 OK OK 112 108 128 111 144 C2' A A 5 OK OK 146 142 161 145 177 C2' G A 6 OK OK 179 175 195 178 211 C2' U A 7 OK OK 213 209 226 212 241 C2' A A 8 OK OK 243 239 258 242 274 C2' C A 9 OK OK 276 272 289 275 305 C2' G A 10 OK OK 307 303 323 306 339 C2' G A 11 OK OK 341 337 357 340 373 C2' C A 12 OK OK 375 371 388 374 404 C2' C A 13 OK OK 406 402 419 405 435 C2' G A 14 OK OK 437 433 453 436 469 C2' C A 15 OK OK 471 467 484 470 500 C2' A A 16 OK OK 502 498 517 501 533 C2' A A 17 OK OK 535 531 550 534 566 C2' G A 18 OK OK 568 564 584 567 600 C2' G A 19 OK OK 602 598 618 601 634 C2' U A 20 OK OK 636 632 649 635 664 C2' U A 21 OK OK 666 662 679 665 694 C2' A A 22 OK OK 696 692 711 695 727 C2' A A 23 OK OK 729 725 744 728 760 C2' A A 24 OK OK 762 758 777 761 793 C2' A A 25 OK OK 795 791 810 794 826 C2' C A 26 OK OK 828 824 841 827 857 C2' U A 27 OK OK 859 855 872 858 887 C2' C A 28 OK OK 889 885 902 888 918 C2' C A 29 OK OK 920 916 933 919 949 C2' C A 30 OK OK 951 947 964 950 980 C2' C A 31 OK OK 982 978 996 981 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' G A 4 OK OK 106 127 109 110 142 C3' A A 5 OK OK 140 160 143 144 175 C3' G A 6 OK OK 173 194 176 177 209 C3' U A 7 OK OK 207 225 210 211 239 C3' A A 8 OK OK 237 257 240 241 272 C3' C A 9 OK OK 270 288 273 274 303 C3' G A 10 OK OK 301 322 304 305 337 C3' G A 11 OK OK 335 356 338 339 371 C3' C A 12 OK OK 369 387 372 373 402 C3' C A 13 OK OK 400 418 403 404 433 C3' G A 14 OK OK 431 452 434 435 467 C3' C A 15 OK OK 465 483 468 469 498 C3' A A 16 OK OK 496 516 499 500 531 C3' A A 17 OK OK 529 549 532 533 564 C3' G A 18 OK OK 562 583 565 566 598 C3' G A 19 OK OK 596 617 599 600 632 C3' U A 20 OK OK 630 648 633 634 662 C3' U A 21 OK OK 660 678 663 664 692 C3' A A 22 OK OK 690 710 693 694 725 C3' A A 23 OK OK 723 743 726 727 758 C3' A A 24 OK OK 756 776 759 760 791 C3' A A 25 OK OK 789 809 792 793 824 C3' C A 26 OK OK 822 840 825 826 855 C3' U A 27 OK OK 853 871 856 857 885 C3' C A 28 OK OK 883 901 886 887 916 C3' C A 29 OK OK 914 932 917 918 947 C3' C A 30 OK OK 945 963 948 949 978 C3' C A 31 OK OK 976 994 979 980 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' G A 4 OK OK 108 126 105 107 140 C4' A A 5 OK OK 142 159 139 141 173 C4' G A 6 OK OK 175 193 172 174 207 C4' U A 7 OK OK 209 224 206 208 237 C4' A A 8 OK OK 239 256 236 238 270 C4' C A 9 OK OK 272 287 269 271 301 C4' G A 10 OK OK 303 321 300 302 335 C4' G A 11 OK OK 337 355 334 336 369 C4' C A 12 OK OK 371 386 368 370 400 C4' C A 13 OK OK 402 417 399 401 431 C4' G A 14 OK OK 433 451 430 432 465 C4' C A 15 OK OK 467 482 464 466 496 C4' A A 16 OK OK 498 515 495 497 529 C4' A A 17 OK OK 531 548 528 530 562 C4' G A 18 OK OK 564 582 561 563 596 C4' G A 19 OK OK 598 616 595 597 630 C4' U A 20 OK OK 632 647 629 631 660 C4' U A 21 OK OK 662 677 659 661 690 C4' A A 22 OK OK 692 709 689 691 723 C4' A A 23 OK OK 725 742 722 