ID code: '4J50' 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' U A 1 alpha beta 4 24 10 7 40 C1' U A 2 alpha beta 35 55 41 38 70 C1' G A 3 alpha beta 65 88 71 68 104 C1' G A 4 alpha beta 99 122 105 102 138 C1' G A 5 alpha beta 133 156 139 136 172 C1' C A 6 alpha beta 167 187 173 170 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' A A 8 alpha beta 229 251 235 232 267 C1' G A 9 alpha beta 262 285 268 265 301 C1' C A 10 alpha beta 296 316 302 299 332 C1' A A 11 alpha beta 327 349 333 330 365 C1' G A 12 alpha beta 360 383 366 363 399 C1' C A 13 alpha beta 394 414 400 397 430 C1' A A 14 alpha beta 425 447 431 428 463 C1' G A 15 alpha beta 458 481 464 461 497 C1' G A 16 alpha beta 492 515 498 495 531 C1' U A 17 alpha beta 526 546 532 529 561 C1' C A 18 alpha beta 556 576 562 559 592 C1' C A 19 alpha beta 587 608 593 590 622 C1' U B 1 alpha beta 617 637 623 620 653 C1' U B 2 alpha beta 648 668 654 651 683 C1' G B 3 alpha beta 678 701 684 681 717 C1' G B 4 alpha beta 712 735 718 715 751 C1' G B 5 alpha beta 746 769 752 749 785 C1' C B 6 alpha beta 780 800 786 783 816 C1' C B 7 alpha beta 811 831 817 814 847 C1' A B 8 alpha beta 842 864 848 845 880 C1' G B 9 alpha beta 875 898 881 878 914 C1' C B 10 alpha beta 909 929 915 912 945 C1' A B 11 alpha beta 940 962 946 943 978 C1' G B 12 alpha beta 973 996 979 976 1012 C1' C B 13 alpha beta 1007 1027 1013 1010 1043 C1' A B 14 alpha beta 1038 1060 1044 1041 1076 C1' G B 15 alpha beta 1071 1094 1077 1074 1110 C1' G B 16 alpha beta 1105 1128 1111 1108 1144 C1' U B 17 alpha beta 1139 1159 1145 1142 1174 C1' C B 18 alpha beta 1169 1189 1175 1172 1205 C1' C B 19 alpha beta 1200 1221 1206 1203 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK OK 9 5 22 8 38 C2' U A 2 OK OK 40 36 53 39 68 C2' G A 3 OK OK 70 66 86 69 102 C2' G A 4 OK OK 104 100 120 103 136 C2' G A 5 OK OK 138 134 154 137 170 C2' C A 6 OK OK 172 168 185 171 201 C2' C A 7 OK OK 203 199 216 202 232 C2' A A 8 OK OK 234 230 249 233 265 C2' G A 9 OK OK 267 263 283 266 299 C2' C A 10 OK OK 301 297 314 300 330 C2' A A 11 OK OK 332 328 347 331 363 C2' G A 12 OK OK 365 361 381 364 397 C2' C A 13 OK OK 399 395 412 398 428 C2' A A 14 OK OK 430 426 445 429 461 C2' G A 15 OK OK 463 459 479 462 495 C2' G A 16 OK OK 497 493 513 496 529 C2' U A 17 OK OK 531 527 544 530 559 C2' C A 18 OK OK 561 557 574 560 590 C2' C A 19 OK OK 592 588 606 591 620 C2' U B 1 OK OK 622 618 635 621 651 C2' U B 2 OK OK 653 649 666 652 681 C2' G B 3 OK OK 683 679 699 682 715 C2' G B 4 OK OK 717 713 733 716 749 C2' G B 5 OK OK 751 747 767 750 783 C2' C B 6 OK OK 785 781 798 784 814 C2' C B 7 OK OK 816 812 829 815 845 C2' A B 8 OK OK 847 843 862 846 878 C2' G B 9 OK OK 880 876 896 879 912 C2' C B 10 OK OK 914 910 927 913 943 C2' A B 11 OK OK 945 941 960 944 976 C2' G B 12 OK OK 978 974 994 977 1010 C2' C B 13 OK OK 1012 1008 1025 1011 1041 C2' A B 14 OK OK 1043 1039 1058 1042 1074 C2' G B 15 OK OK 1076 1072 1092 1075 1108 C2' G B 16 OK OK 1110 1106 1126 1109 1142 C2' U B 17 OK OK 1144 1140 1157 1143 1172 C2' C B 18 OK OK 1174 1170 1187 1173 1203 C2' C B 19 OK OK 1205 1201 1219 1204 