ID code: '2NPZ' 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' A 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' G B 8 beta 419 425 422 447 C1' A B 9 beta 442 448 445 469 C1' A B 10 beta 464 470 467 491 C1' G B 11 beta 486 492 489 514 C1' G B 12 beta 509 515 512 537 C1' G B 13 beta 532 538 535 561 C1' G C 15 beta 556 562 559 584 C1' G C 16 beta 579 585 582 607 C1' C C 17 beta 602 608 605 627 C1' A C 18 beta 622 628 625 649 C1' G C 19 beta 644 650 647 672 C1' A C 20 beta 667 673 670 694 C1' G C 21 beta 689 695 692 717 C1' A C 22 beta 712 718 715 739 C1' A C 23 beta 734 740 737 761 C1' A C 24 beta 756 762 759 783 C1' C C 25 beta 778 784 781 803 C1' A C 26 beta 798 804 801 825 C1' C C 27 beta 820 826 823 845 C1' A C 28 beta 840 846 843 867 C1' C C 29 beta 862 868 865 887 C1' G C 30 beta 882 888 885 910 C1' A C 31 beta 905 911 908 930 C1' U D 31 beta 925 931 928 950 C1' C D 32 beta 945 951 948 970 C1' G D 33 beta 965 971 968 993 C1' U D 34 beta 988 994 991 1013 C1' G D 35 beta 1008 1014 1011 1036 C1' G D 36 beta 1031 1037 1034 1059 C1' U D 37 beta 1054 1060 1057 1079 C1' A D 38 beta 1074 1080 1077 1101 C1' C D 39 beta 1096 1102 1099 1121 C1' A D 40 beta 1116 1122 1119 1143 C1' U D 41 beta 1138 1144 1141 1163 C1' U D 42 beta 1158 1164 1161 1183 C1' A D 43 beta 1178 1184 1181 1205 C1' C D 44 beta 1200 1206 1203 1225 C1' C D 45 beta 1220 1226 1223 1245 C1' U D 46 beta 1240 1246 1243 1265 C1' G D 47 beta 1260 1266 1263 1288 C1' C D 48 beta 1283 1289 1286 1308 C1' C D 49 beta 1303 1309 1306 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A 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' G B 8 OK 424 420 423 445 C2' A B 9 OK 447 443 446 467 C2' A B 10 OK 469 465 468 489 C2' G B 11 OK 491 487 490 512 C2' G B 12 OK 514 510 513 535 C2' G B 13 OK 537 533 536 559 C2' G C 15 OK 561 557 560 582 C2' G C 16 OK 584 580 583 605 C2' C C 17 OK 607 603 606 625 C2' A C 18 OK 627 623 626 647 C2' G C 19 OK 649 645 648 670 C2' A C 20 OK 672 668 671 692 C2' G C 21 OK 694 690 693 715 C2' A C 22 OK 717 713 716 737 C2' A C 23 OK 739 735 738 759 C2' A C 24 OK 761 757 760 781 C2' C C 25 OK 783 779 782 801 C2' A C 26 OK 803 799 802 823 C2' C C 27 OK 825 821 824 843 C2' A C 28 OK 845 841 844 865 C2' C C 29 OK 867 863 866 885 C2' G C 30 OK 887 883 886 908 C2' A C 31 OK 910 906 909 928 C2' U D 31 OK 930 926 929 948 C2' C D 32 OK 950 946 949 968 C2' G D 33 OK 970 966 969 991 C2' U D 34 OK 993 989 992 1011 C2' G D 35 OK 1013 1009 1012 1034 C2' G D 36 OK 1036 1032 1035 1057 C2' U D 37 OK 1059 1055 1058 1077 C2' A D 38 OK 1079 1075 1078 1099 C2' C D 39 OK 1101 1097 1100 1119 C2' A D 40 OK 1121 1117 1120 1141 C2' U D 41 OK 1143 1139 1142 1161 C2' U D 42 OK 1163 1159 1162 1181 C2' A D 43 OK 1183 1179 1182 1203 C2' C D 44 OK 1205 1201 1204 1223 C2' C D 45 OK 1225 1221 1224 1243 C2' U D 46 OK 1245 1241 1244 1263 C2' G D 47 OK 1265 1261 1264 1286 C2' C D 48 OK 1288 1284 1287 1306 C2' C D 49 OK 1308 1304 1307 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A 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' G B 8 OK 