ID code: '5DHC' 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' --------------------------------------------------------------------------------- 5 C1' LCC A 1 beta 4 6 16 24 C1' LCC A 2 beta 23 25 35 57 C1' LCA A 3 beta 60 48 54 80 C1' LCG A 4 beta 83 71 77 100 C1' A A 5 beta 95 101 98 122 C1' C A 6 beta 117 123 120 142 C1' U A 7 beta 137 143 140 162 C1' U A 8 beta 157 163 160 182 C1' A A 9 beta 177 183 180 204 C1' A A 10 beta 199 205 202 226 C1' G A 11 beta 221 227 224 249 C1' U A 12 beta 244 250 247 269 C1' C A 13 beta 264 270 267 289 C1' U A 14 beta 284 290 287 303 C1' LCC B 1 beta 302 304 314 322 C1' LCC B 2 beta 321 323 333 355 C1' LCA B 3 beta 358 346 352 378 C1' LCG B 4 beta 381 369 375 398 C1' A B 5 beta 393 399 396 420 C1' C B 6 beta 415 421 418 440 C1' U B 7 beta 435 441 438 460 C1' U B 8 beta 455 461 458 480 C1' A B 9 beta 475 481 478 502 C1' A B 10 beta 497 503 500 524 C1' G B 11 beta 519 525 522 547 C1' U B 12 beta 542 548 545 567 C1' C B 13 beta 562 568 565 587 C1' U B 14 beta 582 588 585 601 C1' LCC C 1 beta 600 602 612 620 C1' LCC C 2 beta 619 621 631 653 C1' LCA C 3 beta 656 644 650 676 C1' LCG C 4 beta 679 667 673 696 C1' A C 5 beta 691 697 694 718 C1' C C 6 beta 713 719 716 738 C1' U C 7 beta 733 739 736 758 C1' U C 8 beta 753 759 756 778 C1' A C 9 beta 773 779 776 800 C1' A C 10 beta 795 801 798 822 C1' G C 11 beta 817 823 820 845 C1' U C 12 beta 840 846 843 865 C1' C C 13 beta 860 866 863 885 C1' U C 14 beta 880 886 883 899 C1' LCC D 1 beta 898 900 910 918 C1' LCC D 2 beta 917 919 929 951 C1' LCA D 3 beta 954 942 948 974 C1' LCG D 4 beta 977 965 971 994 C1' A D 5 beta 989 995 992 1016 C1' C D 6 beta 1011 1017 1014 1036 C1' U D 7 beta 1031 1037 1034 1056 C1' U D 8 beta 1051 1057 1054 1076 C1' A D 9 beta 1071 1077 1074 1098 C1' A D 10 beta 1093 1099 1096 1120 C1' G D 11 beta 1115 1121 1118 1143 C1' U D 12 beta 1138 1144 1141 1163 C1' C D 13 beta 1158 1164 1161 1183 C1' U D 14 beta 1178 1184 1181 1208 C1' 5GP A 104 beta 1203 1209 1206 1232 C1' 5GP A 105 beta 1227 1233 1230 1260 C1' 5GP B 105 beta 1255 1261 1258 1284 C1' 5GP B 106 beta 1279 1285 1282 1312 C1' 5GP C 105 beta 1307 1313 1310 1336 C1' 5GP C 106 beta 1331 1337 1334 1364 C1' 5GP D 105 beta 1359 1365 1362 1388 C1' 5GP D 106 beta 1383 1389 1386 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 16 C2' LCC A 1 OK 5 15 17 35 C2' LCC A 2 OK 24 34 36 54 C2' LCA A 3 OK 57 46 64 77 C2' LCG A 4 OK 80 69 87 98 C2' A A 5 OK 100 96 99 120 C2' C A 6 OK 122 118 121 140 C2' U A 7 OK 142 138 141 160 C2' U A 8 OK 162 158 161 180 C2' A A 9 OK 182 178 181 202 C2' A A 10 OK 204 