ID code: '4E48' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 beta 8 14 11 36 C1' C A 2 beta 31 37 34 56 C1' U A 3 beta 51 57 54 76 C1' G A 4 beta 71 77 74 99 C1' C A 5 beta 94 100 97 119 C1' U A 6 beta 114 120 117 139 C1' G A 7 beta 134 140 137 162 C1' C A 8 beta 157 163 160 182 C1' U A 9 beta 177 183 180 202 C1' G A 10 beta 197 203 200 225 C1' C A 11 beta 220 226 223 245 C1' U A 12 beta 240 246 243 265 C1' G A 13 beta 260 266 263 288 C1' C A 14 beta 283 289 286 308 C1' U A 15 beta 303 309 306 328 C1' G A 16 beta 323 329 326 351 C1' C A 17 beta 346 352 349 371 C1' U A 18 beta 366 372 369 391 C1' G A 19 beta 386 392 389 414 C1' C A 20 beta 409 415 412 436 C1' G B 21 beta 431 437 434 459 C1' C B 22 beta 454 460 457 479 C1' U B 23 beta 474 480 477 499 C1' G B 24 beta 494 500 497 522 C1' C B 25 beta 517 523 520 542 C1' U B 26 beta 537 543 540 562 C1' G B 27 beta 557 563 560 585 C1' C B 28 beta 580 586 583 605 C1' U B 29 beta 600 606 603 625 C1' G B 30 beta 620 626 623 648 C1' C B 31 beta 643 649 646 668 C1' U B 32 beta 663 669 666 688 C1' G B 33 beta 683 689 686 711 C1' C B 34 beta 706 712 709 731 C1' U B 35 beta 726 732 729 751 C1' G B 36 beta 746 752 749 774 C1' C B 37 beta 769 775 772 794 C1' U B 38 beta 789 795 792 814 C1' G B 39 beta 809 815 812 837 C1' C B 40 beta 832 838 835 859 C1' G D 1 beta 854 860 857 882 C1' C D 2 beta 877 883 880 902 C1' U D 3 beta 897 903 900 922 C1' G D 4 beta 917 923 920 945 C1' C D 5 beta 940 946 943 965 C1' U D 6 beta 960 966 963 985 C1' G D 7 beta 980 986 983 1008 C1' C D 8 beta 1003 1009 1006 1028 C1' U D 9 beta 1023 1029 1026 1048 C1' G D 10 beta 1043 1049 1046 1071 C1' C D 11 beta 1066 1072 1069 1091 C1' U D 12 beta 1086 1092 1089 1111 C1' G D 13 beta 1106 1112 1109 1134 C1' C D 14 beta 1129 1135 1132 1154 C1' U D 15 beta 1149 1155 1152 1174 C1' G D 16 beta 1169 1175 1172 1197 C1' C D 17 beta 1192 1198 1195 1217 C1' U D 18 beta 1212 1218 1215 1237 C1' G D 19 beta 1232 1238 1235 1260 C1' C D 20 beta 1255 1261 1258 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK 13 9 12 34 C2' C A 2 OK 36 32 35 54 C2' U A 3 OK 56 52 55 74 C2' G A 4 OK 76 72 75 97 C2' C A 5 OK 99 95 98 117 C2' U A 6 OK 119 115 118 137 C2' G A 7 OK 139 135 138 160 C2' C A 8 OK 162 158 161 180 C2' U A 9 OK 182 178 181 200 C2' G A 10 OK 202 198 201 223 C2' C A 11 OK 225 221 224 243 C2' U A 12 OK 245 241 244 263 C2' G A 13 OK 265 261 264 286 C2' C A 14 OK 288 284 287 306 C2' U A 15 OK 308 304 307 326 C2' G A 16 OK 328 324 327 349 C2' C A 17 OK 351 347 350 369 C2' U A 18 OK 371 367 370 389 C2' G A 19 OK 391 387 390 412 C2' C A 20 OK 414 410 413 434 C2' G B 21 OK 436 432 435 457 C2' C B 22 OK 459 455 458 477 C2' U B 23 OK 479 475 478 497 C2' G B 24 OK 499 495 498 520 C2' C B 25 OK 522 518 521 540 C2' U B 26 OK 542 538 541 560 C2' G B 27 OK 562 558 561 583 C2' C B 28 OK 585 581 584 603 C2' U B 29 OK 605 601 604 623 C2' G B 30 OK 625 621 624 646 C2' C B 31 OK 648 644 647 666 C2' U B 32 OK 668 664 667 686 C2' G B 33 OK 688 684 687 709 C2' C B 