ID code: '2L94' 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 alpha beta 8 31 14 11 48 C1' G A 2 alpha beta 43 66 49 46 82 C1' G A 3 alpha beta 77 100 83 80 116 C1' A A 4 alpha beta 111 133 117 114 149 C1' A A 5 alpha beta 144 166 150 147 182 C1' G A 6 alpha beta 177 200 183 180 216 C1' A A 7 alpha beta 211 233 217 214 249 C1' U A 8 alpha beta 244 264 250 247 279 C1' C A 9 alpha beta 274 294 280 277 310 C1' U A 10 alpha beta 305 325 311 308 340 C1' G A 11 alpha beta 335 358 341 338 374 C1' G A 12 alpha beta 369 392 375 372 408 C1' C A 13 alpha beta 403 423 409 406 439 C1' C A 14 alpha beta 434 454 440 437 470 C1' U A 15 alpha beta 465 485 471 468 500 C1' U A 16 alpha beta 495 515 501 498 530 C1' C A 17 alpha beta 525 545 531 528 561 C1' C A 18 alpha beta 556 576 562 559 592 C1' C A 19 alpha beta 587 607 593 590 623 C1' A A 20 alpha beta 618 640 624 621 656 C1' C A 21 alpha beta 651 671 657 654 687 C1' A A 22 alpha beta 682 704 688 685 720 C1' A A 23 alpha beta 715 737 721 718 753 C1' G A 24 alpha beta 748 771 754 751 787 C1' G A 25 alpha beta 782 805 788 785 821 C1' G A 26 alpha beta 816 839 822 819 855 C1' A A 27 alpha beta 850 872 856 853 888 C1' A A 28 alpha beta 883 905 889 886 921 C1' G A 29 alpha beta 916 939 922 919 955 C1' G A 30 alpha beta 950 973 956 953 989 C1' C A 31 alpha beta 984 1004 990 987 1020 C1' C A 32 alpha beta 1015 1035 1021 1018 1051 C1' A A 33 alpha beta 1046 1068 1052 1049 1084 C1' G A 34 alpha beta 1079 1102 1085 1082 1118 C1' G A 35 alpha beta 1113 1136 1119 1116 1152 C1' G A 36 alpha beta 1147 1170 1153 1150 1186 C1' A A 37 alpha beta 1181 1203 1187 1184 1219 C1' A A 38 alpha beta 1214 1236 1220 1217 1252 C1' U A 39 alpha beta 1247 1267 1253 1250 1282 C1' C A 40 alpha beta 1277 1297 1283 1280 1313 C1' U A 41 alpha beta 1308 1328 1314 1311 1343 C1' U A 42 alpha beta 1338 1358 1344 1341 1373 C1' C A 43 alpha beta 1368 1388 1374 1371 1404 C1' C A 44 alpha beta 1399 1419 1405 1402 1435 C1' C A 45 alpha beta 1430 1451 1436 1433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 13 9 29 12 46 C2' G A 2 OK OK 48 44 64 47 80 C2' G A 3 OK OK 82 78 98 81 114 C2' A A 4 OK OK 116 112 131 115 147 C2' A A 5 OK OK 149 145 164 148 180 C2' G A 6 OK OK 182 178 198 181 214 C2' A A 7 OK OK 216 212 231 215 247 C2' U A 8 OK OK 249 245 262 248 277 C2' C A 9 OK OK 279 275 292 278 308 C2' U A 10 OK OK 310 306 323 309 338 C2' G A 11 OK OK 340 336 356 339 372 C2' G A 12 OK OK 374 370 390 373 406 C2' C A 13 OK OK 408 404 421 407 437 C2' C A 14 OK OK 439 435 452 438 468 C2' U A 15 OK OK 470 466 483 469 498 C2' U A 16 OK OK 500 496 513 499 528 C2' C A 17 OK OK 530 526 543 529 559 C2' C A 18 OK OK 561 557 574 560 590 C2' C A 19 OK OK 592 588 605 591 621 C2' A A 20 OK OK 623 619 638 622 654 C2' C A 21 OK OK 656 652 669 655 685 C2' A A 22 OK OK 687 683 702 686 