418 421 422 443 C3' A B 9 OK 441 444 445 465 C3' A B 10 OK 463 466 467 487 C3' G B 11 OK 485 488 489 510 C3' G B 12 OK 508 511 512 533 C3' G B 13 OK 531 534 535 557 C3' G C 15 OK 555 558 559 580 C3' G C 16 OK 578 581 582 603 C3' C C 17 OK 601 604 605 623 C3' A C 18 OK 621 624 625 645 C3' G C 19 OK 643 646 647 668 C3' A C 20 OK 666 669 670 690 C3' G C 21 OK 688 691 692 713 C3' A C 22 OK 711 714 715 735 C3' A C 23 OK 733 736 737 757 C3' A C 24 OK 755 758 759 779 C3' C C 25 OK 777 780 781 799 C3' A C 26 OK 797 800 801 821 C3' C C 27 OK 819 822 823 841 C3' A C 28 OK 839 842 843 863 C3' C C 29 OK 861 864 865 883 C3' G C 30 OK 881 884 885 906 C3' A C 31 OK 904 907 908 926 C3' U D 31 OK 924 927 928 946 C3' C D 32 OK 944 947 948 966 C3' G D 33 OK 964 967 968 989 C3' U D 34 OK 987 990 991 1009 C3' G D 35 OK 1007 1010 1011 1032 C3' G D 36 OK 1030 1033 1034 1055 C3' U D 37 OK 1053 1056 1057 1075 C3' A D 38 OK 1073 1076 1077 1097 C3' C D 39 OK 1095 1098 1099 1117 C3' A D 40 OK 1115 1118 1119 1139 C3' U D 41 OK 1137 1140 1141 1159 C3' U D 42 OK 1157 1160 1161 1179 C3' A D 43 OK 1177 1180 1181 1201 C3' C D 44 OK 1199 1202 1203 1221 C3' C D 45 OK 1219 1222 1223 1241 C3' U D 46 OK 1239 1242 1243 1261 C3' G D 47 OK 1259 1262 1263 1284 C3' C D 48 OK 1282 1285 1286 1304 C3' C D 49 OK 1302 1305 1306 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A 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' G B 8 OK 420 417 419 441 C4' A B 9 OK 443 440 442 463 C4' A B 10 OK 465 462 464 485 C4' G B 11 OK 487 484 486 508 C4' G B 12 OK 510 507 509 531 C4' G B 13 OK 533 530 532 555 C4' G C 15 OK 557 554 556 578 C4' G C 16 OK 580 577 579 601 C4' C C 17 OK 603 600 602 621 C4' A C 18 OK 623 620 622 643 C4' G C 19 OK 645 642 644 666 C4' A C 20 OK 668 665 667 688 C4' G C 21 OK 690 687 689 711 C4' A C 22 OK 713 710 712 733 C4' A C 23 OK 735 732 734 755 C4' A C 24 OK 757 754 756 777 C4' C C 25 OK 779 776 778 797 C4' A C 26 OK 799 796 798 819 C4' C C 27 OK 821 818 820 839 C4' A C 28 OK 841 838 840 861 C4' C C 29 OK 863 860 862 881 C4' G C 30 OK 883 880 882 904 C4' A C 31 OK 906 903 905 924 C4' U D 31 OK 926 923 925 944 C4' C D 32 OK 946 943 945 964 C4' G D 33 OK 966 963 965 987 C4' U D 34 OK 989 986 988 1007 C4' G D 35 OK 1009 1006 1008 1030 C4' G D 36 OK 1032 1029 1031 1053 C4' U D 37 OK 1055 1052 1054 1073 C4' A D 38 OK 1075 1072 1074 1095 C4' C D 39 OK 1097 1094 1096 1115 C4' A D 40 OK 1117 1114 1116 1137 C4' U D 41 OK 1139 1136 1138 1157 C4' U D 42 OK 1159 1156 1158 1177 C4' A D 43 OK 1179 1176 1178 1199 C4' C D 44 OK 1201 1198 1200 1219 C4' C D 45 OK 1221 1218 1220 1239 C4' U D 46 OK 1241 1238 1240 1259 C4' G D 47 OK 1261 1258 1260 1282 C4' C D 48 OK 1284 1281 1283 1302 C4' C D 49 OK 1304 1301 1303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A 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' G B 8 416 418 440 C5' A B 9 439 441 462 C5' A B 10 461 463 484 C5' G B 11 483 485 507 C5' G B 12 506 508 530 C5' G B 13 529 531 554 C5' G C 15 553 555 577 C5' G C 16 576 578 600 C5' C C 17 599 601 620 C5' A C 18 619 621 642 C5' G C 19 