ID code: '2BCZ' 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' --------------------------------------------------------------------------------- 46 C1' C A 2 beta 41 47 44 66 C1' C A 3 beta 61 67 64 86 C1' C A 4 beta 81 87 84 105 C1' DA A 5 beta 101 106 104 127 C1' G A 6 beta 122 128 125 150 C1' U A 7 beta 145 151 148 170 C1' C A 8 beta 165 171 168 190 C1' C A 9 beta 185 191 188 210 C1' A A 10 beta 205 211 208 232 C1' C A 11 beta 227 233 230 252 C1' C A 12 beta 247 253 250 272 C1' G A 13 beta 267 273 270 293 C1' C B 2 beta 288 294 291 313 C1' G B 3 beta 308 314 311 336 C1' G B 4 beta 331 337 334 359 C1' U B 5 beta 354 360 357 379 C1' G B 6 beta 374 380 377 402 C1' A B 7 beta 397 403 400 424 C1' I B 8 beta 419 425 422 446 C1' A B 9 beta 441 447 444 468 C1' A B 10 beta 463 469 466 490 C1' G B 11 beta 485 491 488 513 C1' G B 12 beta 508 514 511 536 C1' G B 13 beta 531 537 534 557 C1' G C 15 beta 552 558 555 580 C1' G C 16 beta 575 581 578 603 C1' C C 17 beta 598 604 601 623 C1' A C 18 beta 618 624 621 645 C1' G C 19 beta 640 646 643 668 C1' A C 20 beta 663 669 666 690 C1' G C 21 beta 685 691 688 713 C1' A C 22 beta 708 714 711 735 C1' A C 23 beta 730 736 733 757 C1' A C 24 beta 752 758 755 779 C1' C C 25 beta 774 780 777 799 C1' A C 26 beta 794 800 797 821 C1' C C 27 beta 816 822 819 841 C1' A C 28 beta 836 842 839 863 C1' C C 29 beta 858 864 861 883 C1' G C 30 beta 878 884 881 906 C1' A C 31 beta 901 907 904 926 C1' U D 31 beta 921 927 924 946 C1' C D 32 beta 941 947 944 966 C1' G D 33 beta 961 967 964 989 C1' U D 34 beta 984 990 987 1009 C1' G D 35 beta 1004 1010 1007 1032 C1' G D 36 beta 1027 1033 1030 1055 C1' U D 37 beta 1050 1056 1053 1075 C1' A D 38 beta 1070 1076 1073 1097 C1' C D 39 beta 1092 1098 1095 1117 C1' A D 40 beta 1112 1118 1115 1139 C1' U D 41 beta 1134 1140 1137 1159 C1' U D 42 beta 1154 1160 1157 1179 C1' A D 43 beta 1174 1180 1177 1201 C1' C D 44 beta 1196 1202 1199 1221 C1' C D 45 beta 1216 1222 1219 1241 C1' U D 46 beta 1236 1242 1239 1261 C1' G D 47 beta 1256 1262 1259 1284 C1' C D 48 beta 1279 1285 1282 1304 C1' C D 49 beta 1299 1305 1302 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 44 C2' C A 2 OK 46 42 45 64 C2' C A 3 OK 66 62 65 84 C2' C A 4 OK 86 82 85 104 C2' DA A 5 105 102 125 C2' G A 6 OK 127 123 126 148 C2' U A 7 OK 150 146 149 168 C2' C A 8 OK 170 166 169 188 C2' C A 9 OK 190 186 189 208 C2' A A 10 OK 210 206 209 230 C2' C A 11 OK 232 228 231 250 C2' C A 12 OK 252 248 251 270 C2' G A 13 OK 272 268 271 291 C2' C B 2 OK 293 289 292 311 C2' G B 3 OK 313 309 312 334 C2' G B 4 OK 336 332 335 357 C2' U B 5 OK 359 355 358 377 C2' G B 6 OK 379 375 378 400 C2' A B 7 OK 402 398 401 422 C2' I B 8 OK 424 420 423 444 C2' A B 9 OK 446 442 445 466 C2' A B 10 OK 468 464 467 488 C2' G B 11 OK 490 486 489 511 C2' G B 12 OK 513 509 512 534 C2' G B 13 OK 536 532 535 555 C2' G C 15 OK 557 553 556 578 C2' G C 16 OK 580 576 579 601 C2' C C 17 OK 603 599 602 621 C2' A C 18 OK 623 619 622 643 C2' G C 19 OK 645 641 644 666 C2' A C 20 OK 668 664 667 688 C2' G C 21 OK 