ID code: '2RFK' 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 D 1 beta 4 10 7 32 C1' G D 2 beta 27 33 30 55 C1' G D 3 beta 50 56 53 78 C1' C D 4 beta 73 79 76 98 C1' U D 5 beta 93 99 96 118 C1' C D 6 beta 113 119 116 138 C1' C D 7 beta 133 139 136 158 C1' G D 8 beta 153 159 156 181 C1' G D 9 beta 176 182 179 204 C1' A D 10 beta 199 205 202 226 C1' A D 11 beta 221 227 224 248 C1' A D 12 beta 243 249 246 270 C1' C D 13 beta 265 271 268 290 C1' C D 14 beta 285 291 288 310 C1' G D 15 beta 305 311 308 333 C1' C D 16 beta 328 334 331 353 C1' G D 17 beta 348 354 351 376 C1' G D 18 beta 371 377 374 399 C1' C D 19 beta 394 400 397 419 C1' G D 20 beta 414 420 417 442 C1' C D 21 beta 437 443 440 460 C1' G E 1 beta 455 461 458 483 C1' C E 2 beta 478 484 481 503 C1' G E 3 beta 498 504 501 526 C1' C E 4 beta 521 527 524 546 C1' U E 5 beta 541 547 544 566 C1' U E 6 beta 561 567 564 586 C1' C E 7 beta 581 587 584 606 C1' G E 8 beta 601 607 604 629 C1' C E 9 beta 624 630 627 649 C1' U E 10 beta 644 650 647 669 C1' C E 11 beta 664 670 667 689 C1' C E 12 beta 684 690 687 709 C1' C E 13 beta 704 710 707 729 C1' G E 14 beta 724 730 727 752 C1' G E 15 beta 747 753 750 775 C1' A E 16 beta 770 776 773 797 C1' G E 17 beta 792 798 795 820 C1' C E 18 beta 815 821 818 840 C1' C E 19 beta 835 841 838 860 C1' C E 20 beta 855 861 858 880 C1' A E 21 beta 875 881 878 902 C1' C E 22 beta 897 903 900 922 C1' A E 23 beta 917 923 920 944 C1' C E 24 beta 939 945 942 964 C1' U E 25 beta 959 965 962 984 C1' A E 26 beta 979 985 982 1004 C1' G F 4 beta 999 1005 1002 1027 C1' G F 5 beta 1022 1028 1025 1050 C1' A F 6 beta 1045 1051 1048 1072 C1' G F 7 beta 1067 1073 1070 1095 C1' C F 8 beta 1090 1096 1093 1115 C1' G F 9 beta 1110 1116 1113 1138 C1' U F 10 beta 1133 1139 1136 1158 C1' G F 11 beta 1153 1159 1156 1181 C1' C F 12 beta 1176 1182 1179 1201 C1' G F 13 beta 1196 1202 1199 1224 C1' G F 14 beta 1219 1225 1222 1247 C1' U F 15 beta 1242 1248 1245 1267 C1' U F 16 beta 1262 1268 1265 1287 C1' U F 17 beta 1282 1288 1285 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G D 1 OK 9 5 8 30 C2' G D 2 OK 32 28 31 53 C2' G D 3 OK 55 51 54 76 C2' C D 4 OK 78 74 77 96 C2' U D 5 OK 98 94 97 116 C2' C D 6 OK 118 114 117 136 C2' C D 7 OK 138 134 137 156 C2' G D 8 OK 158 154 157 179 C2' G D 9 OK 181 177 180 202 C2' A D 10 OK 204 200 203 224 C2' A D 11 OK 226 222 225 246 C2' A D 12 OK 248 244 247 268 C2' C D 13 OK 270 266 269 288 C2' C D 14 OK 290 286 289 308 C2' G D 15 OK 310 306 309 331 C2' C D 16 OK 333 329 332 351 C2' G D 17 OK 353 349 352 374 C2' G D 18 OK 376 372 375 397 C2' C D 19 OK 399 395 398 417 C2' G D 20 OK 419 415 418 440 C2' C D 21 OK 442 438 441 458 C2' G E 1 OK 460 456 459 481 C2' C E 2 OK 483 479 482 501 C2' G E 3 OK 503 499 502 524 C2' C E 4 OK 526 522 525 544 C2' U E 5 OK 546 542 545 564 C2' U E 6 OK 566 562 565 584 C2' C E 7 OK 586 582 585 604 C2' G E 8 OK 606 602 605 627 C2' C E 9 OK 629 625 628 647 C2' U E 10 OK 649 645 648 667 C2' C E 11 OK 669 665 668 687 C2' C E 12 OK 689 685 688 707 C2' C E 