ID code: '1E95' 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' G A 3 alpha beta 70 93 76 73 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' C A 5 alpha beta 138 158 144 141 174 C1' C A 6 alpha beta 169 189 175 172 205 C1' A A 7 alpha beta 200 222 206 203 238 C1' G A 8 alpha beta 233 256 239 236 272 C1' C A 9 alpha beta 267 287 273 270 303 C1' U A 10 alpha beta 298 318 304 301 333 C1' C A 11 alpha beta 328 348 334 331 364 C1' C A 12 alpha beta 359 379 365 362 395 C1' A A 13 alpha beta 390 412 396 393 428 C1' G A 14 alpha beta 423 446 429 426 462 C1' G A 15 alpha beta 457 480 463 460 496 C1' C A 16 alpha beta 491 511 497 494 527 C1' C A 17 alpha beta 522 542 528 525 558 C1' G A 18 alpha beta 553 576 559 556 592 C1' C A 19 alpha beta 587 607 593 590 623 C1' C A 20 alpha beta 618 638 624 621 654 C1' A A 21 alpha beta 649 671 655 652 687 C1' A A 22 alpha beta 682 704 688 685 720 C1' A A 23 alpha beta 715 737 721 718 753 C1' C A 24 alpha beta 748 768 754 751 784 C1' A A 25 alpha beta 779 801 785 782 817 C1' A A 26 alpha beta 812 834 818 815 850 C1' U A 27 alpha beta 845 865 851 848 880 C1' A A 28 alpha beta 875 897 881 878 913 C1' U A 29 alpha beta 908 928 914 911 943 C1' G A 30 alpha beta 938 961 944 941 977 C1' G A 31 alpha beta 972 995 978 975 1011 C1' A A 32 alpha beta 1006 1028 1012 1009 1044 C1' G A 33 alpha beta 1039 1062 1045 1042 1078 C1' C A 34 alpha beta 1073 1093 1079 1076 1109 C1' A A 35 alpha beta 1104 1126 1110 1107 1142 C1' C A 36 alpha beta 1137 1157 1143 1140 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 75 71 91 74 107 C2' G A 4 OK OK 109 105 125 108 141 C2' C A 5 OK OK 143 139 156 142 172 C2' C A 6 OK OK 174 170 187 173 203 C2' A A 7 OK OK 205 201 220 204 236 C2' G A 8 OK OK 238 234 254 237 270 C2' C A 9 OK OK 272 268 285 271 301 C2' U A 10 OK OK 303 299 316 302 331 C2' C A 11 OK OK 333 329 346 332 362 C2' C A 12 OK OK 364 360 377 363 393 C2' A A 13 OK OK 395 391 410 394 426 C2' G A 14 OK OK 428 424 444 427 460 C2' G A 15 OK OK 462 458 478 461 494 C2' C A 16 OK OK 496 492 509 495 525 C2' C A 17 OK OK 527 523 540 526 556 C2' G A 18 OK OK 558 554 574 557 590 C2' C A 19 OK OK 592 588 605 591 621 C2' C A 20 OK OK 623 619 636 622 652 C2' A A 21 OK OK 654 650 669 653 685 C2' A A 22 OK OK 687 683 702 686 718 C2' A A 23 OK OK 720 716 735 719 751 C2' C A 24 OK OK 753 749 766 752 782 C2' A A 25 OK OK 784 780 799 783 815 C2' A A 26 OK OK 817 813 832 816 848 C2' U A 27 OK OK 850 846 863 849 878 C2' A A 28 OK OK 880 876 895 879 911 C2' U A 29 OK OK 913 909 926 912 941 C2' G A 30 OK OK 943 939 959 942 975 C2' G A 31 OK OK 977 973 993 976 1009 C2' A A 32 OK OK 1011 1007 1026 1010 1042 C2' G A 33 OK OK 1044 1040 1060 1043 1076 C2' C A 34 OK OK 1078 1074 1091 1077 1107 C2' A A 35 OK OK 1109 1105 1124 1108 1140 C2' C A 36 OK OK 1142 1138 1155 1141 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 69 90 72 73 