690 686 689 711 C2' A C 22 OK 713 709 712 733 C2' A C 23 OK 735 731 734 755 C2' A C 24 OK 757 753 756 777 C2' C C 25 OK 779 775 778 797 C2' A C 26 OK 799 795 798 819 C2' C C 27 OK 821 817 820 839 C2' A C 28 OK 841 837 840 861 C2' C C 29 OK 863 859 862 881 C2' G C 30 OK 883 879 882 904 C2' A C 31 OK 906 902 905 924 C2' U D 31 OK 926 922 925 944 C2' C D 32 OK 946 942 945 964 C2' G D 33 OK 966 962 965 987 C2' U D 34 OK 989 985 988 1007 C2' G D 35 OK 1009 1005 1008 1030 C2' G D 36 OK 1032 1028 1031 1053 C2' U D 37 OK 1055 1051 1054 1073 C2' A D 38 OK 1075 1071 1074 1095 C2' C D 39 OK 1097 1093 1096 1115 C2' A D 40 OK 1117 1113 1116 1137 C2' U D 41 OK 1139 1135 1138 1157 C2' U D 42 OK 1159 1155 1158 1177 C2' A D 43 OK 1179 1175 1178 1199 C2' C D 44 OK 1201 1197 1200 1219 C2' C D 45 OK 1221 1217 1220 1239 C2' U D 46 OK 1241 1237 1240 1259 C2' G D 47 OK 1261 1257 1260 1282 C2' C D 48 OK 1284 1280 1283 1302 C2' C D 49 OK 1304 1300 1303 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 42 C3' C A 2 OK 40 43 44 62 C3' C A 3 OK 60 63 64 82 C3' C A 4 OK 80 83 84 102 C3' DA A 5 OK 100 103 104 123 C3' G A 6 OK 121 124 125 146 C3' U A 7 OK 144 147 148 166 C3' C A 8 OK 164 167 168 186 C3' C A 9 OK 184 187 188 206 C3' A A 10 OK 204 207 208 228 C3' C A 11 OK 226 229 230 248 C3' C A 12 OK 246 249 250 268 C3' G A 13 OK 266 269 270 289 C3' C B 2 OK 287 290 291 309 C3' G B 3 OK 307 310 311 332 C3' G B 4 OK 330 333 334 355 C3' U B 5 OK 353 356 357 375 C3' G B 6 OK 373 376 377 398 C3' A B 7 OK 396 399 400 420 C3' I B 8 OK 418 421 422 442 C3' A B 9 OK 440 443 444 464 C3' A B 10 OK 462 465 466 486 C3' G B 11 OK 484 487 488 509 C3' G B 12 OK 507 510 511 532 C3' G B 13 OK 530 533 534 553 C3' G C 15 OK 551 554 555 576 C3' G C 16 OK 574 577 578 599 C3' C C 17 OK 597 600 601 619 C3' A C 18 OK 617 620 621 641 C3' G C 19 OK 639 642 643 664 C3' A C 20 OK 662 665 666 686 C3' G C 21 OK 684 687 688 709 C3' A C 22 OK 707 710 711 731 C3' A C 23 OK 729 732 733 753 C3' A C 24 OK 751 754 755 775 C3' C C 25 OK 773 776 777 795 C3' A C 26 OK 793 796 797 817 C3' C C 27 OK 815 818 819 837 C3' A C 28 OK 835 838 839 859 C3' C C 29 OK 857 860 861 879 C3' G C 30 OK 877 880 881 902 C3' A C 31 OK 900 903 904 922 C3' U D 31 OK 920 923 924 942 C3' C D 32 OK 940 943 944 962 C3' G D 33 OK 960 963 964 985 C3' U D 34 OK 983 986 987 1005 C3' G D 35 OK 1003 1006 1007 1028 C3' G D 36 OK 1026 1029 1030 1051 C3' U D 37 OK 1049 1052 1053 1071 C3' A D 38 OK 1069 1072 1073 1093 C3' C D 39 OK 1091 1094 1095 1113 C3' A D 40 OK 1111 1114 1115 1135 C3' U D 41 OK 1133 1136 1137 1155 C3' U D 42 OK 1153 1156 1157 1175 C3' A D 43 OK 1173 1176 1177 1197 C3' C D 44 OK 1195 1198 1199 1217 C3' C D 45 OK 1215 1218 1219 1237 C3' U D 46 OK 1235 1238 1239 1257 C3' G D 47 OK 1255 1258 1259 1280 C3' C D 48 OK 1278 1281 1282 1300 C3' C D 49 OK 1298 1301 1302 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 40 C4' C A 2 OK 42 39 41 60 C4' C A 3 OK 62 59 61 80 C4' C A 4 OK 82 79 81 100 C4' DA A 5 OK 102 99 101 121 C4' G A 6 OK 123 120 122 144 C4' U A 7 OK 146 143 145 