641 643 665 C5' A C 20 664 666 687 C5' G C 21 686 688 710 C5' A C 22 709 711 732 C5' A C 23 731 733 754 C5' A C 24 753 755 776 C5' C C 25 775 777 796 C5' A C 26 795 797 818 C5' C C 27 817 819 838 C5' A C 28 837 839 860 C5' C C 29 859 861 880 C5' G C 30 879 881 903 C5' A C 31 902 904 923 C5' U D 31 922 924 943 C5' C D 32 942 944 963 C5' G D 33 962 964 986 C5' U D 34 985 987 1006 C5' G D 35 1005 1007 1029 C5' G D 36 1028 1030 1052 C5' U D 37 1051 1053 1072 C5' A D 38 1071 1073 1094 C5' C D 39 1093 1095 1114 C5' A D 40 1113 1115 1136 C5' U D 41 1135 1137 1156 C5' U D 42 1155 1157 1176 C5' A D 43 1175 1177 1198 C5' C D 44 1197 1199 1218 C5' C D 45 1217 1219 1238 C5' U D 46 1237 1239 1258 C5' G D 47 1257 1259 1281 C5' C D 48 1280 1282 1301 C5' C D 49 1300 1302 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A 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 G B 8 distorted distorted 399 414 415 416 436 P A B 9 distorted distorted 421 437 438 439 458 P A B 10 distorted distorted 444 459 460 461 480 P G B 11 distorted distorted 466 481 482 483 503 P G B 12 distorted distorted 488 504 505 506 526 P G B 13 distorted distorted 511 527 528 529 550 P G C 15 OK OK 551 552 553 573 P G C 16 distorted distorted 558 574 575 576 596 P C C 17 distorted distorted 581 597 598 599 616 P A C 18 distorted distorted 604 617 618 619 638 P G C 19 distorted distorted 624 639 640 641 661 P A C 20 distorted distorted 646 662 663 664 683 P G C 21 distorted distorted 669 684 685 686 706 P A C 22 distorted distorted 691 707 708 709 728 P A C 23 distorted distorted 714 729 730 731 750 P A C 24 distorted distorted 736 751 752 753 772 P C C 25 distorted distorted 758 773 774 775 792 P A C 26 distorted distorted 780 793 794 795 814 P C C 27 distorted distorted 800 815 816 817 834 P A C 28 distorted distorted 822 835 836 837 856 P C C 29 distorted distorted 842 857 858 859 876 P G C 30 distorted distorted 864 877 878 879 899 P A C 31 distorted distorted 884 900 901 902 939 P C D 32 distorted distorted 927 940 941 942 959 P G D 33 distorted distorted 947 960 961 962 982 P U D 34 distorted distorted 967 983 984 985 1002 P G D 35 distorted distorted 990 1003 1004 1005 1025 P G D 36 distorted distorted 1010 1026 1027 1028 1048 P U D 37 distorted distorted 1033 1049 1050 1051 1068 P A D 38 distorted distorted 1056 1069 1070 1071 1090 P C D 39 distorted distorted 1076 1091 1092 1093 1110 P A D 40 distorted distorted 1098 1111 1112 1113 1132 P U D 41 distorted distorted 1118 1133 1134 1135 1152 P U D 42 distorted distorted 1140 1153 1154 1155 1172 P A D 43 distorted distorted 1160 1173 1174 1175 1194 P C D 44 distorted distorted 1180 1195 1196 1197 1214 P C D 45 distorted distorted 1202 1215 1216 1217 1234 P U D 46 distorted distorted 1222 1235 1236 1237 1254 P G D 47 distorted distorted 1242 1255 1256 1257 1277 P C D 48 distorted distorted 1262 1278 1279 1280 1297 P C D 49 distorted distorted 1285 1298 1299 1300 1318 P PDI B 14 distorted distorted 534 1321 1320 ---------------------------------------------------------------------------------