105 C3' G A 4 OK OK 103 124 106 107 139 C3' C A 5 OK OK 137 155 140 141 170 C3' C A 6 OK OK 168 186 171 172 201 C3' A A 7 OK OK 199 219 202 203 234 C3' G A 8 OK OK 232 253 235 236 268 C3' C A 9 OK OK 266 284 269 270 299 C3' U A 10 OK OK 297 315 300 301 329 C3' C A 11 OK OK 327 345 330 331 360 C3' C A 12 OK OK 358 376 361 362 391 C3' A A 13 OK OK 389 409 392 393 424 C3' G A 14 OK OK 422 443 425 426 458 C3' G A 15 OK OK 456 477 459 460 492 C3' C A 16 OK OK 490 508 493 494 523 C3' C A 17 OK OK 521 539 524 525 554 C3' G A 18 OK OK 552 573 555 556 588 C3' C A 19 OK OK 586 604 589 590 619 C3' C A 20 OK OK 617 635 620 621 650 C3' A A 21 OK OK 648 668 651 652 683 C3' A A 22 OK OK 681 701 684 685 716 C3' A A 23 OK OK 714 734 717 718 749 C3' C A 24 OK OK 747 765 750 751 780 C3' A A 25 OK OK 778 798 781 782 813 C3' A A 26 OK OK 811 831 814 815 846 C3' U A 27 OK OK 844 862 847 848 876 C3' A A 28 OK OK 874 894 877 878 909 C3' U A 29 OK OK 907 925 910 911 939 C3' G A 30 OK OK 937 958 940 941 973 C3' G A 31 OK OK 971 992 974 975 1007 C3' A A 32 OK OK 1005 1025 1008 1009 1040 C3' G A 33 OK OK 1038 1059 1041 1042 1074 C3' C A 34 OK OK 1072 1090 1075 1076 1105 C3' A A 35 OK OK 1103 1123 1106 1107 1138 C3' C A 36 OK OK 1136 1154 1139 1140 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 71 89 68 70 103 C4' G A 4 OK OK 105 123 102 104 137 C4' C A 5 OK OK 139 154 136 138 168 C4' C A 6 OK OK 170 185 167 169 199 C4' A A 7 OK OK 201 218 198 200 232 C4' G A 8 OK OK 234 252 231 233 266 C4' C A 9 OK OK 268 283 265 267 297 C4' U A 10 OK OK 299 314 296 298 327 C4' C A 11 OK OK 329 344 326 328 358 C4' C A 12 OK OK 360 375 357 359 389 C4' A A 13 OK OK 391 408 388 390 422 C4' G A 14 OK OK 424 442 421 423 456 C4' G A 15 OK OK 458 476 455 457 490 C4' C A 16 OK OK 492 507 489 491 521 C4' C A 17 OK OK 523 538 520 522 552 C4' G A 18 OK OK 554 572 551 553 586 C4' C A 19 OK OK 588 603 585 587 617 C4' C A 20 OK OK 619 634 616 618 648 C4' A A 21 OK OK 650 667 647 649 681 C4' A A 22 OK OK 683 700 680 682 714 C4' A A 23 OK OK 716 733 713 715 747 C4' C A 24 OK OK 749 764 746 748 778 C4' A A 25 OK OK 780 797 777 779 811 C4' A A 26 OK OK 813 830 810 812 844 C4' U A 27 OK OK 846 861 843 845 874 C4' A A 28 OK OK 876 893 873 875 907 C4' U A 29 OK OK 909 924 906 908 937 C4' G A 30 OK OK 939 957 936 938 971 C4' G A 31 OK OK 973 991 970 972 1005 C4' A A 32 OK OK 1007 1024 1004 1006 1038 C4' G A 33 OK OK 1040 1058 1037 1039 1072 C4' C A 34 OK OK 1074 1089 1071 1073 1103 C4' A A 35 OK OK 1105 1122 1102 1104 1136 C4' C A 36 OK OK 1138 1153 1135 1137 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 67 87 88 69 102 C5' G A 4 OK OK 101 121 122 103 136 C5' C A 5 OK OK 135 152 153 137 167 C5' C A 6 OK OK 166 183 184 168 198 C5' A A 7 distorted distorted 197 216 217 199 231 C5' G A 8 OK OK 230 250 251 232 265 C5' C A 9 OK OK 264 281 282 266 296 C5' U A 10 OK OK 295 312 313 297 326 