164 C4' C A 8 OK 166 163 165 184 C4' C A 9 OK 186 183 185 204 C4' A A 10 OK 206 203 205 226 C4' C A 11 OK 228 225 227 246 C4' C A 12 OK 248 245 247 266 C4' G A 13 OK 268 265 267 287 C4' C B 2 OK 289 286 288 307 C4' G B 3 OK 309 306 308 330 C4' G B 4 OK 332 329 331 353 C4' U B 5 OK 355 352 354 373 C4' G B 6 OK 375 372 374 396 C4' A B 7 OK 398 395 397 418 C4' I B 8 OK 420 417 419 440 C4' A B 9 OK 442 439 441 462 C4' A B 10 OK 464 461 463 484 C4' G B 11 OK 486 483 485 507 C4' G B 12 OK 509 506 508 530 C4' G B 13 OK 532 529 531 551 C4' G C 15 OK 553 550 552 574 C4' G C 16 OK 576 573 575 597 C4' C C 17 OK 599 596 598 617 C4' A C 18 OK 619 616 618 639 C4' G C 19 OK 641 638 640 662 C4' A C 20 OK 664 661 663 684 C4' G C 21 OK 686 683 685 707 C4' A C 22 OK 709 706 708 729 C4' A C 23 OK 731 728 730 751 C4' A C 24 OK 753 750 752 773 C4' C C 25 OK 775 772 774 793 C4' A C 26 OK 795 792 794 815 C4' C C 27 OK 817 814 816 835 C4' A C 28 OK 837 834 836 857 C4' C C 29 OK 859 856 858 877 C4' G C 30 OK 879 876 878 900 C4' A C 31 OK 902 899 901 920 C4' U D 31 OK 922 919 921 940 C4' C D 32 OK 942 939 941 960 C4' G D 33 OK 962 959 961 983 C4' U D 34 OK 985 982 984 1003 C4' G D 35 OK 1005 1002 1004 1026 C4' G D 36 OK 1028 1025 1027 1049 C4' U D 37 OK 1051 1048 1050 1069 C4' A D 38 OK 1071 1068 1070 1091 C4' C D 39 OK 1093 1090 1092 1111 C4' A D 40 OK 1113 1110 1112 1133 C4' U D 41 OK 1135 1132 1134 1153 C4' U D 42 OK 1155 1152 1154 1173 C4' A D 43 OK 1175 1172 1174 1195 C4' C D 44 OK 1197 1194 1196 1215 C4' C D 45 OK 1217 1214 1216 1235 C4' U D 46 OK 1237 1234 1236 1255 C4' G D 47 OK 1257 1254 1256 1278 C4' C D 48 OK 1280 1277 1279 1298 C4' C D 49 OK 1300 1297 1299 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 39 C5' C A 2 38 40 59 C5' C A 3 58 60 79 C5' C A 4 78 80 99 C5' DA A 5 98 100 120 C5' G A 6 119 121 143 C5' U A 7 142 144 163 C5' C A 8 162 164 183 C5' C A 9 182 184 203 C5' A A 10 202 204 225 C5' C A 11 224 226 245 C5' C A 12 244 246 265 C5' G A 13 264 266 286 C5' C B 2 285 287 306 C5' G B 3 305 307 329 C5' G B 4 328 330 352 C5' U B 5 351 353 372 C5' G B 6 371 373 395 C5' A B 7 394 396 417 C5' I B 8 416 418 439 C5' A B 9 438 440 461 C5' A B 10 460 462 483 C5' G B 11 482 484 506 C5' G B 12 505 507 529 C5' G B 13 528 530 550 C5' G C 15 549 551 573 C5' G C 16 572 574 596 C5' C C 17 595 597 616 C5' A C 18 615 617 638 C5' G C 19 637 639 661 C5' A C 20 660 662 683 C5' G C 21 682 684 706 C5' A C 22 705 707 728 C5' A C 23 727 729 750 C5' A C 24 749 751 772 C5' C C 25 771 773 792 C5' A C 26 791 793 814 C5' C C 27 813 815 834 C5' A C 28 833 835 856 C5' C C 29 855 857 876 C5' G C 30 875 877 899 C5' A C 31 898 900 919 C5' U D 31 918 920 939 C5' C D 32 938 940 959 C5' G D 33 958 960 982 C5' U D 34 981 983 1002 C5' G D 35 1001 1003 1025 C5' G D 36 1024 1026 1048 C5' U D 37 1047 1049 1068 C5' A D 38 1067 1069 1090 C5' C D 39 1089 1091 1110 C5' A D 40 1109 1111 1132 C5' U D 41 1131 1133 1152 C5' U D 42 1151 1153 1172 C5' A D 43 1171 1173 1194 C5' C D 44 1193 1195 1214 C5' C D 45 1213 1215 1234 C5' U D 46 1233 