ID code: '1N8X' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 alpha beta 7 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' A A 3 alpha beta 75 97 81 78 113 C1' C A 4 alpha beta 108 128 114 111 144 C1' U A 5 alpha beta 139 159 145 142 174 C1' C A 6 alpha beta 169 189 175 172 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' C A 9 alpha beta 268 288 274 271 304 C1' U A 10 alpha beta 299 319 305 302 334 C1' U A 11 alpha beta 329 349 335 332 364 C1' G A 12 alpha beta 359 382 365 362 398 C1' C A 13 alpha beta 393 413 399 396 429 C1' U A 14 alpha beta 424 444 430 427 459 C1' G A 15 alpha beta 454 477 460 457 493 C1' G A 16 alpha beta 488 511 494 491 527 C1' A A 17 alpha beta 522 544 528 525 560 C1' G A 18 alpha beta 555 578 561 558 594 C1' A A 19 alpha beta 589 611 595 592 627 C1' C A 20 alpha beta 622 642 628 625 658 C1' G A 21 alpha beta 653 676 659 656 692 C1' G A 22 alpha beta 687 710 693 690 726 C1' C A 23 alpha beta 721 741 727 724 757 C1' A A 24 alpha beta 752 774 758 755 790 C1' A A 25 alpha beta 785 807 791 788 823 C1' G A 26 alpha beta 818 841 824 821 857 C1' A A 27 alpha beta 852 874 858 855 890 C1' G A 28 alpha beta 885 908 891 888 924 C1' G A 29 alpha beta 919 942 925 922 958 C1' C A 30 alpha beta 953 973 959 956 989 C1' G A 31 alpha beta 984 1007 990 987 1023 C1' A A 32 alpha beta 1018 1040 1024 1021 1056 C1' G A 33 alpha beta 1051 1074 1057 1054 1090 C1' U A 34 alpha beta 1085 1105 1091 1088 1120 C1' C A 35 alpha beta 1115 1135 1121 1118 1151 C1' C A 36 alpha beta 1146 1166 1152 1149 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' G A 2 OK OK 46 42 62 45 78 C2' A A 3 OK OK 80 76 95 79 111 C2' C A 4 OK OK 113 109 126 112 142 C2' U A 5 OK OK 144 140 157 143 172 C2' C A 6 OK OK 174 170 187 173 203 C2' G A 7 OK OK 205 201 221 204 237 C2' G A 8 OK OK 239 235 255 238 271 C2' C A 9 OK OK 273 269 286 272 302 C2' U A 10 OK OK 304 300 317 303 332 C2' U A 11 OK OK 334 330 347 333 362 C2' G A 12 OK OK 364 360 380 363 396 C2' C A 13 OK OK 398 394 411 397 427 C2' U A 14 OK OK 429 425 442 428 457 C2' G A 15 OK OK 459 455 475 458 491 C2' G A 16 OK OK 493 489 509 492 525 C2' A A 17 OK OK 527 523 542 526 558 C2' G A 18 OK OK 560 556 576 559 592 C2' A A 19 OK OK 594 590 609 593 625 C2' C A 20 OK OK 627 623 640 626 656 C2' G A 21 OK OK 658 654 674 657 690 C2' G A 22 OK OK 692 688 708 691 724 C2' C A 23 OK OK 726 722 739 725 755 C2' A A 24 OK OK 757 753 772 756 788 C2' A A 25 OK OK 790 786 805 789 821 C2' G A 26 OK OK 823 819 839 822 855 C2' A A 27 OK OK 857 853 872 856 888 C2' G A 28 OK OK 890 886 906 889 922 C2' G A 29 OK OK 924 920 940 923 956 C2' C A 30 OK OK 958 954 971 957 987 C2' G A 31 OK OK 989 985 1005 988 1021 C2' A A 32 OK OK 1023 1019 1038 1022 1054 C2' G A 33 OK OK 1056 1052 1072 1055 1088 C2' U A 34 OK OK 1090 1086 1103 1089 1118 C2' C A 35 OK OK 1120 1116 1133 1119 1149 C2' C A 36 OK OK 1151 1147 1164 1150 