34 OK 711 707 710 729 C2' U B 35 OK 731 727 730 749 C2' G B 36 OK 751 747 750 772 C2' C B 37 OK 774 770 773 792 C2' U B 38 OK 794 790 793 812 C2' G B 39 OK 814 810 813 835 C2' C B 40 OK 837 833 836 857 C2' G D 1 OK 859 855 858 880 C2' C D 2 OK 882 878 881 900 C2' U D 3 OK 902 898 901 920 C2' G D 4 OK 922 918 921 943 C2' C D 5 OK 945 941 944 963 C2' U D 6 OK 965 961 964 983 C2' G D 7 OK 985 981 984 1006 C2' C D 8 OK 1008 1004 1007 1026 C2' U D 9 OK 1028 1024 1027 1046 C2' G D 10 OK 1048 1044 1047 1069 C2' C D 11 OK 1071 1067 1070 1089 C2' U D 12 OK 1091 1087 1090 1109 C2' G D 13 OK 1111 1107 1110 1132 C2' C D 14 OK 1134 1130 1133 1152 C2' U D 15 OK 1154 1150 1153 1172 C2' G D 16 OK 1174 1170 1173 1195 C2' C D 17 OK 1197 1193 1196 1215 C2' U D 18 OK 1217 1213 1216 1235 C2' G D 19 OK 1237 1233 1236 1258 C2' C D 20 OK 1260 1256 1259 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK 7 10 11 32 C3' C A 2 OK 30 33 34 52 C3' U A 3 OK 50 53 54 72 C3' G A 4 OK 70 73 74 95 C3' C A 5 OK 93 96 97 115 C3' U A 6 OK 113 116 117 135 C3' G A 7 OK 133 136 137 158 C3' C A 8 OK 156 159 160 178 C3' U A 9 OK 176 179 180 198 C3' G A 10 OK 196 199 200 221 C3' C A 11 OK 219 222 223 241 C3' U A 12 OK 239 242 243 261 C3' G A 13 OK 259 262 263 284 C3' C A 14 OK 282 285 286 304 C3' U A 15 OK 302 305 306 324 C3' G A 16 OK 322 325 326 347 C3' C A 17 OK 345 348 349 367 C3' U A 18 OK 365 368 369 387 C3' G A 19 OK 385 388 389 410 C3' C A 20 OK 408 411 412 432 C3' G B 21 OK 430 433 434 455 C3' C B 22 OK 453 456 457 475 C3' U B 23 OK 473 476 477 495 C3' G B 24 OK 493 496 497 518 C3' C B 25 OK 516 519 520 538 C3' U B 26 OK 536 539 540 558 C3' G B 27 OK 556 559 560 581 C3' C B 28 OK 579 582 583 601 C3' U B 29 OK 599 602 603 621 C3' G B 30 OK 619 622 623 644 C3' C B 31 OK 642 645 646 664 C3' U B 32 OK 662 665 666 684 C3' G B 33 OK 682 685 686 707 C3' C B 34 OK 705 708 709 727 C3' U B 35 OK 725 728 729 747 C3' G B 36 OK 745 748 749 770 C3' C B 37 OK 768 771 772 790 C3' U B 38 OK 788 791 792 810 C3' G B 39 OK 808 811 812 833 C3' C B 40 OK 831 834 835 855 C3' G D 1 OK 853 856 857 878 C3' C D 2 OK 876 879 880 898 C3' U D 3 OK 896 899 900 918 C3' G D 4 OK 916 919 920 941 C3' C D 5 OK 939 942 943 961 C3' U D 6 OK 959 962 963 981 C3' G D 7 OK 979 982 983 1004 C3' C D 8 OK 1002 1005 1006 1024 C3' U D 9 OK 1022 1025 1026 1044 C3' G D 10 OK 1042 1045 1046 1067 C3' C D 11 OK 1065 1068 1069 1087 C3' U D 12 OK 1085 1088 1089 1107 C3' G D 13 OK 1105 1108 1109 1130 C3' C D 14 OK 1128 1131 1132 1150 C3' U D 15 OK 1148 1151 1152 1170 C3' G D 16 OK 1168 1171 1172 1193 C3' C D 17 OK 1191 1194 1195 1213 C3' U D 18 OK 1211 1214 1215 1233 C3' G D 19 OK 1231 1234 1235 1256 C3' C D 20 OK 1254 1257 1258 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK 9 6 8 30 C4' C A 2 OK 32 29 31 50 C4' U A 3 OK 52 49 51 70 C4' G A 4 OK 72 69 71 93 C4' C A 5 OK 95 92 94 113 C4' U A 6 OK 115 112 114 133 C4' G A 7 OK 135 132 134 156 C4' C A 8 OK 158 155 157 176 C4' U A 9 OK 178 175 177 196 C4' G A 10 OK 198 195 197 219 