ID code: '1MDM' 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' T C 2 beta 7 12 10 31 C1' G C 3 beta 27 32 30 53 C1' C C 4 beta 49 54 52 72 C1' C C 5 beta 68 73 71 91 C1' G C 6 beta 87 92 90 113 C1' G C 7 beta 109 114 112 135 C1' A C 8 beta 131 136 134 156 C1' G C 9 beta 152 157 155 178 C1' A C 10 beta 174 179 177 199 C1' T C 11 beta 195 200 198 219 C1' G C 12 beta 215 220 218 241 C1' G C 13 beta 237 242 240 263 C1' G C 14 beta 259 264 262 285 C1' C C 15 beta 281 286 284 304 C1' T C 16 beta 300 305 303 324 C1' C C 17 beta 320 325 323 343 C1' C C 18 beta 339 344 342 362 C1' A C 19 beta 358 363 361 383 C1' G C 20 beta 379 384 382 405 C1' T C 21 beta 401 406 404 425 C1' G C 22 beta 421 426 424 447 C1' G C 23 beta 443 448 446 469 C1' C C 24 beta 465 470 468 488 C1' C C 25 beta 484 489 487 507 C1' T C 26 beta 503 508 506 528 C1' A D 2 beta 524 529 527 549 C1' G D 3 beta 545 550 548 571 C1' G D 4 beta 567 572 570 593 C1' C D 5 beta 589 594 592 612 C1' C D 6 beta 608 613 611 631 C1' A D 7 beta 627 632 630 652 C1' C D 8 beta 648 653 651 671 C1' T D 9 beta 667 672 670 691 C1' G D 10 beta 687 692 690 713 C1' G D 11 beta 709 714 712 735 C1' A D 12 beta 731 736 734 756 C1' G D 13 beta 752 757 755 778 C1' C D 14 beta 774 779 777 797 C1' C D 15 beta 793 798 796 816 C1' C D 16 beta 812 817 815 835 C1' A D 17 beta 831 836 834 856 C1' T D 18 beta 852 857 855 876 C1' C D 19 beta 872 877 875 895 C1' T D 20 beta 891 896 894 915 C1' C D 21 beta 911 916 914 934 C1' C D 22 beta 930 935 933 953 C1' G D 23 beta 949 954 952 975 C1' G D 24 beta 971 976 974 997 C1' C D 25 beta 993 998 996 1016 C1' A D 26 beta 1012 1017 1015 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T C 2 11 8 30 C2' G C 3 31 28 52 C2' C C 4 53 50 71 C2' C C 5 72 69 90 C2' G C 6 91 88 112 C2' G C 7 113 110 134 C2' A C 8 135 132 155 C2' G C 9 156 153 177 C2' A C 10 178 175 198 C2' T C 11 199 196 218 C2' G C 12 219 216 240 C2' G C 13 241 238 262 C2' G C 14 263 260 284 C2' C C 15 285 282 303 C2' T C 16 304 301 323 C2' C C 17 324 321 342 C2' C C 18 343 340 361 C2' A C 19 362 359 382 C2' G C 20 383 380 404 C2' T C 21 405 402 424 C2' G C 22 425 422 446 C2' G C 23 447 444 468 C2' C C 24 469 466 487 C2' C C 25 488 485 506 C2' T C 26 507 504 527 C2' A D 2 528 525 548 C2' G D 3 549 546 570 C2' G D 4 571 568 592 C2' C D 5 593 590 611 C2' C D 6 612 609 630 C2' A D 7 631 628 651 C2' C D 8 652 649 670 C2' T D 9 671 668 690 C2' G D 10 691 688 712 C2' G D 11 713 710 734 C2' A D 12 735 732 755 C2' G D 13 756 753 777 C2' C D 14 778 775 796 C2' C D 15 797 794 815 C2' C D 16 816 813 834 C2' A D 17 835 832 855 C2' T D 18 856 853 875 C2' C D 19 876 873 894 C2' T D 20 895 892 914 C2' C D 21 915 912 933 C2' C D 22 934 931 952 C2' G D 23 953 950 974 C2' G D 24 975 972 996 C2' C D 25 997 994 1015 C2' A D 26 1016 1013 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T C 2 OK 6 9 10 28 C3' G C 3 OK 26 29 30 50 C3' C C 4 OK 48 51 52 69 C3' C C 5 OK 67 70 71 88 C3' G C 6 OK 86 89 90 110 C3' G C 7 OK 108 111 112 132 C3' A C 8 OK 130 133 134 153 C3' G C 9 OK 151 154 155 175 C3' A C 10 OK 173 176 177 196 C3' T C 11 OK 194 197 198 216 C3' G C 12 OK 214 217 218 238 C3' G C 13 OK 236 239 240 