200 203 224 C2' G A 11 OK 226 222 225 247 C2' U A 12 OK 249 245 248 267 C2' C A 13 OK 269 265 268 287 C2' U A 14 OK 289 285 288 314 C2' LCC B 1 OK 303 313 315 333 C2' LCC B 2 OK 322 332 334 352 C2' LCA B 3 OK 355 344 362 375 C2' LCG B 4 OK 378 367 385 396 C2' A B 5 OK 398 394 397 418 C2' C B 6 OK 420 416 419 438 C2' U B 7 OK 440 436 439 458 C2' U B 8 OK 460 456 459 478 C2' A B 9 OK 480 476 479 500 C2' A B 10 OK 502 498 501 522 C2' G B 11 OK 524 520 523 545 C2' U B 12 OK 547 543 546 565 C2' C B 13 OK 567 563 566 585 C2' U B 14 OK 587 583 586 612 C2' LCC C 1 OK 601 611 613 631 C2' LCC C 2 OK 620 630 632 650 C2' LCA C 3 OK 653 642 660 673 C2' LCG C 4 OK 676 665 683 694 C2' A C 5 OK 696 692 695 716 C2' C C 6 OK 718 714 717 736 C2' U C 7 OK 738 734 737 756 C2' U C 8 OK 758 754 757 776 C2' A C 9 OK 778 774 777 798 C2' A C 10 OK 800 796 799 820 C2' G C 11 OK 822 818 821 843 C2' U C 12 OK 845 841 844 863 C2' C C 13 OK 865 861 864 883 C2' U C 14 OK 885 881 884 910 C2' LCC D 1 OK 899 909 911 929 C2' LCC D 2 OK 918 928 930 948 C2' LCA D 3 OK 951 940 958 971 C2' LCG D 4 OK 974 963 981 992 C2' A D 5 OK 994 990 993 1014 C2' C D 6 OK 1016 1012 1015 1034 C2' U D 7 OK 1036 1032 1035 1054 C2' U D 8 OK 1056 1052 1055 1074 C2' A D 9 OK 1076 1072 1075 1096 C2' A D 10 OK 1098 1094 1097 1118 C2' G D 11 OK 1120 1116 1119 1141 C2' U D 12 OK 1143 1139 1142 1161 C2' C D 13 OK 1163 1159 1162 1181 C2' U D 14 OK 1183 1179 1182 1206 C2' 5GP A 104 OK 1208 1204 1207 1230 C2' 5GP A 105 OK 1232 1228 1231 1258 C2' 5GP B 105 OK 1260 1256 1259 1282 C2' 5GP B 106 OK 1284 1280 1283 1310 C2' 5GP C 105 OK 1312 1308 1311 1334 C2' 5GP C 106 OK 1336 1332 1335 1362 C2' 5GP D 105 OK 1364 1360 1363 1386 C2' 5GP D 106 OK 1388 1384 1387 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 15 C3' LCC A 1 OK 3 18 16 34 C3' LCC A 2 OK 22 37 35 46 C3' LCA A 3 OK 56 63 54 69 C3' LCG A 4 OK 79 88 77 96 C3' A A 5 OK 94 97 98 118 C3' C A 6 OK 116 119 120 138 C3' U A 7 OK 136 139 140 158 C3' U A 8 OK 156 159 160 178 C3' A A 9 OK 176 179 180 200 C3' A A 10 OK 198 201 202 222 C3' G A 11 OK 220 223 224 245 C3' U A 12 OK 243 246 247 265 C3' C A 13 OK 263 266 267 285 C3' U A 14 OK 283 286 287 313 C3' LCC B 1 OK 301 316 314 332 C3' LCC B 2 OK 320 335 333 344 C3' LCA B 3 OK 354 361 352 367 C3' LCG B 4 OK 377 386 375 394 C3' A B 5 OK 392 395 396 416 C3' C B 6 OK 414 417 418 436 C3' U B 7 OK 434 437 438 456 C3' U B 8 OK 454 457 458 476 C3' A B 9 OK 474 477 478 498 C3' A B 10 OK 496 499 500 520 C3' G B 11 OK 518 521 522 543 C3' U B 12 OK 541 544 545 563 C3' C B 13 OK 561 564 565 583 C3' U B 14 OK 581 584 585 611 C3' LCC