724 756 C4' A A 24 OK OK 758 775 755 757 789 C4' A A 25 OK OK 791 808 788 790 822 C4' C A 26 OK OK 824 839 821 823 853 C4' U A 27 OK OK 855 870 852 854 883 C4' C A 28 OK OK 885 900 882 884 914 C4' C A 29 OK OK 916 931 913 915 945 C4' C A 30 OK OK 947 962 944 946 976 C4' C A 31 OK OK 978 993 975 977 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' G A 4 OK OK 104 124 125 106 139 C5' A A 5 OK OK 138 157 158 140 172 C5' G A 6 OK OK 171 191 192 173 206 C5' U A 7 OK OK 205 222 223 207 236 C5' A A 8 OK OK 235 254 255 237 269 C5' C A 9 OK OK 268 285 286 270 300 C5' G A 10 OK OK 299 319 320 301 334 C5' G A 11 OK OK 333 353 354 335 368 C5' C A 12 OK OK 367 384 385 369 399 C5' C A 13 OK OK 398 415 416 400 430 C5' G A 14 OK OK 429 449 450 431 464 C5' C A 15 OK OK 463 480 481 465 495 C5' A A 16 OK OK 494 513 514 496 528 C5' A A 17 OK OK 527 546 547 529 561 C5' G A 18 OK OK 560 580 581 562 595 C5' G A 19 OK OK 594 614 615 596 629 C5' U A 20 OK OK 628 645 646 630 659 C5' U A 21 OK OK 658 675 676 660 689 C5' A A 22 OK OK 688 707 708 690 722 C5' A A 23 OK OK 721 740 741 723 755 C5' A A 24 OK OK 754 773 774 756 788 C5' A A 25 OK OK 787 806 807 789 821 C5' C A 26 OK OK 820 837 838 822 852 C5' U A 27 OK OK 851 868 869 853 882 C5' C A 28 OK OK 881 898 899 883 913 C5' C A 29 OK OK 912 929 930 914 944 C5' C A 30 OK OK 943 960 961 945 975 C5' C A 31 OK OK 974 991 992 976 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P G A 4 distorted distorted 75 102 103 104 135 P A A 5 distorted distorted 109 136 137 138 168 P G A 6 distorted distorted 143 169 170 171 202 P U A 7 distorted distorted 176 203 204 205 232 P A A 8 distorted distorted 210 233 234 235 265 P C A 9 distorted distorted 240 266 267 268 296 P G A 10 distorted distorted 273 297 298 299 330 P G A 11 distorted distorted 304 331 332 333 364 P C A 12 distorted distorted 338 365 366 367 395 P C A 13 distorted distorted 372 396 397 398 426 P G A 14 distorted distorted 403 427 428 429 460 P C A 15 distorted distorted 434 461 462 463 491 P A A 16 distorted distorted 468 492 493 494 524 P A A 17 distorted distorted 499 525 526 527 557 P G A 18 distorted distorted 532 558 559 560 591 P G A 19 distorted distorted 565 592 593 594 625 P U A 20 distorted distorted 599 626 627 628 655 P U A 21 distorted distorted 633 656 657 658 685 P A A 22 distorted distorted 663 686 687 688 718 P A A 23 distorted distorted 693 719 720 721 751 P A A 24 distorted distorted 726 752 753 754 784 P A A 25 distorted distorted 759 785 786 787 817 P C A 26 distorted distorted 792 818 819 820 848 P U A 27 distorted distorted 825 849 850 851 878 P C A 28 distorted distorted 856 879 880 881 909 P C A 29 distorted distorted 886 910 911 912 940 P C A 30 distorted distorted 917 941 942 943 971 P C A 31 distorted distorted 948 972 973 974 ---------------------------------------------------------------------------------