13 OK 709 705 708 727 C2' G E 14 OK 729 725 728 750 C2' G E 15 OK 752 748 751 773 C2' A E 16 OK 775 771 774 795 C2' G E 17 OK 797 793 796 818 C2' C E 18 OK 820 816 819 838 C2' C E 19 OK 840 836 839 858 C2' C E 20 OK 860 856 859 878 C2' A E 21 OK 880 876 879 900 C2' C E 22 OK 902 898 901 920 C2' A E 23 OK 922 918 921 942 C2' C E 24 OK 944 940 943 962 C2' U E 25 OK 964 960 963 982 C2' A E 26 OK 984 980 983 1002 C2' G F 4 OK 1004 1000 1003 1025 C2' G F 5 OK 1027 1023 1026 1048 C2' A F 6 OK 1050 1046 1049 1070 C2' G F 7 OK 1072 1068 1071 1093 C2' C F 8 OK 1095 1091 1094 1113 C2' G F 9 OK 1115 1111 1114 1136 C2' U F 10 OK 1138 1134 1137 1156 C2' G F 11 OK 1158 1154 1157 1179 C2' C F 12 OK 1181 1177 1180 1199 C2' G F 13 OK 1201 1197 1200 1222 C2' G F 14 OK 1224 1220 1223 1245 C2' U F 15 OK 1247 1243 1246 1265 C2' U F 16 OK 1267 1263 1266 1285 C2' U F 17 OK 1287 1283 1286 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G D 1 OK 3 6 7 28 C3' G D 2 OK 26 29 30 51 C3' G D 3 OK 49 52 53 74 C3' C D 4 OK 72 75 76 94 C3' U D 5 OK 92 95 96 114 C3' C D 6 OK 112 115 116 134 C3' C D 7 OK 132 135 136 154 C3' G D 8 OK 152 155 156 177 C3' G D 9 OK 175 178 179 200 C3' A D 10 OK 198 201 202 222 C3' A D 11 OK 220 223 224 244 C3' A D 12 OK 242 245 246 266 C3' C D 13 OK 264 267 268 286 C3' C D 14 OK 284 287 288 306 C3' G D 15 OK 304 307 308 329 C3' C D 16 OK 327 330 331 349 C3' G D 17 OK 347 350 351 372 C3' G D 18 OK 370 373 374 395 C3' C D 19 OK 393 396 397 415 C3' G D 20 OK 413 416 417 438 C3' C D 21 OK 436 439 440 456 C3' G E 1 OK 454 457 458 479 C3' C E 2 OK 477 480 481 499 C3' G E 3 OK 497 500 501 522 C3' C E 4 OK 520 523 524 542 C3' U E 5 OK 540 543 544 562 C3' U E 6 OK 560 563 564 582 C3' C E 7 OK 580 583 584 602 C3' G E 8 OK 600 603 604 625 C3' C E 9 OK 623 626 627 645 C3' U E 10 OK 643 646 647 665 C3' C E 11 OK 663 666 667 685 C3' C E 12 OK 683 686 687 705 C3' C E 13 OK 703 706 707 725 C3' G E 14 OK 723 726 727 748 C3' G E 15 OK 746 749 750 771 C3' A E 16 OK 769 772 773 793 C3' G E 17 OK 791 794 795 816 C3' C E 18 OK 814 817 818 836 C3' C E 19 OK 834 837 838 856 C3' C E 20 OK 854 857 858 876 C3' A E 21 OK 874 877 878 898 C3' C E 22 OK 896 899 900 918 C3' A E 23 OK 916 919 920 940 C3' C E 24 OK 938 941 942 960 C3' U E 25 OK 958 961 962 980 C3' A E 26 OK 978 981 982 1000 C3' G F 4 OK 998 1001 1002 1023 C3' G F 5 OK 1021 1024 1025 1046 C3' A F 6 OK 1044 1047 1048 1068 C3' G F 7 OK 1066 1069 1070 1091 C3' C F 8 OK 1089 1092 1093 1111 C3' G F 9 OK 1109 1112 1113 1134 C3' U F 10 OK 1132 1135 1136 1154 C3' G F 11 OK 1152 1155 1156 1177 C3' C F 12 OK 1175 1178 1179 1197 C3' G F 13 OK 1195 1198 1199 1220 C3' G F 14 OK 1218 1221 1222 1243 C3' U F 15 OK 1241 1244 1245 1263 C3' U F 16 OK 1261 1264 1265 1283 C3' U F 17 OK 1281 1284 1285 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G D 1 OK 5 2 4 26 C4' G D 2 OK 28 25 27 49 C4' G D 3 OK 51 48 50 72 C4' C D 4 OK 74 71 73 92 C4' U D 5 OK 94 91 93 112 C4' C D 6 OK 114 111 113 132 C4' C D 7 OK 134 131 133 152 C4' G D 8 OK 154 151 153 175 C4' G