718 C2' A A 23 OK OK 720 716 735 719 751 C2' G A 24 OK OK 753 749 769 752 785 C2' G A 25 OK OK 787 783 803 786 819 C2' G A 26 OK OK 821 817 837 820 853 C2' A A 27 OK OK 855 851 870 854 886 C2' A A 28 OK OK 888 884 903 887 919 C2' G A 29 OK OK 921 917 937 920 953 C2' G A 30 OK OK 955 951 971 954 987 C2' C A 31 OK OK 989 985 1002 988 1018 C2' C A 32 OK OK 1020 1016 1033 1019 1049 C2' A A 33 OK OK 1051 1047 1066 1050 1082 C2' G A 34 OK OK 1084 1080 1100 1083 1116 C2' G A 35 OK OK 1118 1114 1134 1117 1150 C2' G A 36 OK OK 1152 1148 1168 1151 1184 C2' A A 37 OK OK 1186 1182 1201 1185 1217 C2' A A 38 OK OK 1219 1215 1234 1218 1250 C2' U A 39 OK OK 1252 1248 1265 1251 1280 C2' C A 40 OK OK 1282 1278 1295 1281 1311 C2' U A 41 OK OK 1313 1309 1326 1312 1341 C2' U A 42 OK OK 1343 1339 1356 1342 1371 C2' C A 43 OK OK 1373 1369 1386 1372 1402 C2' C A 44 OK OK 1404 1400 1417 1403 1433 C2' C A 45 OK OK 1435 1431 1449 1434 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' G A 2 OK OK 42 63 45 46 78 C3' G A 3 OK OK 76 97 79 80 112 C3' A A 4 OK OK 110 130 113 114 145 C3' A A 5 OK OK 143 163 146 147 178 C3' G A 6 OK OK 176 197 179 180 212 C3' A A 7 OK OK 210 230 213 214 245 C3' U A 8 OK OK 243 261 246 247 275 C3' C A 9 OK OK 273 291 276 277 306 C3' U A 10 OK OK 304 322 307 308 336 C3' G A 11 OK OK 334 355 337 338 370 C3' G A 12 OK OK 368 389 371 372 404 C3' C A 13 OK OK 402 420 405 406 435 C3' C A 14 OK OK 433 451 436 437 466 C3' U A 15 OK OK 464 482 467 468 496 C3' U A 16 OK OK 494 512 497 498 526 C3' C A 17 OK OK 524 542 527 528 557 C3' C A 18 OK OK 555 573 558 559 588 C3' C A 19 OK OK 586 604 589 590 619 C3' A A 20 OK OK 617 637 620 621 652 C3' C A 21 OK OK 650 668 653 654 683 C3' A A 22 OK OK 681 701 684 685 716 C3' A A 23 OK OK 714 734 717 718 749 C3' G A 24 OK OK 747 768 750 751 783 C3' G A 25 OK OK 781 802 784 785 817 C3' G A 26 OK OK 815 836 818 819 851 C3' A A 27 OK OK 849 869 852 853 884 C3' A A 28 OK OK 882 902 885 886 917 C3' G A 29 OK OK 915 936 918 919 951 C3' G A 30 OK OK 949 970 952 953 985 C3' C A 31 OK OK 983 1001 986 987 1016 C3' C A 32 OK OK 1014 1032 1017 1018 1047 C3' A A 33 OK OK 1045 1065 1048 1049 1080 C3' G A 34 OK OK 1078 1099 1081 1082 1114 C3' G A 35 OK OK 1112 1133 1115 1116 1148 C3' G A 36 OK OK 1146 1167 1149 1150 1182 C3' A A 37 OK OK 1180 1200 1183 1184 1215 C3' A A 38 OK OK 1213 1233 1216 1217 1248 C3' U A 39 OK OK 1246 1264 1249 1250 1278 C3' C A 40 OK OK 1276 1294 1279 1280 1309 C3' U A 41 OK OK 1307 1325 1310 1311 1339 C3' U A 42 OK OK 1337 1355 1340 1341 1369 C3' C A 43 OK OK 1367 1385 1370 1371 1400 C3' C A 44 OK OK 1398 1416 1401 1402 1431 C3' C A 45 OK OK 1429 1447 1432 1433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' G A 2 OK OK 44 62 41 43 76 C4' G A 3 OK OK 78 96 75 77 110 C4' A A 4 OK OK 112 129 109 111 143 C4' A A 5 OK OK 145 