ID code: '2D19' 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' C A 2 alpha beta 39 59 45 42 75 C1' U A 3 alpha beta 70 90 76 73 105 C1' G A 4 alpha beta 100 123 106 103 139 C1' A A 5 alpha beta 134 156 140 137 172 C1' A A 6 alpha beta 167 189 173 170 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' U A 8 alpha beta 234 254 240 237 269 C1' G A 9 alpha beta 264 287 270 267 303 C1' C A 10 alpha beta 298 318 304 301 334 C1' A A 11 alpha beta 329 351 335 332 367 C1' C A 12 alpha beta 362 382 368 365 398 C1' A A 13 alpha beta 393 415 399 396 431 C1' C A 14 alpha beta 426 446 432 429 462 C1' G A 15 alpha beta 457 480 463 460 496 C1' G A 16 alpha beta 491 514 497 494 530 C1' C A 17 alpha beta 525 545 531 528 559 C1' G B 1 alpha beta 554 577 560 557 594 C1' C B 2 alpha beta 589 609 595 592 625 C1' U B 3 alpha beta 620 640 626 623 655 C1' G B 4 alpha beta 650 673 656 653 689 C1' A B 5 alpha beta 684 706 690 687 722 C1' A B 6 alpha beta 717 739 723 720 755 C1' G B 7 alpha beta 750 773 756 753 789 C1' U B 8 alpha beta 784 804 790 787 819 C1' G B 9 alpha beta 814 837 820 817 853 C1' C B 10 alpha beta 848 868 854 851 884 C1' A B 11 alpha beta 879 901 885 882 917 C1' C B 12 alpha beta 912 932 918 915 948 C1' A B 13 alpha beta 943 965 949 946 981 C1' C B 14 alpha beta 976 996 982 979 1012 C1' G B 15 alpha beta 1007 1030 1013 1010 1046 C1' G B 16 alpha beta 1041 1064 1047 1044 1080 C1' C B 17 alpha beta 1075 1095 1081 1078 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 2 OK OK 44 40 57 43 73 C2' U A 3 OK OK 75 71 88 74 103 C2' G A 4 OK OK 105 101 121 104 137 C2' A A 5 OK OK 139 135 154 138 170 C2' A A 6 OK OK 172 168 187 171 203 C2' G A 7 OK OK 205 201 221 204 237 C2' U A 8 OK OK 239 235 252 238 267 C2' G A 9 OK OK 269 265 285 268 301 C2' C A 10 OK OK 303 299 316 302 332 C2' A A 11 OK OK 334 330 349 333 365 C2' C A 12 OK OK 367 363 380 366 396 C2' A A 13 OK OK 398 394 413 397 429 C2' C A 14 OK OK 431 427 444 430 460 C2' G A 15 OK OK 462 458 478 461 494 C2' G A 16 OK OK 496 492 512 495 528 C2' C A 17 OK OK 530 526 543 529 557 C2' G B 1 OK OK 559 555 575 558 592 C2' C B 2 OK OK 594 590 607 593 623 C2' U B 3 OK OK 625 621 638 624 653 C2' G B 4 OK OK 655 651 671 654 687 C2' A B 5 OK OK 689 685 704 688 720 C2' A B 6 OK OK 722 718 737 721 753 C2' G B 7 OK OK 755 751 771 754 787 C2' U B 8 OK OK 789 785 802 788 817 C2' G B 9 OK OK 819 815 835 818 851 C2' C B 10 OK OK 853 849 866 852 882 C2' A B 11 OK OK 884 880 899 883 915 C2' C B 12 OK OK 917 913 930 916 946 C2' A B 13 OK OK 948 944 963 947 979 C2' C B 14 OK OK 981 977 994 980 1010 C2' G B 15 OK OK 1012 1008 1028 1011 1044 C2' G B 16 OK OK 1046 1042 1062 1045 1078 C2' C B 17 OK OK 1080 1076 1093 1079 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' U A 3 OK OK 69 87 72 73 101 C3' G A 4 OK OK 99 120 102 103 135 C3' A A 5 OK OK 133 153 136 137 168 C3' A A 6 OK OK 166 186 169 170 201 C3' G A 7 OK OK 199 220 202 203 235 C3' U A 8 OK OK 233 251 236 237 265 C3' G A 9 OK OK 263 284 266 267 299 C3' C A 10 OK OK 297 315 300 301 330 C3' A A 11 OK OK 328 348 331 332 363 C3' C A 12 OK OK 361 379 364 365 394 C3' A A 13 OK OK 392 412 395 396 427 C3' C A 14 OK OK 425 443 428 429 458 C3' G A 15 OK OK 456 477 459 460 492 C3' G A 16 OK OK 490 511 493 494 526 C3' C A 17 OK OK 524 542 527 528 555 C3' G B 1 OK OK 553 574 556 557 590 C3' C B 2 OK OK 588 606 591 592 621 C3' U B 3 OK OK 619 637 622 623 651 C3' G B 4 OK OK 649 670 652 653 685 C3' A B 5 OK OK 683 703 686 687 718 C3' A B 6 OK OK 716 736 719 720 751 C3' G B 7 OK OK 749 770 752 753 785 C3' U B 8 OK OK 783 801 786 787 815 C3' G B 9 OK OK 813 834 816 817 849 C3' C B 10 OK OK 847 865 850 851 880 C3' A B 11 OK OK 878 898 881 882 913 C3' C B 12 OK OK 911 929 914 915 944 C3' A B 13 OK OK 942 962 945 946 977 C3' C B 14 OK OK 975 993 978 979 1008 C3' G B 15 OK OK 1006 1027 1009 1010 1042 C3' G B 16 OK OK 1040 1061 1043 1044 1076 C3' C B 17 OK OK 1074 1092 1077 1078 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' U A 3 OK OK 71 86 68 70 99 C4' G A 4 OK