C 1 OK 599 614 612 630 C3' LCC C 2 OK 618 633 631 642 C3' LCA C 3 OK 652 659 650 665 C3' LCG C 4 OK 675 684 673 692 C3' A C 5 OK 690 693 694 714 C3' C C 6 OK 712 715 716 734 C3' U C 7 OK 732 735 736 754 C3' U C 8 OK 752 755 756 774 C3' A C 9 OK 772 775 776 796 C3' A C 10 OK 794 797 798 818 C3' G C 11 OK 816 819 820 841 C3' U C 12 OK 839 842 843 861 C3' C C 13 OK 859 862 863 881 C3' U C 14 OK 879 882 883 909 C3' LCC D 1 OK 897 912 910 928 C3' LCC D 2 OK 916 931 929 940 C3' LCA D 3 OK 950 957 948 963 C3' LCG D 4 OK 973 982 971 990 C3' A D 5 OK 988 991 992 1012 C3' C D 6 OK 1010 1013 1014 1032 C3' U D 7 OK 1030 1033 1034 1052 C3' U D 8 OK 1050 1053 1054 1072 C3' A D 9 OK 1070 1073 1074 1094 C3' A D 10 OK 1092 1095 1096 1116 C3' G D 11 OK 1114 1117 1118 1139 C3' U D 12 OK 1137 1140 1141 1159 C3' C D 13 OK 1157 1160 1161 1179 C3' U D 14 OK 1177 1180 1181 1204 C3' 5GP A 104 OK 1202 1205 1206 1228 C3' 5GP A 105 OK 1226 1229 1230 1256 C3' 5GP B 105 OK 1254 1257 1258 1280 C3' 5GP B 106 OK 1278 1281 1282 1308 C3' 5GP C 105 OK 1306 1309 1310 1332 C3' 5GP C 106 OK 1330 1333 1334 1360 C3' 5GP D 105 OK 1358 1361 1362 1384 C3' 5GP D 106 OK 1382 1385 1386 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' LCC A 1 OK 15 2 4 22 C4' LCC A 2 OK 34 21 23 56 C4' LCA A 3 OK 46 45 60 79 C4' LCG A 4 OK 69 68 83 94 C4' A A 5 OK 96 93 95 116 C4' C A 6 OK 118 115 117 136 C4' U A 7 OK 138 135 137 156 C4' U A 8 OK 158 155 157 176 C4' A A 9 OK 178 175 177 198 C4' A A 10 OK 200 197 199 220 C4' G A 11 OK 222 219 221 243 C4' U A 12 OK 245 242 244 263 C4' C A 13 OK 265 262 264 283 C4' U A 14 OK 285 282 284 301 C4' LCC B 1 OK 313 300 302 320 C4' LCC B 2 OK 332 319 321 354 C4' LCA B 3 OK 344 343 358 377 C4' LCG B 4 OK 367 366 381 392 C4' A B 5 OK 394 391 393 414 C4' C B 6 OK 416 413 415 434 C4' U B 7 OK 436 433 435 454 C4' U B 8 OK 456 453 455 474 C4' A B 9 OK 476 473 475 496 C4' A B 10 OK 498 495 497 518 C4' G B 11 OK 520 517 519 541 C4' U B 12 OK 543 540 542 561 C4' C B 13 OK 563 560 562 581 C4' U B 14 OK 583 580 582 599 C4' LCC C 1 OK 611 598 600 618 C4' LCC C 2 OK 630 617 619 652 C4' LCA C 3 OK 642 641 656 675 C4' LCG C 4 OK 665 664 679 690 C4' A C 5 OK 692 689 691 712 C4' C C 6 OK 714 711 713 732 C4' U C 7 OK 734 731 733 752 C4' U C 8 OK 754 751 753 772 C4' A C 9 OK 774 771 773 794 C4' A C 10 OK 796 793 795 816 C4' G C 11 OK 818 815 817 839 C4' U C 12 OK 841 838 840 859 C4' C C 13 OK 861 858 860 879 C4' U C 14 OK 881 878 880 897 C4' LCC D 1 OK 909 896 898 916 C4' LCC D 2 OK 928 915 917 950 C4' LCA D 3 OK 940 939 954 973 C4' LCG D 4 OK 963 962 977 988 C4' A D 5 OK 990 987 