260 C3' G C 14 OK 258 261 262 282 C3' C C 15 OK 280 283 284 301 C3' T C 16 OK 299 302 303 321 C3' C C 17 OK 319 322 323 340 C3' C C 18 OK 338 341 342 359 C3' A C 19 OK 357 360 361 380 C3' G C 20 OK 378 381 382 402 C3' T C 21 OK 400 403 404 422 C3' G C 22 OK 420 423 424 444 C3' G C 23 OK 442 445 446 466 C3' C C 24 OK 464 467 468 485 C3' C C 25 OK 483 486 487 504 C3' T C 26 OK 502 505 506 525 C3' A D 2 OK 523 526 527 546 C3' G D 3 OK 544 547 548 568 C3' G D 4 OK 566 569 570 590 C3' C D 5 OK 588 591 592 609 C3' C D 6 OK 607 610 611 628 C3' A D 7 OK 626 629 630 649 C3' C D 8 OK 647 650 651 668 C3' T D 9 OK 666 669 670 688 C3' G D 10 OK 686 689 690 710 C3' G D 11 OK 708 711 712 732 C3' A D 12 OK 730 733 734 753 C3' G D 13 OK 751 754 755 775 C3' C D 14 OK 773 776 777 794 C3' C D 15 OK 792 795 796 813 C3' C D 16 OK 811 814 815 832 C3' A D 17 OK 830 833 834 853 C3' T D 18 OK 851 854 855 873 C3' C D 19 OK 871 874 875 892 C3' T D 20 OK 890 893 894 912 C3' C D 21 OK 910 913 914 931 C3' C D 22 OK 929 932 933 950 C3' G D 23 OK 948 951 952 972 C3' G D 24 OK 970 973 974 994 C3' C D 25 OK 992 995 996 1013 C3' A D 26 OK 1011 1014 1015 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T C 2 OK 8 5 7 26 C4' G C 3 OK 28 25 27 48 C4' C C 4 OK 50 47 49 67 C4' C C 5 OK 69 66 68 86 C4' G C 6 OK 88 85 87 108 C4' G C 7 OK 110 107 109 130 C4' A C 8 OK 132 129 131 151 C4' G C 9 OK 153 150 152 173 C4' A C 10 OK 175 172 174 194 C4' T C 11 OK 196 193 195 214 C4' G C 12 OK 216 213 215 236 C4' G C 13 OK 238 235 237 258 C4' G C 14 OK 260 257 259 280 C4' C C 15 OK 282 279 281 299 C4' T C 16 OK 301 298 300 319 C4' C C 17 OK 321 318 320 338 C4' C C 18 OK 340 337 339 357 C4' A C 19 OK 359 356 358 378 C4' G C 20 OK 380 377 379 400 C4' T C 21 OK 402 399 401 420 C4' G C 22 OK 422 419 421 442 C4' G C 23 OK 444 441 443 464 C4' C C 24 OK 466 463 465 483 C4' C C 25 OK 485 482 484 502 C4' T C 26 OK 504 501 503 523 C4' A D 2 OK 525 522 524 544 C4' G D 3 OK 546 543 545 566 C4' G D 4 OK 568 565 567 588 C4' C D 5 OK 590 587 589 607 C4' C D 6 OK 609 606 608 626 C4' A D 7 OK 628 625 627 647 C4' C D 8 OK 649 646 648 666 C4' T D 9 OK 668 665 667 686 C4' G D 10 OK 688 685 687 708 C4' G D 11 OK 710 707 709 730 C4' A D 12 OK 732 729 731 751 C4' G D 13 OK 753 750 752 773 C4' C D 14 OK 775 772 774 792 C4' C D 15 OK 794 791 793 811 C4' C D 16 OK 813 810 812 830 C4' A D 17 OK 832 829 831 851 C4' T D 18 OK 853 850 852 871 C4' C D 19 OK 873 870 872 890 C4' T D 20 OK 892 889 891 910 C4' C D 21 OK 912 909 911 929 C4' C D 22 OK 931 928 930 948 C4' G D 23 OK 950 947 949 970 C4' G D 24 OK 972 969 971 992 C4' C D 25 OK 994 991 993 1011 C4' A D 26 OK 1013 1010 1012 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T C 2 4 6 25 C5' G C 3 24 26 47 C5' C C 4 46 48 66 C5' C C 5 65 67 85 C5' G C 6 84 86 107 C5' G C 7 106 108 129 C5' A C 8 128 130 150 C5' G C 9 149 151 172 C5' A C 10 171 173 193 C5' T C 11 192 194 213 C5' G C 12 212 214 235 C5' G C 13 234 236 257 C5' G C 14 256 258 279 C5' C C 15 278 280 298 C5' T C 16 297 299 318 C5' C C 17 317 319 337 C5' C C 18 336 338 356 C5' A C 19 355 357 377 C5' G C 20 376 378 399 C5' T C 21 398 400 419 C5' G C 22 418 420 441 C5' G C 23 440 