ID code: '5KRG' 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 46 C1' LCC A 3 beta 45 47 57 79 C1' LCG A 4 beta 82 70 76 99 C1' A A 5 beta 94 100 97 121 C1' C A 6 beta 116 122 119 141 C1' U A 7 beta 136 142 139 161 C1' U A 8 beta 156 162 159 181 C1' A A 9 beta 176 182 179 203 C1' A A 10 beta 198 204 201 225 C1' G A 11 beta 220 226 223 248 C1' U A 12 beta 243 249 246 268 C1' C A 13 beta 263 269 266 288 C1' G A 14 beta 283 289 286 311 C1' G A 15 beta 306 312 309 328 C1' LCC B 1 beta 327 329 339 347 C1' LCC B 2 beta 346 348 358 369 C1' LCC B 3 beta 368 370 380 402 C1' LCG B 4 beta 405 393 399 422 C1' A B 5 beta 417 423 420 444 C1' C B 6 beta 439 445 442 464 C1' U B 7 beta 459 465 462 484 C1' U B 8 beta 479 485 482 504 C1' A B 9 beta 499 505 502 526 C1' A B 10 beta 521 527 524 548 C1' G B 11 beta 543 549 546 571 C1' U B 12 beta 566 572 569 591 C1' C B 13 beta 586 592 589 611 C1' G B 14 beta 606 612 609 634 C1' G B 15 beta 629 635 632 651 C1' LCC C 1 beta 650 652 662 670 C1' LCC C 2 beta 669 671 681 692 C1' LCC C 3 beta 691 693 703 725 C1' LCG C 4 beta 728 716 722 745 C1' A C 5 beta 740 746 743 767 C1' C C 6 beta 762 768 765 787 C1' U C 7 beta 782 788 785 807 C1' U C 8 beta 802 808 805 827 C1' A C 9 beta 822 828 825 849 C1' A C 10 beta 844 850 847 871 C1' G C 11 beta 866 872 869 894 C1' U C 12 beta 889 895 892 914 C1' C C 13 beta 909 915 912 934 C1' G C 14 beta 929 935 932 957 C1' G C 15 beta 952 958 955 974 C1' LCC D 1 beta 973 975 985 993 C1' LCC D 2 beta 992 994 1004 1015 C1' LCC D 3 beta 1014 1016 1026 1048 C1' LCG D 4 beta 1051 1039 1045 1068 C1' A D 5 beta 1063 1069 1066 1090 C1' C D 6 beta 1085 1091 1088 1110 C1' U D 7 beta 1105 1111 1108 1130 C1' U D 8 beta 1125 1131 1128 1150 C1' A D 9 beta 1145 1151 1148 1172 C1' A D 10 beta 1167 1173 1170 1194 C1' G D 11 beta 1189 1195 1192 1217 C1' U D 12 beta 1212 1218 1215 1237 C1' C D 13 beta 1232 1238 1235 1257 C1' G D 14 beta 1252 1258 1255 1280 C1' G D 15 beta 1275 1281 1278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 57 C2' LCC A 3 OK 46 56 58 76 C2' LCG A 4 OK 79 68 86 97 C2' A A 5 OK 99 95 98 119 C2' C A 6 OK 121 117 120 139 C2' U A 7 OK 141 137 140 159 C2' U A 8 OK 161 157 160 179 C2' A A 9 OK 181 177 180 201 C2' A A 10 OK 203 199 202 223 C2' G A 11 OK 225 221 224 246 C2' U A 12 OK 248 244 247 266 C2' C A 13 OK 268 264 267 286 C2' G A 14 OK 288 284 287 309 C2' G A 15 OK 311 307 310 339 C2' LCC B 1 OK 328 338 340 358 C2' LCC B 2 OK 347 357 359 380 C2' LCC B 3 OK 369 379 381 399 C2' LCG B 4 OK 402 391 409 420 C2' A B 5 OK 422 418 421 442 C2' C B 6 OK 444 440 443 462 C2' U B 7 OK 464 460 463 482 C2' U B 8 OK 484 480 483 502 C2' A B 9 OK 504 500 503 524 C2' A B 10 OK 526 522 525 546 C2' G B 11 OK 548 544 547 569 C2' U B 12 OK 571 567 570 589 C2' C B 13 OK 591 587 590 609 C2' G B 14 OK 611 607 610 632 C2' G B 15 OK 634 630 633 662 C2' LCC C 1 OK 651 661 663 681 C2' LCC C 2 OK 670 680 682 703 C2' LCC C 3 OK 692 702 704 722 C2' LCG C 4 OK 725 714 732 743 C2' A C 5 OK 745 741 744 765 C2' C C 6 OK 767 763 766 785 C2' U C 7 OK 787 783 786 805 C2' U C 8 OK 807 803 806 825 C2' A C 9 OK 827 823 826 847 C2' A C 10 OK 849 845 848 869 C2' G C 11 OK 871 867 870 892 C2' U C 12 OK 894 890 893 912 C2' C C 13 OK 914 910 913 932 C2' G C 14 OK 934 930 933 955 C2' G C 15 OK 957 953 956 985 