D 9 OK 177 174 176 198 C4' A D 10 OK 200 197 199 220 C4' A D 11 OK 222 219 221 242 C4' A D 12 OK 244 241 243 264 C4' C D 13 OK 266 263 265 284 C4' C D 14 OK 286 283 285 304 C4' G D 15 OK 306 303 305 327 C4' C D 16 OK 329 326 328 347 C4' G D 17 OK 349 346 348 370 C4' G D 18 OK 372 369 371 393 C4' C D 19 OK 395 392 394 413 C4' G D 20 OK 415 412 414 436 C4' C D 21 OK 438 435 437 454 C4' G E 1 OK 456 453 455 477 C4' C E 2 OK 479 476 478 497 C4' G E 3 OK 499 496 498 520 C4' C E 4 OK 522 519 521 540 C4' U E 5 OK 542 539 541 560 C4' U E 6 OK 562 559 561 580 C4' C E 7 OK 582 579 581 600 C4' G E 8 OK 602 599 601 623 C4' C E 9 OK 625 622 624 643 C4' U E 10 OK 645 642 644 663 C4' C E 11 OK 665 662 664 683 C4' C E 12 OK 685 682 684 703 C4' C E 13 OK 705 702 704 723 C4' G E 14 OK 725 722 724 746 C4' G E 15 OK 748 745 747 769 C4' A E 16 OK 771 768 770 791 C4' G E 17 OK 793 790 792 814 C4' C E 18 OK 816 813 815 834 C4' C E 19 OK 836 833 835 854 C4' C E 20 OK 856 853 855 874 C4' A E 21 OK 876 873 875 896 C4' C E 22 OK 898 895 897 916 C4' A E 23 OK 918 915 917 938 C4' C E 24 OK 940 937 939 958 C4' U E 25 OK 960 957 959 978 C4' A E 26 OK 980 977 979 998 C4' G F 4 OK 1000 997 999 1021 C4' G F 5 OK 1023 1020 1022 1044 C4' A F 6 OK 1046 1043 1045 1066 C4' G F 7 OK 1068 1065 1067 1089 C4' C F 8 OK 1091 1088 1090 1109 C4' G F 9 OK 1111 1108 1110 1132 C4' U F 10 OK 1134 1131 1133 1152 C4' G F 11 OK 1154 1151 1153 1175 C4' C F 12 OK 1177 1174 1176 1195 C4' G F 13 OK 1197 1194 1196 1218 C4' G F 14 OK 1220 1217 1219 1241 C4' U F 15 OK 1243 1240 1242 1261 C4' U F 16 OK 1263 1260 1262 1281 C4' U F 17 OK 1283 1280 1282 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G D 1 1 3 25 C5' G D 2 24 26 48 C5' G D 3 47 49 71 C5' C D 4 70 72 91 C5' U D 5 90 92 111 C5' C D 6 110 112 131 C5' C D 7 130 132 151 C5' G D 8 150 152 174 C5' G D 9 173 175 197 C5' A D 10 196 198 219 C5' A D 11 218 220 241 C5' A D 12 240 242 263 C5' C D 13 262 264 283 C5' C D 14 282 284 303 C5' G D 15 302 304 326 C5' C D 16 325 327 346 C5' G D 17 345 347 369 C5' G D 18 368 370 392 C5' C D 19 391 393 412 C5' G D 20 411 413 435 C5' C D 21 434 436 453 C5' G E 1 452 454 476 C5' C E 2 475 477 496 C5' G E 3 495 497 519 C5' C E 4 518 520 539 C5' U E 5 538 540 559 C5' U E 6 558 560 579 C5' C E 7 578 580 599 C5' G E 8 598 600 622 C5' C E 9 621 623 642 C5' U E 10 641 643 662 C5' C E 11 661 663 682 C5' C E 12 681 683 702 C5' C E 13 701 703 722 C5' G E 14 721 723 745 C5' G E 15 744 746 768 C5' A E 16 767 769 790 C5' G E 17 789 791 813 C5' C E 18 812 814 833 C5' C E 19 832 834 853 C5' C E 20 852 854 873 C5' A E 21 872 874 895 C5' C E 22 894 896 915 C5' A E 23 914 916 937 C5' C E 24 936 938 957 C5' U E 25 956 958 977 C5' A E 26 976 978 997 C5' G F 4 996 998 1020 C5' G F 5 1019 1021 1043 C5' A F 6 1042 1044 1065 C5' G F 7 1064 1066 1088 C5' C F 8 1087 1089 1108 C5' G F 9 1107 1109 1131 C5' U F 10 1130 1132 1151 C5' G F 11 1150 1152 1174 C5' C F 12 1173 1175 1194 C5' G F 13 1193 1195 1217 C5' G F 14 1216 1218 1240 C5' U F 15 1239 1241 1260 C5' U F 16 