442 463 C5' C C 24 462 464 482 C5' C C 25 481 483 501 C5' T C 26 500 502 522 C5' A D 2 521 523 543 C5' G D 3 542 544 565 C5' G D 4 564 566 587 C5' C D 5 586 588 606 C5' C D 6 605 607 625 C5' A D 7 624 626 646 C5' C D 8 645 647 665 C5' T D 9 664 666 685 C5' G D 10 684 686 707 C5' G D 11 706 708 729 C5' A D 12 728 730 750 C5' G D 13 749 751 772 C5' C D 14 771 773 791 C5' C D 15 790 792 810 C5' C D 16 809 811 829 C5' A D 17 828 830 850 C5' T D 18 849 851 870 C5' C D 19 869 871 889 C5' T D 20 888 890 909 C5' C D 21 908 910 928 C5' C D 22 927 929 947 C5' G D 23 946 948 969 C5' G D 24 968 970 991 C5' C D 25 990 992 1010 C5' A D 26 1009 1011 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T C 2 distorted distorted 2 3 4 21 P G C 3 distorted distorted 9 22 23 24 43 P C C 4 distorted distorted 29 44 45 46 62 P C C 5 distorted distorted 51 63 64 65 81 P G C 6 distorted distorted 70 82 83 84 103 P G C 7 distorted distorted 89 104 105 106 125 P A C 8 distorted distorted 111 126 127 128 146 P G C 9 distorted distorted 133 147 148 149 168 P A C 10 distorted distorted 154 169 170 171 189 P T C 11 distorted distorted 176 190 191 192 209 P G C 12 distorted distorted 197 210 211 212 231 P G C 13 distorted distorted 217 232 233 234 253 P G C 14 distorted distorted 239 254 255 256 275 P C C 15 distorted distorted 261 276 277 278 294 P T C 16 distorted distorted 283 295 296 297 314 P C C 17 distorted distorted 302 315 316 317 333 P C C 18 distorted distorted 322 334 335 336 352 P A C 19 distorted distorted 341 353 354 355 373 P G C 20 distorted distorted 360 374 375 376 395 P T C 21 distorted distorted 381 396 397 398 415 P G C 22 distorted distorted 403 416 417 418 437 P G C 23 distorted distorted 423 438 439 440 459 P C C 24 distorted distorted 445 460 461 462 478 P C C 25 distorted distorted 467 479 480 481 497 P T C 26 distorted distorted 486 498 499 500 518 P A D 2 distorted distorted 519 520 521 539 P G D 3 distorted distorted 526 540 541 542 561 P G D 4 distorted distorted 547 562 563 564 583 P C D 5 distorted distorted 569 584 585 586 602 P C D 6 distorted distorted 591 603 604 605 621 P A D 7 distorted distorted 610 622 623 624 642 P C D 8 distorted distorted 629 643 644 645 661 P T D 9 distorted distorted 650 662 663 664 681 P G D 10 distorted distorted 669 682 683 684 703 P G D 11 distorted distorted 689 704 705 706 725 P A D 12 distorted distorted 711 726 727 728 746 P G D 13 distorted distorted 733 747 748 749 768 P C D 14 distorted distorted 754 769 770 771 787 P C D 15 distorted distorted 776 788 789 790 806 P C D 16 distorted distorted 795 807 808 809 825 P A D 17 distorted distorted 814 826 827 828 846 P T D 18 distorted distorted 833 847 848 849 866 P C D 19 distorted distorted 854 867 868 869 885 P T D 20 distorted distorted 874 886 887 888 905 P C D 21 distorted distorted 893 906 907 908 924 P C D 22 distorted distorted 913 925 926 927 943 P G D 23 distorted distorted 932 944 945 946 965 P G D 24 distorted distorted 951 966 967 968 987 P C D 25 distorted distorted 973 988 989 990 1006 P A D 26 distorted distorted 995 1007 1008 1009 ---------------------------------------------------------------------------------