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK OK 3 21 6 7 36 C3' U A 2 OK OK 34 52 37 38 66 C3' G A 3 OK OK 64 85 67 68 100 C3' G A 4 OK OK 98 119 101 102 134 C3' G A 5 OK OK 132 153 135 136 168 C3' C A 6 OK OK 166 184 169 170 199 C3' C A 7 OK OK 197 215 200 201 230 C3' A A 8 OK OK 228 248 231 232 263 C3' G A 9 OK OK 261 282 264 265 297 C3' C A 10 OK OK 295 313 298 299 328 C3' A A 11 OK OK 326 346 329 330 361 C3' G A 12 OK OK 359 380 362 363 395 C3' C A 13 OK OK 393 411 396 397 426 C3' A A 14 OK OK 424 444 427 428 459 C3' G A 15 OK OK 457 478 460 461 493 C3' G A 16 OK OK 491 512 494 495 527 C3' U A 17 OK OK 525 543 528 529 557 C3' C A 18 OK OK 555 573 558 559 588 C3' C A 19 OK OK 586 604 589 590 618 C3' U B 1 OK OK 616 634 619 620 649 C3' U B 2 OK OK 647 665 650 651 679 C3' G B 3 OK OK 677 698 680 681 713 C3' G B 4 OK OK 711 732 714 715 747 C3' G B 5 OK OK 745 766 748 749 781 C3' C B 6 OK OK 779 797 782 783 812 C3' C B 7 OK OK 810 828 813 814 843 C3' A B 8 OK OK 841 861 844 845 876 C3' G B 9 OK OK 874 895 877 878 910 C3' C B 10 OK OK 908 926 911 912 941 C3' A B 11 OK OK 939 959 942 943 974 C3' G B 12 OK OK 972 993 975 976 1008 C3' C B 13 OK OK 1006 1024 1009 1010 1039 C3' A B 14 OK OK 1037 1057 1040 1041 1072 C3' G B 15 OK OK 1070 1091 1073 1074 1106 C3' G B 16 OK OK 1104 1125 1107 1108 1140 C3' U B 17 OK OK 1138 1156 1141 1142 1170 C3' C B 18 OK OK 1168 1186 1171 1172 1201 C3' C B 19 OK OK 1199 1217 1202 1203 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK OK 5 20 2 4 34 C4' U A 2 OK OK 36 51 33 35 64 C4' G A 3 OK OK 66 84 63 65 98 C4' G A 4 OK OK 100 118 97 99 132 C4' G A 5 OK OK 134 152 131 133 166 C4' C A 6 OK OK 168 183 165 167 197 C4' C A 7 OK OK 199 214 196 198 228 C4' A A 8 OK OK 230 247 227 229 261 C4' G A 9 OK OK 263 281 260 262 295 C4' C A 10 OK OK 297 312 294 296 326 C4' A A 11 OK OK 328 345 325 327 359 C4' G A 12 OK OK 361 379 358 360 393 C4' C A 13 OK OK 395 410 392 394 424 C4' A A 14 OK OK 426 443 423 425 457 C4' G A 15 OK OK 459 477 456 458 491 C4' G A 16 OK OK 493 511 490 492 525 C4' U A 17 OK OK 527 542 524 526 555 C4' C A 18 OK OK 557 572 554 556 586 C4' C A 19 OK OK 588 603 585 587 616 C4' U B 1 OK OK 618 633 615 617 647 C4' U B 2 OK OK 649 664 646 648 677 C4' G B 3 OK OK 679 697 676 678 711 C4' G B 4 OK OK 713 731 710 712 745 C4' G B 5 OK OK 747 765 744 746 779 C4' C B 6 OK OK 781 796 778 780 810 C4' C B 7 OK OK 812 827 809 811 841 C4' A B 8 OK OK 843 860 840 842 874 C4' G B 9 OK OK 876 894 873 875 908 C4' C B 10 OK OK 910 925 907 909 939 C4' A B 11 OK OK 941 958 938 940 972 C4' G B 12 OK OK 974 992 971 973 1006 C4' C B 13 OK OK 1008 1023 1005 1007 1037 C4' A B 14 OK OK 1039 1056 1036 1038 1070 C4' G B 15 OK OK 1072 1090 1069 1071 1104 C4' G B 16 OK OK 1106 1124 1103 1105 1138 C4' U B 17 OK OK 1140 1155 1137 1139 1168 C4' C B 18 OK OK 1170 1185 1167 1169 1199 C4' C B 19 OK OK 1201 1216 1198 1200 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 OK OK 1 18 19 3 33 C5' U A 2 OK OK 32 49 50 34 63 C5' G A 3 OK OK 62 82 83 64 97 C5' G A 4 OK OK 96 116 117 98 131 C5' G A 5 OK OK 130 150 151 132 165 C5' C A 6 OK OK 164 181 182 166 196 C5' C A 7 