ID code: '3SZX' 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' U A 1 alpha beta 7 27 13 10 42 C1' U A 2 alpha beta 37 57 43 40 72 C1' G A 3 alpha beta 67 90 73 70 106 C1' G A 4 alpha beta 101 124 107 104 140 C1' G A 5 alpha beta 135 158 141 138 174 C1' C A 6 alpha beta 169 189 175 172 205 C1' C A 7 alpha beta 200 220 206 203 236 C1' U A 8 alpha beta 231 251 237 234 266 C1' G A 9 alpha beta 261 284 267 264 300 C1' C A 10 alpha beta 295 315 301 298 331 C1' U A 11 alpha beta 326 346 332 329 361 C1' G A 12 alpha beta 356 379 362 359 395 C1' C A 13 alpha beta 390 410 396 393 426 C1' U A 14 alpha beta 421 441 427 424 456 C1' G A 15 alpha beta 451 474 457 454 490 C1' G A 16 alpha beta 485 508 491 488 524 C1' U A 17 alpha beta 519 539 525 522 554 C1' C A 18 alpha beta 549 569 555 552 585 C1' C A 19 alpha beta 580 601 586 583 618 C1' U B 1 alpha beta 613 633 619 616 648 C1' U B 2 alpha beta 643 663 649 646 678 C1' G B 3 alpha beta 673 696 679 676 712 C1' G B 4 alpha beta 707 730 713 710 746 C1' G B 5 alpha beta 741 764 747 744 780 C1' C B 6 alpha beta 775 795 781 778 811 C1' C B 7 alpha beta 806 826 812 809 842 C1' U B 8 alpha beta 837 857 843 840 872 C1' G B 9 alpha beta 867 890 873 870 906 C1' C B 10 alpha beta 901 921 907 904 937 C1' U B 11 alpha beta 932 952 938 935 967 C1' G B 12 alpha beta 962 985 968 965 1001 C1' C B 13 alpha beta 996 1016 1002 999 1032 C1' U B 14 alpha beta 1027 1047 1033 1030 1062 C1' G B 15 alpha beta 1057 1080 1063 1060 1096 C1' G B 16 alpha beta 1091 1114 1097 1094 1130 C1' U B 17 alpha beta 1125 1145 1131 1128 1160 C1' C B 18 alpha beta 1155 1175 1161 1158 1191 C1' C B 19 alpha beta 1186 1207 1192 1189 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U A 1 OK OK 12 8 25 11 40 C2' U A 2 OK OK 42 38 55 41 70 C2' G A 3 OK OK 72 68 88 71 104 C2' G A 4 OK OK 106 102 122 105 138 C2' G A 5 OK OK 140 136 156 139 172 C2' C A 6 OK OK 174 170 187 173 203 C2' C A 7 OK OK 205 201 218 204 234 C2' U A 8 OK OK 236 232 249 235 264 C2' G A 9 OK OK 266 262 282 265 298 C2' C A 10 OK OK 300 296 313 299 329 C2' U A 11 OK OK 331 327 344 330 359 C2' G A 12 OK OK 361 357 377 360 393 C2' C A 13 OK OK 395 391 408 394 424 C2' U A 14 OK OK 426 422 439 425 454 C2' G A 15 OK OK 456 452 472 455 488 C2' G A 16 OK OK 490 486 506 489 522 C2' U A 17 OK OK 524 520 537 523 552 C2' C A 18 OK OK 554 550 567 553 583 C2' C A 19 OK OK 585 581 599 584 616 C2' U B 1 OK OK 618 614 631 617 646 C2' U B 2 OK OK 648 644 661 647 676 C2' G B 3 OK OK 678 674 694 677 710 C2' G B 4 OK OK 712 708 728 711 744 C2' G B 5 OK OK 746 742 762 745 778 C2' C B 6 OK OK 780 776 793 779 809 C2' C B 7 OK OK 811 807 824 810 840 C2' U B 8 OK OK 842 838 855 841 870 C2' G B 9 OK OK 872 868 888 871 904 C2' C B 10 OK OK 906 902 919 905 935 C2' U B 11 OK OK 937 933 950 936 965 C2' G B 12 OK OK 967 963 983 966 999 C2' C B 13 OK OK 1001 997 1014 1000 1030 C2' U B 14 OK OK 1032 1028 1045 1031 1060 C2' G B 15 OK OK 1062 1058 1078 1061 1094 C2' G B 16 OK OK 1096 1092 1112 1095 1128 C2' U B 17 OK OK 1130 1126 1143 1129 1158 C2' C B 18 OK OK 1160 1156 1173 1159 1189 C2' C B 19 OK OK 1191 1187 1205 1190 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U