989 1010 C4' C D 6 OK 1012 1009 1011 1030 C4' U D 7 OK 1032 1029 1031 1050 C4' U D 8 OK 1052 1049 1051 1070 C4' A D 9 OK 1072 1069 1071 1092 C4' A D 10 OK 1094 1091 1093 1114 C4' G D 11 OK 1116 1113 1115 1137 C4' U D 12 OK 1139 1136 1138 1157 C4' C D 13 OK 1159 1156 1158 1177 C4' U D 14 OK 1179 1176 1178 1202 C4' 5GP A 104 OK 1204 1201 1203 1226 C4' 5GP A 105 OK 1228 1225 1227 1254 C4' 5GP B 105 OK 1256 1253 1255 1278 C4' 5GP B 106 OK 1280 1277 1279 1306 C4' 5GP C 105 OK 1308 1305 1307 1330 C4' 5GP C 106 OK 1332 1329 1331 1358 C4' 5GP D 105 OK 1360 1357 1359 1382 C4' 5GP D 106 OK 1384 1381 1383 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' LCC A 1 1 3 21 C5' LCC A 2 20 22 45 C5' LCA A 3 44 56 68 C5' LCG A 4 67 79 93 C5' A A 5 92 94 115 C5' C A 6 114 116 135 C5' U A 7 134 136 155 C5' U A 8 154 156 175 C5' A A 9 174 176 197 C5' A A 10 196 198 219 C5' G A 11 218 220 242 C5' U A 12 241 243 262 C5' C A 13 261 263 282 C5' U A 14 281 283 300 C5' LCC B 1 299 301 319 C5' LCC B 2 318 320 343 C5' LCA B 3 342 354 366 C5' LCG B 4 365 377 391 C5' A B 5 390 392 413 C5' C B 6 412 414 433 C5' U B 7 432 434 453 C5' U B 8 452 454 473 C5' A B 9 472 474 495 C5' A B 10 494 496 517 C5' G B 11 516 518 540 C5' U B 12 539 541 560 C5' C B 13 559 561 580 C5' U B 14 579 581 598 C5' LCC C 1 597 599 617 C5' LCC C 2 616 618 641 C5' LCA C 3 640 652 664 C5' LCG C 4 663 675 689 C5' A C 5 688 690 711 C5' C C 6 710 712 731 C5' U C 7 730 732 751 C5' U C 8 750 752 771 C5' A C 9 770 772 793 C5' A C 10 792 794 815 C5' G C 11 814 816 838 C5' U C 12 837 839 858 C5' C C 13 857 859 878 C5' U C 14 877 879 896 C5' LCC D 1 895 897 915 C5' LCC D 2 914 916 939 C5' LCA D 3 938 950 962 C5' LCG D 4 961 973 987 C5' A D 5 986 988 1009 C5' C D 6 1008 1010 1029 C5' U D 7 1028 1030 1049 C5' U D 8 1048 1050 1069 C5' A D 9 1068 1070 1091 C5' A D 10 1090 1092 1113 C5' G D 11 1112 1114 1136 C5' U D 12 1135 1137 1156 C5' C D 13 1155 1157 1176 C5' U D 14 1175 1177 1201 C5' 5GP A 104 1200 1202 1225 C5' 5GP A 105 1224 1226 1253 C5' 5GP B 105 1252 1254 1277 C5' 5GP B 106 1276 1278 1305 C5' 5GP C 105 1304 1306 1329 C5' 5GP C 106 1328 1330 1357 C5' 5GP D 105 1356 1358 1381 C5' 5GP D 106 1380 1382 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 39 P LCC A 2 OK OK 18 40 41 20 42 P LCA A 3 OK OK 37 43 61 44 65 P LCG A 4 distorted distorted 63 66 84 67 89 P A A 5 distorted distorted 88 90 91 92 111 P C A 6 distorted distorted 97 112 113 114 131 P U A 7 distorted distorted 119 132 133 134 151 P U A 8 distorted distorted 139 152 153 154 171 P A A 9 distorted distorted 159 172 173 174 193 P A A 10 distorted