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' A A 3 OK OK 74 94 77 78 109 C3' C A 4 OK OK 107 125 110 111 140 C3' U A 5 OK OK 138 156 141 142 170 C3' C A 6 OK OK 168 186 171 172 201 C3' G A 7 OK OK 199 220 202 203 235 C3' G A 8 OK OK 233 254 236 237 269 C3' C A 9 OK OK 267 285 270 271 300 C3' U A 10 OK OK 298 316 301 302 330 C3' U A 11 OK OK 328 346 331 332 360 C3' G A 12 OK OK 358 379 361 362 394 C3' C A 13 OK OK 392 410 395 396 425 C3' U A 14 OK OK 423 441 426 427 455 C3' G A 15 OK OK 453 474 456 457 489 C3' G A 16 OK OK 487 508 490 491 523 C3' A A 17 OK OK 521 541 524 525 556 C3' G A 18 OK OK 554 575 557 558 590 C3' A A 19 OK OK 588 608 591 592 623 C3' C A 20 OK OK 621 639 624 625 654 C3' G A 21 OK OK 652 673 655 656 688 C3' G A 22 OK OK 686 707 689 690 722 C3' C A 23 OK OK 720 738 723 724 753 C3' A A 24 OK OK 751 771 754 755 786 C3' A A 25 OK OK 784 804 787 788 819 C3' G A 26 OK OK 817 838 820 821 853 C3' A A 27 OK OK 851 871 854 855 886 C3' G A 28 OK OK 884 905 887 888 920 C3' G A 29 OK OK 918 939 921 922 954 C3' C A 30 OK OK 952 970 955 956 985 C3' G A 31 OK OK 983 1004 986 987 1019 C3' A A 32 OK OK 1017 1037 1020 1021 1052 C3' G A 33 OK OK 1050 1071 1053 1054 1086 C3' U A 34 OK OK 1084 1102 1087 1088 1116 C3' C A 35 OK OK 1114 1132 1117 1118 1147 C3' C A 36 OK OK 1145 1163 1148 1149 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' A A 3 OK OK 76 93 73 75 107 C4' C A 4 OK OK 109 124 106 108 138 C4' U A 5 OK OK 140 155 137 139 168 C4' C A 6 OK OK 170 185 167 169 199 C4' G A 7 OK OK 201 219 198 200 233 C4' G A 8 OK OK 235 253 232 234 267 C4' C A 9 OK OK 269 284 266 268 298 C4' U A 10 OK OK 300 315 297 299 328 C4' U A 11 OK OK 330 345 327 329 358 C4' G A 12 OK OK 360 378 357 359 392 C4' C A 13 OK OK 394 409 391 393 423 C4' U A 14 OK OK 425 440 422 424 453 C4' G A 15 OK OK 455 473 452 454 487 C4' G A 16 OK OK 489 507 486 488 521 C4' A A 17 OK OK 523 540 520 522 554 C4' G A 18 OK OK 556 574 553 555 588 C4' A A 19 OK OK 590 607 587 589 621 C4' C A 20 OK OK 623 638 620 622 652 C4' G A 21 OK OK 654 672 651 653 686 C4' G A 22 OK OK 688 706 685 687 720 C4' C A 23 OK OK 722 737 719 721 751 C4' A A 24 OK OK 753 770 750 752 784 C4' A A 25 OK OK 786 803 783 785 817 C4' G A 26 OK OK 819 837 816 818 851 C4' A A 27 OK OK 853 870 850 852 884 C4' G A 28 OK OK 886 904 883 885 918 C4' G A 29 OK OK 920 938 917 919 952 C4' C A 30 OK OK 954 969 951 953 983 C4' G A 31 OK OK 985 1003 982 984 1017 C4' A A 32 OK OK 1019 1036 1016 1018 1050 C4' G A 33 OK OK 1052 1070 1049 1051 1084 C4' U A 34 OK OK 1086 1101 1083 1085 1114 C4' C A 35 OK OK 1116 1131 1113 1115 1145 C4' C A 36 OK OK 1147 1162 1144 1146 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' G A 2 OK OK 38 58 59 40 73 C5' A A 3 OK OK 72 91 92 74 106 C5' C A 4 OK OK 105 122 123 107 137 C5' U A 5 OK OK 136 153 154 138 167 C5' C A 6 OK OK 166 183 184 168 198 C5' G A 7 OK OK 197 217 218 199 232 C5' G