OK OK 195 212 213 197 227 C5' A A 8 OK OK 226 245 246 228 260 C5' G A 9 OK OK 259 279 280 261 294 C5' C A 10 OK OK 293 310 311 295 325 C5' A A 11 OK OK 324 343 344 326 358 C5' G A 12 OK OK 357 377 378 359 392 C5' C A 13 OK OK 391 408 409 393 423 C5' A A 14 OK OK 422 441 442 424 456 C5' G A 15 OK OK 455 475 476 457 490 C5' G A 16 OK OK 489 509 510 491 524 C5' U A 17 OK OK 523 540 541 525 554 C5' C A 18 OK OK 553 570 571 555 585 C5' C A 19 OK OK 584 601 602 586 615 C5' U B 1 OK OK 614 631 632 616 646 C5' U B 2 OK OK 645 662 663 647 676 C5' G B 3 OK OK 675 695 696 677 710 C5' G B 4 OK OK 709 729 730 711 744 C5' G B 5 OK OK 743 763 764 745 778 C5' C B 6 OK OK 777 794 795 779 809 C5' C B 7 OK OK 808 825 826 810 840 C5' A B 8 OK OK 839 858 859 841 873 C5' G B 9 OK OK 872 892 893 874 907 C5' C B 10 OK OK 906 923 924 908 938 C5' A B 11 OK OK 937 956 957 939 971 C5' G B 12 OK OK 970 990 991 972 1005 C5' C B 13 OK OK 1004 1021 1022 1006 1036 C5' A B 14 OK OK 1035 1054 1055 1037 1069 C5' G B 15 OK OK 1068 1088 1089 1070 1103 C5' G B 16 OK OK 1102 1122 1123 1104 1137 C5' U B 17 OK OK 1136 1153 1154 1138 1167 C5' C B 18 OK OK 1166 1183 1184 1168 1198 C5' C B 19 OK OK 1197 1214 1215 1199 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P U A 2 distorted distorted 6 30 31 32 59 P G A 3 distorted distorted 37 60 61 62 93 P G A 4 distorted distorted 67 94 95 96 127 P G A 5 distorted distorted 101 128 129 130 161 P C A 6 distorted distorted 135 162 163 164 192 P C A 7 distorted distorted 169 193 194 195 223 P A A 8 distorted distorted 200 224 225 226 256 P G A 9 distorted distorted 231 257 258 259 290 P C A 10 distorted distorted 264 291 292 293 321 P A A 11 distorted distorted 298 322 323 324 354 P G A 12 distorted distorted 329 355 356 357 388 P C A 13 distorted distorted 362 389 390 391 419 P A A 14 distorted distorted 396 420 421 422 452 P G A 15 distorted distorted 427 453 454 455 486 P G A 16 distorted distorted 460 487 488 489 520 P U A 17 distorted distorted 494 521 522 523 550 P C A 18 distorted distorted 528 551 552 553 581 P C A 19 distorted distorted 558 582 583 584 642 P U B 2 distorted distorted 619 643 644 645 672 P G B 3 distorted distorted 650 673 674 675 706 P G B 4 distorted distorted 680 707 708 709 740 P G B 5 distorted distorted 714 741 742 743 774 P C B 6 distorted distorted 748 775 776 777 805 P C B 7 distorted distorted 782 806 807 808 836 P A B 8 distorted distorted 813 837 838 839 869 P G B 9 distorted distorted 844 870 871 872 903 P C B 10 distorted distorted 877 904 905 906 934 P A B 11 distorted distorted 911 935 936 937 967 P G B 12 distorted distorted 942 968 969 970 1001 P C B 13 distorted distorted 975 1002 1003 1004 1032 P A B 14 distorted distorted 1009 1033 1034 1035 1065 P G B 15 distorted distorted 1040 1066 1067 1068 1099 P G B 16 distorted distorted 1073 1100 1101 1102 1133 P U B 17 distorted distorted 1107 1134 1135 1136 1163 P C B 18 distorted distorted 1141 1164 1165 1166 1194 P C B 19 distorted distorted 1171 1195 1196 1197 1227 P PO4 A 101 1232 P PO4 B 101 ---------------------------------------------------------------------------------