distorted 179 194 195 196 215 P G A 11 distorted distorted 201 216 217 218 238 P U A 12 distorted distorted 223 239 240 241 258 P C A 13 distorted distorted 246 259 260 261 278 P U A 14 distorted distorted 266 279 280 281 337 P LCC B 2 distorted distorted 316 338 339 318 340 P LCA B 3 distorted distorted 335 341 359 342 363 P LCG B 4 distorted distorted 361 364 382 365 387 P A B 5 distorted distorted 386 388 389 390 409 P C B 6 distorted distorted 395 410 411 412 429 P U B 7 distorted distorted 417 430 431 432 449 P U B 8 distorted distorted 437 450 451 452 469 P A B 9 distorted distorted 457 470 471 472 491 P A B 10 distorted distorted 477 492 493 494 513 P G B 11 distorted distorted 499 514 515 516 536 P U B 12 distorted distorted 521 537 538 539 556 P C B 13 distorted distorted 544 557 558 559 576 P U B 14 distorted distorted 564 577 578 579 635 P LCC C 2 distorted distorted 614 636 637 616 638 P LCA C 3 distorted distorted 633 639 657 640 661 P LCG C 4 distorted distorted 659 662 680 663 685 P A C 5 distorted distorted 684 686 687 688 707 P C C 6 distorted distorted 693 708 709 710 727 P U C 7 distorted distorted 715 728 729 730 747 P U C 8 distorted distorted 735 748 749 750 767 P A C 9 distorted distorted 755 768 769 770 789 P A C 10 distorted distorted 775 790 791 792 811 P G C 11 distorted distorted 797 812 813 814 834 P U C 12 distorted distorted 819 835 836 837 854 P C C 13 distorted distorted 842 855 856 857 874 P U C 14 distorted distorted 862 875 876 877 933 P LCC D 2 OK OK 912 934 935 914 936 P LCA D 3 OK OK 931 937 955 938 959 P LCG D 4 distorted distorted 957 960 978 961 983 P A D 5 distorted distorted 982 984 985 986 1005 P C D 6 distorted distorted 991 1006 1007 1008 1025 P U D 7 distorted distorted 1013 1026 1027 1028 1045 P U D 8 distorted distorted 1033 1046 1047 1048 1065 P A D 9 distorted distorted 1053 1066 1067 1068 1087 P A D 10 distorted distorted 1073 1088 1089 1090 1109 P G D 11 distorted distorted 1095 1110 1111 1112 1132 P U D 12 distorted distorted 1117 1133 1134 1135 1152 P C D 13 distorted distorted 1140 1153 1154 1155 1172 P U D 14 distorted distorted 1160 1173 1174 1175 1196 P 5GP A 104 distorted distorted 1197 1198 1200 1220 P 5GP A 105 OK OK 1221 1222 1224 1248 P 5GP B 105 distorted distorted 1249 1250 1252 1272 P 5GP B 106 distorted distorted 1273 1274 1276 1300 P 5GP C 105 OK OK 1301 1302 1304 1324 P 5GP C 106 distorted distorted 1325 1326 1328 1352 P 5GP D 105 OK OK 1353 1354 1356 1376 P 5GP D 106 distorted distorted 1377 1378 1380 ---------------------------------------------------------------------------------