OK 101 119 98 100 133 C4' A A 5 OK OK 135 152 132 134 166 C4' A A 6 OK OK 168 185 165 167 199 C4' G A 7 OK OK 201 219 198 200 233 C4' U A 8 OK OK 235 250 232 234 263 C4' G A 9 OK OK 265 283 262 264 297 C4' C A 10 OK OK 299 314 296 298 328 C4' A A 11 OK OK 330 347 327 329 361 C4' C A 12 OK OK 363 378 360 362 392 C4' A A 13 OK OK 394 411 391 393 425 C4' C A 14 OK OK 427 442 424 426 456 C4' G A 15 OK OK 458 476 455 457 490 C4' G A 16 OK OK 492 510 489 491 524 C4' C A 17 OK OK 526 541 523 525 553 C4' G B 1 OK OK 555 573 552 554 588 C4' C B 2 OK OK 590 605 587 589 619 C4' U B 3 OK OK 621 636 618 620 649 C4' G B 4 OK OK 651 669 648 650 683 C4' A B 5 OK OK 685 702 682 684 716 C4' A B 6 OK OK 718 735 715 717 749 C4' G B 7 OK OK 751 769 748 750 783 C4' U B 8 OK OK 785 800 782 784 813 C4' G B 9 OK OK 815 833 812 814 847 C4' C B 10 OK OK 849 864 846 848 878 C4' A B 11 OK OK 880 897 877 879 911 C4' C B 12 OK OK 913 928 910 912 942 C4' A B 13 OK OK 944 961 941 943 975 C4' C B 14 OK OK 977 992 974 976 1006 C4' G B 15 OK OK 1008 1026 1005 1007 1040 C4' G B 16 OK OK 1042 1060 1039 1041 1074 C4' C B 17 OK OK 1076 1091 1073 1075 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 2 OK OK 36 53 54 38 68 C5' U A 3 OK OK 67 84 85 69 98 C5' G A 4 OK OK 97 117 118 99 132 C5' A A 5 OK OK 131 150 151 133 165 C5' A A 6 OK OK 164 183 184 166 198 C5' G A 7 OK OK 197 217 218 199 232 C5' U A 8 OK OK 231 248 249 233 262 C5' G A 9 OK OK 261 281 282 263 296 C5' C A 10 OK OK 295 312 313 297 327 C5' A A 11 OK OK 326 345 346 328 360 C5' C A 12 OK OK 359 376 377 361 391 C5' A A 13 OK OK 390 409 410 392 424 C5' C A 14 OK OK 423 440 441 425 455 C5' G A 15 OK OK 454 474 475 456 489 C5' G A 16 OK OK 488 508 509 490 523 C5' C A 17 OK OK 522 539 540 524 552 C5' G B 1 OK OK 551 571 572 553 587 C5' C B 2 OK OK 586 603 604 588 618 C5' U B 3 OK OK 617 634 635 619 648 C5' G B 4 OK OK 647 667 668 649 682 C5' A B 5 OK OK 681 700 701 683 715 C5' A B 6 OK OK 714 733 734 716 748 C5' G B 7 OK OK 747 767 768 749 782 C5' U B 8 OK OK 781 798 799 783 812 C5' G B 9 OK OK 811 831 832 813 846 C5' C B 10 OK OK 845 862 863 847 877 C5' A B 11 OK OK 876 895 896 878 910 C5' C B 12 OK OK 909 926 927 911 941 C5' A B 13 OK OK 940 959 960 942 974 C5' C B 14 OK OK 973 990 991 975 1005 C5' G B 15 OK OK 1004 1024 1025 1006 1039 C5' G B 16 OK OK 1038 1058 1059 1040 1073 C5' C B 17 OK OK 1072 1089 1090 1074 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P U A 3 distorted distorted 41 65 66 67 94 P G A 4 distorted distorted 72 95 96 97 128 P A A 5 distorted distorted 102 129 130 131 161 P A A 6 distorted distorted 136 162 163 164 194 P G A 7 distorted distorted 169 195 196 197 228 P U A 8 distorted distorted 202 229 230 231 258 P G A 9 distorted distorted 236 259 260 261 292 P C A 10 distorted distorted 266 293 294 295 323 P A A 11 distorted distorted 300 324 325 326 356 P C A 12 distorted distorted 331 357 358 359 387 P A A 13 distorted distorted 364 388 389 390 420 P C A 14 distorted distorted 395 421 422 423 451 P G A 15 distorted distorted 428 452 453 454 485 P G A 16 distorted distorted 459 486 487 488 519 P C A 17 distorted distorted 493 520 521 522 583 P C B 2 distorted distorted 556 584 585 586 614 P U B 3 distorted distorted 591 615 616 617 644 P G B 4 distorted distorted 622 645 646 647 678 P A B 5 distorted distorted 652 679 680 681 711 P A B 6 distorted distorted 686 712 713 714 744 P G B 7 distorted distorted 719 745 746 747 778 P U B 8 distorted distorted 752 779 780 781 808 P G B 9 distorted distorted 786 809 810 811 842 P C B 10 distorted distorted 816 843 844 845 873 P A B 11 distorted distorted 850 874 875 876 906 P C B 12 distorted distorted 881 907 908 909 937 P A B 13 distorted distorted 914 938 939 940 970 P C B 14 distorted distorted 945 971 972 973 1001 P G B 15 distorted distorted 978 1002 1003 1004 1035 P G B 16 distorted distorted 1009 1036 1037 1038 1069 P C B 17 distorted distorted 1043 1070 1071 1072 ---------------------------------------------------------------------------------