C4' C A 11 OK 221 218 220 239 C4' U A 12 OK 241 238 240 259 C4' G A 13 OK 261 258 260 282 C4' C A 14 OK 284 281 283 302 C4' U A 15 OK 304 301 303 322 C4' G A 16 OK 324 321 323 345 C4' C A 17 OK 347 344 346 365 C4' U A 18 OK 367 364 366 385 C4' G A 19 OK 387 384 386 408 C4' C A 20 OK 410 407 409 430 C4' G B 21 OK 432 429 431 453 C4' C B 22 OK 455 452 454 473 C4' U B 23 OK 475 472 474 493 C4' G B 24 OK 495 492 494 516 C4' C B 25 OK 518 515 517 536 C4' U B 26 OK 538 535 537 556 C4' G B 27 OK 558 555 557 579 C4' C B 28 OK 581 578 580 599 C4' U B 29 OK 601 598 600 619 C4' G B 30 OK 621 618 620 642 C4' C B 31 OK 644 641 643 662 C4' U B 32 OK 664 661 663 682 C4' G B 33 OK 684 681 683 705 C4' C B 34 OK 707 704 706 725 C4' U B 35 OK 727 724 726 745 C4' G B 36 OK 747 744 746 768 C4' C B 37 OK 770 767 769 788 C4' U B 38 OK 790 787 789 808 C4' G B 39 OK 810 807 809 831 C4' C B 40 OK 833 830 832 853 C4' G D 1 OK 855 852 854 876 C4' C D 2 OK 878 875 877 896 C4' U D 3 OK 898 895 897 916 C4' G D 4 OK 918 915 917 939 C4' C D 5 OK 941 938 940 959 C4' U D 6 OK 961 958 960 979 C4' G D 7 OK 981 978 980 1002 C4' C D 8 OK 1004 1001 1003 1022 C4' U D 9 OK 1024 1021 1023 1042 C4' G D 10 OK 1044 1041 1043 1065 C4' C D 11 OK 1067 1064 1066 1085 C4' U D 12 OK 1087 1084 1086 1105 C4' G D 13 OK 1107 1104 1106 1128 C4' C D 14 OK 1130 1127 1129 1148 C4' U D 15 OK 1150 1147 1149 1168 C4' G D 16 OK 1170 1167 1169 1191 C4' C D 17 OK 1193 1190 1192 1211 C4' U D 18 OK 1213 1210 1212 1231 C4' G D 19 OK 1233 1230 1232 1254 C4' C D 20 OK 1256 1253 1255 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 5 7 29 C5' C A 2 28 30 49 C5' U A 3 48 50 69 C5' G A 4 68 70 92 C5' C A 5 91 93 112 C5' U A 6 111 113 132 C5' G A 7 131 133 155 C5' C A 8 154 156 175 C5' U A 9 174 176 195 C5' G A 10 194 196 218 C5' C A 11 217 219 238 C5' U A 12 237 239 258 C5' G A 13 257 259 281 C5' C A 14 280 282 301 C5' U A 15 300 302 321 C5' G A 16 320 322 344 C5' C A 17 343 345 364 C5' U A 18 363 365 384 C5' G A 19 383 385 407 C5' C A 20 406 408 429 C5' G B 21 428 430 452 C5' C B 22 451 453 472 C5' U B 23 471 473 492 C5' G B 24 491 493 515 C5' C B 25 514 516 535 C5' U B 26 534 536 555 C5' G B 27 554 556 578 C5' C B 28 577 579 598 C5' U B 29 597 599 618 C5' G B 30 617 619 641 C5' C B 31 640 642 661 C5' U B 32 660 662 681 C5' G B 33 680 682 704 C5' C B 34 703 705 724 C5' U B 35 723 725 744 C5' G B 36 743 745 767 C5' C B 37 766 768 787 C5' U B 38 786 788 807 C5' G B 39 806 808 830 C5' C B 40 829 831 852 C5' G D 1 851 853 875 C5' C D 2 874 876 895 C5' U D 3 894 896 915 C5' G D 4 914 916 938 C5' C D 5 937 939 958 C5' U D 6 957 959 978 C5' G D 7 977 979 1001 C5' C D 8 1000 1002 1021 C5' U D 9 1020 1022 1041 C5' G D 10 1040 1042 1064 C5' C D 11 1063 1065 1084 C5' U D 12 1083 1085 1104 C5' G D 13 1103 1105 1127 C5' C D 14 1126 1128 1147 C5' U D 15 1146 1148 1167 C5' G D 16 1166 1168 1190 C5' C D 17 1189 1191 1210 C5' U D 18 1209 1211 1230 C5' G D 19 1229 1231 1253 C5' C D 20 1252 1254 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 