C2' LCC D 1 OK 974 984 986 1004 C2' LCC D 2 OK 993 1003 1005 1026 C2' LCC D 3 OK 1015 1025 1027 1045 C2' LCG D 4 OK 1048 1037 1055 1066 C2' A D 5 OK 1068 1064 1067 1088 C2' C D 6 OK 1090 1086 1089 1108 C2' U D 7 OK 1110 1106 1109 1128 C2' U D 8 OK 1130 1126 1129 1148 C2' A D 9 OK 1150 1146 1149 1170 C2' A D 10 OK 1172 1168 1171 1192 C2' G D 11 OK 1194 1190 1193 1215 C2' U D 12 OK 1217 1213 1216 1235 C2' C D 13 OK 1237 1233 1236 1255 C2' G D 14 OK 1257 1253 1256 1278 C2' G D 15 OK 1280 1276 1279 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 56 C3' LCC A 3 OK 44 59 57 68 C3' LCG A 4 OK 78 87 76 95 C3' A A 5 OK 93 96 97 117 C3' C A 6 OK 115 118 119 137 C3' U A 7 OK 135 138 139 157 C3' U A 8 OK 155 158 159 177 C3' A A 9 OK 175 178 179 199 C3' A A 10 OK 197 200 201 221 C3' G A 11 OK 219 222 223 244 C3' U A 12 OK 242 245 246 264 C3' C A 13 OK 262 265 266 284 C3' G A 14 OK 282 285 286 307 C3' G A 15 OK 305 308 309 338 C3' LCC B 1 OK 326 341 339 357 C3' LCC B 2 OK 345 360 358 379 C3' LCC B 3 OK 367 382 380 391 C3' LCG B 4 OK 401 410 399 418 C3' A B 5 OK 416 419 420 440 C3' C B 6 OK 438 441 442 460 C3' U B 7 OK 458 461 462 480 C3' U B 8 OK 478 481 482 500 C3' A B 9 OK 498 501 502 522 C3' A B 10 OK 520 523 524 544 C3' G B 11 OK 542 545 546 567 C3' U B 12 OK 565 568 569 587 C3' C B 13 OK 585 588 589 607 C3' G B 14 OK 605 608 609 630 C3' G B 15 OK 628 631 632 661 C3' LCC C 1 OK 649 664 662 680 C3' LCC C 2 OK 668 683 681 702 C3' LCC C 3 OK 690 705 703 714 C3' LCG C 4 OK 724 733 722 741 C3' A C 5 OK 739 742 743 763 C3' C C 6 OK 761 764 765 783 C3' U C 7 OK 781 784 785 803 C3' U C 8 OK 801 804 805 823 C3' A C 9 OK 821 824 825 845 C3' A C 10 OK 843 846 847 867 C3' G C 11 OK 865 868 869 890 C3' U C 12 OK 888 891 892 910 C3' C C 13 OK 908 911 912 930 C3' G C 14 OK 928 931 932 953 C3' G C 15 OK 951 954 955 984 C3' LCC D 1 OK 972 987 985 1003 C3' LCC D 2 OK 991 1006 1004 1025 C3' LCC D 3 OK 1013 1028 1026 1037 C3' LCG D 4 OK 1047 1056 1045 1064 C3' A D 5 OK 1062 1065 1066 1086 C3' C D 6 OK 1084 1087 1088 1106 C3' U D 7 OK 1104 1107 1108 1126 C3' U D 8 OK 1124 1127 1128 1146 C3' A D 9 OK 1144 1147 1148 1168 C3' A D 10 OK 1166 1169 1170 1190 C3' G D 11 OK 1188 1191 1192 1213 C3' U D 12 OK 1211 1214 1215 1233 C3' C D 13 OK 1231 1234 1235 1253 C3' G D 14 OK 1251 1254 1255 1276 C3' G D 15 OK 1274 1277 1278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 44 C4' LCC A 3 OK 56 43 45 78 C4' LCG A 4 OK 68 67 82 93 C4' A A 5 OK 95 92 94 115 C4' C A 6 OK 117 114 116 135 C4' U A 7 OK 137 134 136 155 C4' U A 8 OK 157 154 156 175 C4' A A 9 OK 177 174 176 197 C4' A A 10 OK 199 196 198 219 C4' G A 11 OK 221 218 220 242 C4' U A 12 OK 244 241 243 262 C4' C A 13 OK 264 261 263 282 C4' G A 14 OK 284 281 283 305 C4' G A 15 OK 307 304 306 326 C4' LCC B 1 OK 338 325 327 345 C4' LCC B 2 OK 357 344 346 367 C4' LCC B 3 OK 379 366 368 401 C4' LCG B 4 OK 391 390 405 416 C4' A B 5 OK 418 415 417 438 C4' C B 6 OK 440 437 439 458 C4' U B 7 OK 460 457 459 478 C4' U B 8 OK 480 477 479 498 C4' A B 9 OK 500 497 499 520 C4' A B 10 OK 522 519 521 542 C4' G B 11 OK 544 541 543 565 C4' U B 12 OK 567 564 566 585 C4' C B 13 OK 587 584 586 605 C4' G B 14 OK 607 604 606 628 C4' G B 15 OK 630 627 629 649 C4' LCC C 1 OK 661 648 650 668 C4' LCC C 2 OK 680 667 669 690 C4' LCC C 3 OK 702 