A 1 OK OK 6 24 9 10 38 C3' U A 2 OK OK 36 54 39 40 68 C3' G A 3 OK OK 66 87 69 70 102 C3' G A 4 OK OK 100 121 103 104 136 C3' G A 5 OK OK 134 155 137 138 170 C3' C A 6 OK OK 168 186 171 172 201 C3' C A 7 OK OK 199 217 202 203 232 C3' U A 8 OK OK 230 248 233 234 262 C3' G A 9 OK OK 260 281 263 264 296 C3' C A 10 OK OK 294 312 297 298 327 C3' U A 11 OK OK 325 343 328 329 357 C3' G A 12 OK OK 355 376 358 359 391 C3' C A 13 OK OK 389 407 392 393 422 C3' U A 14 OK OK 420 438 423 424 452 C3' G A 15 OK OK 450 471 453 454 486 C3' G A 16 OK OK 484 505 487 488 520 C3' U A 17 OK OK 518 536 521 522 550 C3' C A 18 OK OK 548 566 551 552 581 C3' C A 19 OK OK 579 597 582 583 614 C3' U B 1 OK OK 612 630 615 616 644 C3' U B 2 OK OK 642 660 645 646 674 C3' G B 3 OK OK 672 693 675 676 708 C3' G B 4 OK OK 706 727 709 710 742 C3' G B 5 OK OK 740 761 743 744 776 C3' C B 6 OK OK 774 792 777 778 807 C3' C B 7 OK OK 805 823 808 809 838 C3' U B 8 OK OK 836 854 839 840 868 C3' G B 9 OK OK 866 887 869 870 902 C3' C B 10 OK OK 900 918 903 904 933 C3' U B 11 OK OK 931 949 934 935 963 C3' G B 12 OK OK 961 982 964 965 997 C3' C B 13 OK OK 995 1013 998 999 1028 C3' U B 14 OK OK 1026 1044 1029 1030 1058 C3' G B 15 OK OK 1056 1077 1059 1060 1092 C3' G B 16 OK OK 1090 1111 1093 1094 1126 C3' U B 17 OK OK 1124 1142 1127 1128 1156 C3' C B 18 OK OK 1154 1172 1157 1158 1187 C3' C B 19 OK OK 1185 1203 1188 1189 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U A 1 OK OK 8 23 5 7 36 C4' U A 2 OK OK 38 53 35 37 66 C4' G A 3 OK OK 68 86 65 67 100 C4' G A 4 OK OK 102 120 99 101 134 C4' G A 5 OK OK 136 154 133 135 168 C4' C A 6 OK OK 170 185 167 169 199 C4' C A 7 OK OK 201 216 198 200 230 C4' U A 8 OK OK 232 247 229 231 260 C4' G A 9 OK OK 262 280 259 261 294 C4' C A 10 OK OK 296 311 293 295 325 C4' U A 11 OK OK 327 342 324 326 355 C4' G A 12 OK OK 357 375 354 356 389 C4' C A 13 OK OK 391 406 388 390 420 C4' U A 14 OK OK 422 437 419 421 450 C4' G A 15 OK OK 452 470 449 451 484 C4' G A 16 OK OK 486 504 483 485 518 C4' U A 17 OK OK 520 535 517 519 548 C4' C A 18 OK OK 550 565 547 549 579 C4' C A 19 OK OK 581 596 578 580 612 C4' U B 1 OK OK 614 629 611 613 642 C4' U B 2 OK OK 644 659 641 643 672 C4' G B 3 OK OK 674 692 671 673 706 C4' G B 4 OK OK 708 726 705 707 740 C4' G B 5 OK OK 742 760 739 741 774 C4' C B 6 OK OK 776 791 773 775 805 C4' C B 7 OK OK 807 822 804 806 836 C4' U B 8 OK OK 838 853 835 837 866 C4' G B 9 OK OK 868 886 865 867 900 C4' C B 10 OK OK 902 917 899 901 931 C4' U B 11 OK OK 933 948 930 932 961 C4' G B 12 OK OK 963 981 960 962 995 C4' C B 13 OK OK 997 1012 994 996 1026 C4' U B 14 OK OK 1028 1043 1025 1027 1056 C4' G B 15 OK OK 1058 1076 1055 1057 1090 C4' G B 16 OK OK 1092 1110 1089 1091 1124 C4' U B 17 OK OK 1126 1141 1123 1125 1154 C4' C B 18 OK OK 1156 1171 1153 1155 1185 C4' C B 19 OK OK 1187 1202 1184 1186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U A 1 OK OK 4 21 22 6 35 C5' U A 2 OK OK 34 51 52 36 65 C5' G A 3 OK OK 64 84 85 66 99 C5' G A 4 OK OK 98 118 119 100 133 C5' G A 5 OK OK 132 152 153 134 167 C5' C A 6 OK OK 166 183 184 168 198 C5' C A 7 OK OK 197 214 215 199 