A 8 OK OK 231 251 252 233 266 C5' C A 9 OK OK 265 282 283 267 297 C5' U A 10 OK OK 296 313 314 298 327 C5' U A 11 OK OK 326 343 344 328 357 C5' G A 12 OK OK 356 376 377 358 391 C5' C A 13 OK OK 390 407 408 392 422 C5' U A 14 OK OK 421 438 439 423 452 C5' G A 15 OK OK 451 471 472 453 486 C5' G A 16 OK OK 485 505 506 487 520 C5' A A 17 OK OK 519 538 539 521 553 C5' G A 18 OK OK 552 572 573 554 587 C5' A A 19 OK OK 586 605 606 588 620 C5' C A 20 OK OK 619 636 637 621 651 C5' G A 21 OK OK 650 670 671 652 685 C5' G A 22 OK OK 684 704 705 686 719 C5' C A 23 OK OK 718 735 736 720 750 C5' A A 24 OK OK 749 768 769 751 783 C5' A A 25 OK OK 782 801 802 784 816 C5' G A 26 OK OK 815 835 836 817 850 C5' A A 27 OK OK 849 868 869 851 883 C5' G A 28 OK OK 882 902 903 884 917 C5' G A 29 OK OK 916 936 937 918 951 C5' C A 30 OK OK 950 967 968 952 982 C5' G A 31 OK OK 981 1001 1002 983 1016 C5' A A 32 OK OK 1015 1034 1035 1017 1049 C5' G A 33 OK OK 1048 1068 1069 1050 1083 C5' U A 34 OK OK 1082 1099 1100 1084 1113 C5' C A 35 OK OK 1112 1129 1130 1114 1144 C5' C A 36 OK OK 1143 1160 1161 1145 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P A A 3 distorted distorted 43 70 71 72 102 P C A 4 distorted distorted 77 103 104 105 133 P U A 5 distorted distorted 110 134 135 136 163 P C A 6 distorted distorted 141 164 165 166 194 P G A 7 distorted distorted 171 195 196 197 228 P G A 8 distorted distorted 202 229 230 231 262 P C A 9 distorted distorted 236 263 264 265 293 P U A 10 distorted distorted 270 294 295 296 323 P U A 11 distorted distorted 301 324 325 326 353 P G A 12 distorted distorted 331 354 355 356 387 P C A 13 distorted distorted 361 388 389 390 418 P U A 14 distorted distorted 395 419 420 421 448 P G A 15 distorted distorted 426 449 450 451 482 P G A 16 distorted distorted 456 483 484 485 516 P A A 17 distorted distorted 490 517 518 519 549 P G A 18 distorted distorted 524 550 551 552 583 P A A 19 distorted distorted 557 584 585 586 616 P C A 20 distorted distorted 591 617 618 619 647 P G A 21 distorted distorted 624 648 649 650 681 P G A 22 distorted distorted 655 682 683 684 715 P C A 23 distorted distorted 689 716 717 718 746 P A A 24 distorted distorted 723 747 748 749 779 P A A 25 distorted distorted 754 780 781 782 812 P G A 26 distorted distorted 787 813 814 815 846 P A A 27 distorted distorted 820 847 848 849 879 P G A 28 distorted distorted 854 880 881 882 913 P G A 29 distorted distorted 887 914 915 916 947 P C A 30 distorted distorted 921 948 949 950 978 P G A 31 distorted distorted 955 979 980 981 1012 P A A 32 distorted distorted 986 1013 1014 1015 1045 P G A 33 distorted distorted 1020 1046 1047 1048 1079 P U A 34 distorted distorted 1053 1080 1081 1082 1109 P C A 35 distorted distorted 1087 1110 1111 1112 1140 P C A 36 distorted distorted 1117 1141 1142 1143 ---------------------------------------------------------------------------------