C5' C A 11 OK OK 325 342 343 327 357 C5' C A 12 OK OK 356 373 374 358 388 C5' A A 13 OK OK 387 406 407 389 421 C5' G A 14 OK OK 420 440 441 422 455 C5' G A 15 OK OK 454 474 475 456 489 C5' C A 16 OK OK 488 505 506 490 520 C5' C A 17 OK OK 519 536 537 521 551 C5' G A 18 OK OK 550 570 571 552 585 C5' C A 19 OK OK 584 601 602 586 616 C5' C A 20 OK OK 615 632 633 617 647 C5' A A 21 distorted distorted 646 665 666 648 680 C5' A A 22 distorted distorted 679 698 699 681 713 C5' A A 23 OK OK 712 731 732 714 746 C5' C A 24 distorted distorted 745 762 763 747 777 C5' A A 25 distorted distorted 776 795 796 778 810 C5' A A 26 distorted distorted 809 828 829 811 843 C5' U A 27 OK OK 842 859 860 844 873 C5' A A 28 OK OK 872 891 892 874 906 C5' U A 29 distorted distorted 905 922 923 907 936 C5' G A 30 OK OK 935 955 956 937 970 C5' G A 31 OK OK 969 989 990 971 1004 C5' A A 32 OK OK 1003 1022 1023 1005 1037 C5' G A 33 OK OK 1036 1056 1057 1038 1071 C5' C A 34 OK OK 1070 1087 1088 1072 1102 C5' A A 35 distorted distorted 1101 1120 1121 1103 1135 C5' C A 36 OK OK 1134 1151 1152 1136 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P G A 3 distorted distorted 41 65 66 67 98 P G A 4 distorted distorted 72 99 100 101 132 P C A 5 distorted distorted 106 133 134 135 163 P C A 6 distorted distorted 140 164 165 166 194 P A A 7 distorted distorted 171 195 196 197 227 P G A 8 distorted distorted 202 228 229 230 261 P C A 9 distorted distorted 235 262 263 264 292 P U A 10 distorted distorted 269 293 294 295 322 P C A 11 distorted distorted 300 323 324 325 353 P C A 12 distorted distorted 330 354 355 356 384 P A A 13 distorted distorted 361 385 386 387 417 P G A 14 distorted distorted 392 418 419 420 451 P G A 15 distorted distorted 425 452 453 454 485 P C A 16 distorted distorted 459 486 487 488 516 P C A 17 distorted distorted 493 517 518 519 547 P G A 18 distorted distorted 524 548 549 550 581 P C A 19 distorted distorted 555 582 583 584 612 P C A 20 distorted distorted 589 613 614 615 643 P A A 21 distorted distorted 620 644 645 646 676 P A A 22 distorted distorted 651 677 678 679 709 P A A 23 distorted distorted 684 710 711 712 742 P C A 24 distorted distorted 717 743 744 745 773 P A A 25 distorted distorted 750 774 775 776 806 P A A 26 distorted distorted 781 807 808 809 839 P U A 27 distorted distorted 814 840 841 842 869 P A A 28 distorted distorted 847 870 871 872 902 P U A 29 distorted distorted 877 903 904 905 932 P G A 30 distorted distorted 910 933 934 935 966 P G A 31 distorted distorted 940 967 968 969 1000 P A A 32 distorted distorted 974 1001 1002 1003 1033 P G A 33 distorted distorted 1008 1034 1035 1036 1067 P C A 34 distorted distorted 1041 1068 1069 1070 1098 P A A 35 distorted distorted 1075 1099 1100 1101 1131 P C A 36 distorted distorted 1106 1132 1133 1134 ---------------------------------------------------------------------------------