1235 1254 C5' G D 47 1253 1255 1277 C5' C D 48 1276 1278 1297 C5' C D 49 1296 1298 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 35 P C A 2 distorted distorted 36 37 38 55 P C A 3 distorted distorted 43 56 57 58 75 P C A 4 distorted distorted 63 76 77 78 95 P DA A 5 distorted distorted 83 96 97 98 116 P G A 6 distorted distorted 103 117 118 119 139 P U A 7 distorted distorted 124 140 141 142 159 P C A 8 distorted distorted 147 160 161 162 179 P C A 9 distorted distorted 167 180 181 182 199 P A A 10 distorted distorted 187 200 201 202 221 P C A 11 distorted distorted 207 222 223 224 241 P C A 12 distorted distorted 229 242 243 244 261 P G A 13 distorted distorted 249 262 263 264 302 P G B 3 distorted distorted 290 303 304 305 325 P G B 4 distorted distorted 310 326 327 328 348 P U B 5 distorted distorted 333 349 350 351 368 P G B 6 distorted distorted 356 369 370 371 391 P A B 7 distorted distorted 376 392 393 394 413 P I B 8 distorted distorted 399 414 415 416 435 P A B 9 distorted distorted 421 436 437 438 457 P A B 10 distorted distorted 443 458 459 460 479 P G B 11 distorted distorted 465 480 481 482 502 P G B 12 distorted distorted 487 503 504 505 525 P G B 13 distorted distorted 510 526 527 528 569 P G C 16 distorted distorted 554 570 571 572 592 P C C 17 distorted distorted 577 593 594 595 612 P A C 18 distorted distorted 600 613 614 615 634 P G C 19 distorted distorted 620 635 636 637 657 P A C 20 distorted distorted 642 658 659 660 679 P G C 21 distorted distorted 665 680 681 682 702 P A C 22 distorted distorted 687 703 704 705 724 P A C 23 distorted distorted 710 725 726 727 746 P A C 24 distorted distorted 732 747 748 749 768 P C C 25 distorted distorted 754 769 770 771 788 P A C 26 distorted distorted 776 789 790 791 810 P C C 27 distorted distorted 796 811 812 813 830 P A C 28 distorted distorted 818 831 832 833 852 P C C 29 distorted distorted 838 853 854 855 872 P G C 30 distorted distorted 860 873 874 875 895 P A C 31 distorted distorted 880 896 897 898 935 P C D 32 distorted distorted 923 936 937 938 955 P G D 33 distorted distorted 943 956 957 958 978 P U D 34 distorted distorted 963 979 980 981 998 P G D 35 distorted distorted 986 999 1000 1001 1021 P G D 36 distorted distorted 1006 1022 1023 1024 1044 P U D 37 distorted distorted 1029 1045 1046 1047 1064 P A D 38 distorted distorted 1052 1065 1066 1067 1086 P C D 39 distorted distorted 1072 1087 1088 1089 1106 P A D 40 distorted distorted 1094 1107 1108 1109 1128 P U D 41 distorted distorted 1114 1129 1130 1131 1148 P U D 42 distorted distorted 1136 1149 1150 1151 1168 P A D 43 distorted distorted 1156 1169 1170 1171 1190 P C D 44 distorted distorted 1176 1191 1192 1193 1210 P C D 45 distorted distorted 1198 1211 1212 1213 1230 P U D 46 distorted distorted 1218 1231 1232 1233 1250 P G D 47 distorted distorted 1238 1251 1252 1253 1273 P C D 48 distorted distorted 1258 1274 1275 1276 1293 P C D 49 distorted distorted 1281 1294 1295 1296 ---------------------------------------------------------------------------------