229 C5' U A 8 OK OK 228 245 246 230 259 C5' G A 9 OK OK 258 278 279 260 293 C5' C A 10 OK OK 292 309 310 294 324 C5' U A 11 OK OK 323 340 341 325 354 C5' G A 12 OK OK 353 373 374 355 388 C5' C A 13 OK OK 387 404 405 389 419 C5' U A 14 OK OK 418 435 436 420 449 C5' G A 15 OK OK 448 468 469 450 483 C5' G A 16 OK OK 482 502 503 484 517 C5' U A 17 OK OK 516 533 534 518 547 C5' C A 18 OK OK 546 563 564 548 578 C5' C A 19 OK OK 577 594 595 579 611 C5' U B 1 OK OK 610 627 628 612 641 C5' U B 2 OK OK 640 657 658 642 671 C5' G B 3 OK OK 670 690 691 672 705 C5' G B 4 OK OK 704 724 725 706 739 C5' G B 5 OK OK 738 758 759 740 773 C5' C B 6 OK OK 772 789 790 774 804 C5' C B 7 OK OK 803 820 821 805 835 C5' U B 8 OK OK 834 851 852 836 865 C5' G B 9 OK OK 864 884 885 866 899 C5' C B 10 OK OK 898 915 916 900 930 C5' U B 11 OK OK 929 946 947 931 960 C5' G B 12 OK OK 959 979 980 961 994 C5' C B 13 OK OK 993 1010 1011 995 1025 C5' U B 14 OK OK 1024 1041 1042 1026 1055 C5' G B 15 OK OK 1054 1074 1075 1056 1089 C5' G B 16 OK OK 1088 1108 1109 1090 1123 C5' U B 17 OK OK 1122 1139 1140 1124 1153 C5' C B 18 OK OK 1152 1169 1170 1154 1184 C5' C B 19 OK OK 1183 1200 1201 1185 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U A 1 distorted distorted 2 3 4 31 P U A 2 distorted distorted 9 32 33 34 61 P G A 3 distorted distorted 39 62 63 64 95 P G A 4 distorted distorted 69 96 97 98 129 P G A 5 distorted distorted 103 130 131 132 163 P C A 6 distorted distorted 137 164 165 166 194 P C A 7 distorted distorted 171 195 196 197 225 P U A 8 distorted distorted 202 226 227 228 255 P G A 9 distorted distorted 233 256 257 258 289 P C A 10 distorted distorted 263 290 291 292 320 P U A 11 distorted distorted 297 321 322 323 350 P G A 12 distorted distorted 328 351 352 353 384 P C A 13 distorted distorted 358 385 386 387 415 P U A 14 distorted distorted 392 416 417 418 445 P G A 15 distorted distorted 423 446 447 448 479 P G A 16 distorted distorted 453 480 481 482 513 P U A 17 distorted distorted 487 514 515 516 543 P C A 18 distorted distorted 521 544 545 546 574 P C A 19 distorted distorted 551 575 576 577 607 P U B 1 distorted distorted 608 609 610 637 P U B 2 distorted distorted 615 638 639 640 667 P G B 3 distorted distorted 645 668 669 670 701 P G B 4 distorted distorted 675 702 703 704 735 P G B 5 distorted distorted 709 736 737 738 769 P C B 6 distorted distorted 743 770 771 772 800 P C B 7 distorted distorted 777 801 802 803 831 P U B 8 distorted distorted 808 832 833 834 861 P G B 9 distorted distorted 839 862 863 864 895 P C B 10 distorted distorted 869 896 897 898 926 P U B 11 distorted distorted 903 927 928 929 956 P G B 12 distorted distorted 934 957 958 959 990 P C B 13 distorted distorted 964 991 992 993 1021 P U B 14 distorted distorted 998 1022 1023 1024 1051 P G B 15 distorted distorted 1029 1052 1053 1054 1085 P G B 16 distorted distorted 1059 1086 1087 1088 1119 P U B 17 distorted distorted 1093 1120 1121 1122 1149 P C B 18 distorted distorted 1127 1150 1151 1152 1180 P C B 19 distorted distorted 1157 1181 1182 1183 ---------------------------------------------------------------------------------