1259 1261 1280 C5' U F 17 1279 1281 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G D 2 distorted distorted 6 22 23 24 44 P G D 3 distorted distorted 29 45 46 47 67 P C D 4 distorted distorted 52 68 69 70 87 P U D 5 distorted distorted 75 88 89 90 107 P C D 6 distorted distorted 95 108 109 110 127 P C D 7 distorted distorted 115 128 129 130 147 P G D 8 distorted distorted 135 148 149 150 170 P G D 9 distorted distorted 155 171 172 173 193 P A D 10 distorted distorted 178 194 195 196 215 P A D 11 distorted distorted 201 216 217 218 237 P A D 12 distorted distorted 223 238 239 240 259 P C D 13 distorted distorted 245 260 261 262 279 P C D 14 distorted distorted 267 280 281 282 299 P G D 15 distorted distorted 287 300 301 302 322 P C D 16 distorted distorted 307 323 324 325 342 P G D 17 distorted distorted 330 343 344 345 365 P G D 18 distorted distorted 350 366 367 368 388 P C D 19 distorted distorted 373 389 390 391 408 P G D 20 distorted distorted 396 409 410 411 431 P C D 21 distorted distorted 416 432 433 434 472 P C E 2 distorted distorted 457 473 474 475 492 P G E 3 distorted distorted 480 493 494 495 515 P C E 4 distorted distorted 500 516 517 518 535 P U E 5 distorted distorted 523 536 537 538 555 P U E 6 distorted distorted 543 556 557 558 575 P C E 7 distorted distorted 563 576 577 578 595 P G E 8 distorted distorted 583 596 597 598 618 P C E 9 distorted distorted 603 619 620 621 638 P U E 10 distorted distorted 626 639 640 641 658 P C E 11 distorted distorted 646 659 660 661 678 P C E 12 distorted distorted 666 679 680 681 698 P C E 13 distorted distorted 686 699 700 701 718 P G E 14 distorted distorted 706 719 720 721 741 P G E 15 distorted distorted 726 742 743 744 764 P A E 16 distorted distorted 749 765 766 767 786 P G E 17 distorted distorted 772 787 788 789 809 P C E 18 distorted distorted 794 810 811 812 829 P C E 19 distorted distorted 817 830 831 832 849 P C E 20 distorted distorted 837 850 851 852 869 P A E 21 distorted distorted 857 870 871 872 891 P C E 22 distorted distorted 877 892 893 894 911 P A E 23 distorted distorted 899 912 913 914 933 P C E 24 distorted distorted 919 934 935 936 953 P U E 25 distorted distorted 941 954 955 956 973 P A E 26 distorted distorted 961 974 975 976 1016 P G F 5 distorted distorted 1001 1017 1018 1019 1039 P A F 6 distorted distorted 1024 1040 1041 1042 1061 P G F 7 distorted distorted 1047 1062 1063 1064 1084 P C F 8 distorted distorted 1069 1085 1086 1087 1104 P G F 9 distorted distorted 1092 1105 1106 1107 1127 P U F 10 distorted distorted 1112 1128 1129 1130 1147 P G F 11 distorted distorted 1135 1148 1149 1150 1170 P C F 12 distorted distorted 1155 1171 1172 1173 1190 P G F 13 distorted distorted 1178 1191 1192 1193 1213 P G F 14 distorted distorted 1198 1214 1215 1216 1236 P U F 15 distorted distorted 1221 1237 1238 1239 1256 P U F 16 distorted distorted 1244 1257 1258 1259 1276 P U F 17 distorted distorted 1264 1277 1278 1279 ---------------------------------------------------------------------------------