162 142 144 176 C4' G A 6 OK OK 178 196 175 177 210 C4' A A 7 OK OK 212 229 209 211 243 C4' U A 8 OK OK 245 260 242 244 273 C4' C A 9 OK OK 275 290 272 274 304 C4' U A 10 OK OK 306 321 303 305 334 C4' G A 11 OK OK 336 354 333 335 368 C4' G A 12 OK OK 370 388 367 369 402 C4' C A 13 OK OK 404 419 401 403 433 C4' C A 14 OK OK 435 450 432 434 464 C4' U A 15 OK OK 466 481 463 465 494 C4' U A 16 OK OK 496 511 493 495 524 C4' C A 17 OK OK 526 541 523 525 555 C4' C A 18 OK OK 557 572 554 556 586 C4' C A 19 OK OK 588 603 585 587 617 C4' A A 20 OK OK 619 636 616 618 650 C4' C A 21 OK OK 652 667 649 651 681 C4' A A 22 OK OK 683 700 680 682 714 C4' A A 23 OK OK 716 733 713 715 747 C4' G A 24 OK OK 749 767 746 748 781 C4' G A 25 OK OK 783 801 780 782 815 C4' G A 26 OK OK 817 835 814 816 849 C4' A A 27 OK OK 851 868 848 850 882 C4' A A 28 OK OK 884 901 881 883 915 C4' G A 29 OK OK 917 935 914 916 949 C4' G A 30 OK OK 951 969 948 950 983 C4' C A 31 OK OK 985 1000 982 984 1014 C4' C A 32 OK OK 1016 1031 1013 1015 1045 C4' A A 33 OK OK 1047 1064 1044 1046 1078 C4' G A 34 OK OK 1080 1098 1077 1079 1112 C4' G A 35 OK OK 1114 1132 1111 1113 1146 C4' G A 36 OK OK 1148 1166 1145 1147 1180 C4' A A 37 OK OK 1182 1199 1179 1181 1213 C4' A A 38 OK OK 1215 1232 1212 1214 1246 C4' U A 39 OK OK 1248 1263 1245 1247 1276 C4' C A 40 OK OK 1278 1293 1275 1277 1307 C4' U A 41 OK OK 1309 1324 1306 1308 1337 C4' U A 42 OK OK 1339 1354 1336 1338 1367 C4' C A 43 OK OK 1369 1384 1366 1368 1398 C4' C A 44 OK OK 1400 1415 1397 1399 1429 C4' C A 45 OK OK 1431 1446 1428 1430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' G A 2 OK OK 40 60 61 42 75 C5' G A 3 OK OK 74 94 95 76 109 C5' A A 4 OK OK 108 127 128 110 142 C5' A A 5 OK OK 141 160 161 143 175 C5' G A 6 OK OK 174 194 195 176 209 C5' A A 7 OK OK 208 227 228 210 242 C5' U A 8 OK OK 241 258 259 243 272 C5' C A 9 OK OK 271 288 289 273 303 C5' U A 10 OK OK 302 319 320 304 333 C5' G A 11 OK OK 332 352 353 334 367 C5' G A 12 OK OK 366 386 387 368 401 C5' C A 13 OK OK 400 417 418 402 432 C5' C A 14 OK OK 431 448 449 433 463 C5' U A 15 OK OK 462 479 480 464 493 C5' U A 16 OK OK 492 509 510 494 523 C5' C A 17 OK OK 522 539 540 524 554 C5' C A 18 OK OK 553 570 571 555 585 C5' C A 19 OK OK 584 601 602 586 616 C5' A A 20 OK OK 615 634 635 617 649 C5' C A 21 OK OK 648 665 666 650 680 C5' A A 22 OK OK 679 698 699 681 713 C5' A A 23 OK OK 712 731 732 714 746 C5' G A 24 OK OK 745 765 766 747 780 C5' G A 25 OK OK 779 799 800 781 814 C5' G A 26 OK OK 813 833 834 815 848 C5' A A 27 OK OK 847 866 867 849 881 C5' A A 28 OK OK 880 899 900 882 914 C5' G A 29 OK OK 913 933 934 915 948 C5' G A 30 OK OK 947 967 968 949 982 C5' C A 31 OK OK 981 998 999 983 1013 C5' C A 32 OK OK 1012 1029 1030 1014 1044 C5' A A 33 OK OK 1043 1062 1063 1045 1077 C5' G A 34 OK OK 1076 1096 1097 