25 P C A 2 distorted distorted 10 26 27 28 45 P U A 3 distorted distorted 33 46 47 48 65 P G A 4 distorted distorted 53 66 67 68 88 P C A 5 distorted distorted 73 89 90 91 108 P U A 6 distorted distorted 96 109 110 111 128 P G A 7 distorted distorted 116 129 130 131 151 P C A 8 distorted distorted 136 152 153 154 171 P U A 9 distorted distorted 159 172 173 174 191 P G A 10 distorted distorted 179 192 193 194 214 P C A 11 distorted distorted 199 215 216 217 234 P U A 12 distorted distorted 222 235 236 237 254 P G A 13 distorted distorted 242 255 256 257 277 P C A 14 distorted distorted 262 278 279 280 297 P U A 15 distorted distorted 285 298 299 300 317 P G A 16 distorted distorted 305 318 319 320 340 P C A 17 distorted distorted 325 341 342 343 360 P U A 18 distorted distorted 348 361 362 363 380 P G A 19 distorted distorted 368 381 382 383 403 P C A 20 distorted distorted 388 404 405 406 425 P G B 21 distorted distorted 426 427 428 448 P C B 22 distorted distorted 433 449 450 451 468 P U B 23 distorted distorted 456 469 470 471 488 P G B 24 distorted distorted 476 489 490 491 511 P C B 25 distorted distorted 496 512 513 514 531 P U B 26 distorted distorted 519 532 533 534 551 P G B 27 distorted distorted 539 552 553 554 574 P C B 28 distorted distorted 559 575 576 577 594 P U B 29 distorted distorted 582 595 596 597 614 P G B 30 distorted distorted 602 615 616 617 637 P C B 31 distorted distorted 622 638 639 640 657 P U B 32 distorted distorted 645 658 659 660 677 P G B 33 distorted distorted 665 678 679 680 700 P C B 34 distorted distorted 685 701 702 703 720 P U B 35 distorted distorted 708 721 722 723 740 P G B 36 distorted distorted 728 741 742 743 763 P C B 37 distorted distorted 748 764 765 766 783 P U B 38 distorted distorted 771 784 785 786 803 P G B 39 distorted distorted 791 804 805 806 826 P C B 40 distorted distorted 811 827 828 829 848 P G D 1 distorted distorted 849 850 851 871 P C D 2 distorted distorted 856 872 873 874 891 P U D 3 distorted distorted 879 892 893 894 911 P G D 4 distorted distorted 899 912 913 914 934 P C D 5 distorted distorted 919 935 936 937 954 P U D 6 distorted distorted 942 955 956 957 974 P G D 7 distorted distorted 962 975 976 977 997 P C D 8 distorted distorted 982 998 999 1000 1017 P U D 9 distorted distorted 1005 1018 1019 1020 1037 P G D 10 distorted distorted 1025 1038 1039 1040 1060 P C D 11 distorted distorted 1045 1061 1062 1063 1080 P U D 12 distorted distorted 1068 1081 1082 1083 1100 P G D 13 distorted distorted 1088 1101 1102 1103 1123 P C D 14 distorted distorted 1108 1124 1125 1126 1143 P U D 15 distorted distorted 1131 1144 1145 1146 1163 P G D 16 distorted distorted 1151 1164 1165 1166 1186 P C D 17 distorted distorted 1171 1187 1188 1189 1206 P U D 18 distorted distorted 1194 1207 1208 1209 1226 P G D 19 distorted distorted 1214 1227 1228 1229 1249 P C D 20 distorted distorted 1234 1250 1251 1252 ---------------------------------------------------------------------------------