1078 1111 C5' G A 35 OK OK 1110 1130 1131 1112 1145 C5' G A 36 OK OK 1144 1164 1165 1146 1179 C5' A A 37 OK OK 1178 1197 1198 1180 1212 C5' A A 38 OK OK 1211 1230 1231 1213 1245 C5' U A 39 OK OK 1244 1261 1262 1246 1275 C5' C A 40 OK OK 1274 1291 1292 1276 1306 C5' U A 41 OK OK 1305 1322 1323 1307 1336 C5' U A 42 OK OK 1335 1352 1353 1337 1366 C5' C A 43 OK OK 1365 1382 1383 1367 1397 C5' C A 44 OK OK 1396 1413 1414 1398 1428 C5' C A 45 OK OK 1427 1444 1445 1429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 OK OK 3 4 5 37 P G A 2 distorted distorted 10 38 39 40 71 P G A 3 distorted distorted 45 72 73 74 105 P A A 4 distorted distorted 79 106 107 108 138 P A A 5 distorted distorted 113 139 140 141 171 P G A 6 distorted distorted 146 172 173 174 205 P A A 7 distorted distorted 179 206 207 208 238 P U A 8 distorted distorted 213 239 240 241 268 P C A 9 distorted distorted 246 269 270 271 299 P U A 10 distorted distorted 276 300 301 302 329 P G A 11 distorted distorted 307 330 331 332 363 P G A 12 distorted distorted 337 364 365 366 397 P C A 13 distorted distorted 371 398 399 400 428 P C A 14 distorted distorted 405 429 430 431 459 P U A 15 distorted distorted 436 460 461 462 489 P U A 16 distorted distorted 467 490 491 492 519 P C A 17 distorted distorted 497 520 521 522 550 P C A 18 distorted distorted 527 551 552 553 581 P C A 19 distorted distorted 558 582 583 584 612 P A A 20 distorted distorted 589 613 614 615 645 P C A 21 distorted distorted 620 646 647 648 676 P A A 22 distorted distorted 653 677 678 679 709 P A A 23 distorted distorted 684 710 711 712 742 P G A 24 distorted distorted 717 743 744 745 776 P G A 25 distorted distorted 750 777 778 779 810 P G A 26 distorted distorted 784 811 812 813 844 P A A 27 distorted distorted 818 845 846 847 877 P A A 28 distorted distorted 852 878 879 880 910 P G A 29 distorted distorted 885 911 912 913 944 P G A 30 distorted distorted 918 945 946 947 978 P C A 31 distorted distorted 952 979 980 981 1009 P C A 32 distorted distorted 986 1010 1011 1012 1040 P A A 33 distorted distorted 1017 1041 1042 1043 1073 P G A 34 distorted distorted 1048 1074 1075 1076 1107 P G A 35 distorted distorted 1081 1108 1109 1110 1141 P G A 36 distorted distorted 1115 1142 1143 1144 1175 P A A 37 distorted distorted 1149 1176 1177 1178 1208 P A A 38 distorted distorted 1183 1209 1210 1211 1241 P U A 39 distorted distorted 1216 1242 1243 1244 1271 P C A 40 distorted distorted 1249 1272 1273 1274 1302 P U A 41 distorted distorted 1279 1303 1304 1305 1332 P U A 42 distorted distorted 1310 1333 1334 1335 1362 P C A 43 distorted distorted 1340 1363 1364 1365 1393 P C A 44 distorted distorted 1370 1394 1395 1396 1424 P C A 45 distorted distorted 1401 1425 1426 1427 ---------------------------------------------------------------------------------