689 691 724 C4' LCG C 4 OK 714 713 728 739 C4' A C 5 OK 741 738 740 761 C4' C C 6 OK 763 760 762 781 C4' U C 7 OK 783 780 782 801 C4' U C 8 OK 803 800 802 821 C4' A C 9 OK 823 820 822 843 C4' A C 10 OK 845 842 844 865 C4' G C 11 OK 867 864 866 888 C4' U C 12 OK 890 887 889 908 C4' C C 13 OK 910 907 909 928 C4' G C 14 OK 930 927 929 951 C4' G C 15 OK 953 950 952 972 C4' LCC D 1 OK 984 971 973 991 C4' LCC D 2 OK 1003 990 992 1013 C4' LCC D 3 OK 1025 1012 1014 1047 C4' LCG D 4 OK 1037 1036 1051 1062 C4' A D 5 OK 1064 1061 1063 1084 C4' C D 6 OK 1086 1083 1085 1104 C4' U D 7 OK 1106 1103 1105 1124 C4' U D 8 OK 1126 1123 1125 1144 C4' A D 9 OK 1146 1143 1145 1166 C4' A D 10 OK 1168 1165 1167 1188 C4' G D 11 OK 1190 1187 1189 1211 C4' U D 12 OK 1213 1210 1212 1231 C4' C D 13 OK 1233 1230 1232 1251 C4' G D 14 OK 1253 1250 1252 1274 C4' G D 15 OK 1276 1273 1275 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 43 C5' LCC A 3 42 44 67 C5' LCG A 4 66 78 92 C5' A A 5 91 93 114 C5' C A 6 113 115 134 C5' U A 7 133 135 154 C5' U A 8 153 155 174 C5' A A 9 173 175 196 C5' A A 10 195 197 218 C5' G A 11 217 219 241 C5' U A 12 240 242 261 C5' C A 13 260 262 281 C5' G A 14 280 282 304 C5' G A 15 303 305 325 C5' LCC B 1 324 326 344 C5' LCC B 2 343 345 366 C5' LCC B 3 365 367 390 C5' LCG B 4 389 401 415 C5' A B 5 414 416 437 C5' C B 6 436 438 457 C5' U B 7 456 458 477 C5' U B 8 476 478 497 C5' A B 9 496 498 519 C5' A B 10 518 520 541 C5' G B 11 540 542 564 C5' U B 12 563 565 584 C5' C B 13 583 585 604 C5' G B 14 603 605 627 C5' G B 15 626 628 648 C5' LCC C 1 647 649 667 C5' LCC C 2 666 668 689 C5' LCC C 3 688 690 713 C5' LCG C 4 712 724 738 C5' A C 5 737 739 760 C5' C C 6 759 761 780 C5' U C 7 779 781 800 C5' U C 8 799 801 820 C5' A C 9 819 821 842 C5' A C 10 841 843 864 C5' G C 11 863 865 887 C5' U C 12 886 888 907 C5' C C 13 906 908 927 C5' G C 14 926 928 950 C5' G C 15 949 951 971 C5' LCC D 1 970 972 990 C5' LCC D 2 989 991 1012 C5' LCC D 3 1011 1013 1036 C5' LCG D 4 1035 1047 1061 C5' A D 5 1060 1062 1083 C5' C D 6 1082 1084 1103 C5' U D 7 1102 1104 1123 C5' U D 8 1122 1124 1143 C5' A D 9 1142 1144 1165 C5' A D 10 1164 1166 1187 C5' G D 11 1186 1188 1210 C5' U D 12 1209 1211 1230 C5' C D 13 1229 1231 1250 C5' G D 14 1249 1251 1273 C5' G D 15 1272 1274 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 39 P LCC A 2 distorted distorted 18 40 41 20 61 P LCC A 3 distorted distorted 37 62 63 42 64 P LCG A 4 distorted distorted 59 65 83 66 88 P A A 5 distorted distorted 87 89 90 91 110 P C A 6 distorted distorted 96 111 112 113 130 P U A 7 distorted distorted 118 131 132 133 150 P U A 8 distorted distorted 138 151 152 153 170 P A A 9 distorted distorted 158 171 172 173 192 P A A 10 distorted distorted 178 193 194 195 214 P G A 11 distorted distorted 200 215 216 217 237 P U A 12 distorted distorted 222 238 239 240 257 P C A 13 distorted distorted 245 258 259 260 277 P G A 14 distorted distorted 265 278 279 280 300 P G A 15 distorted distorted 285 301 302 303 362 P LCC B 2 OK OK 341 363 364 343 384 P LCC B 3 OK OK 360 385 386 365 387 P LCG B 4 distorted distorted 382 388 406 389 411 P A B 5 distorted distorted 410 412 413 414 433 P C B 6 distorted distorted 419 434 435 436 453 P U B 7 distorted distorted 441 454 455 456 473 P U B 8 distorted distorted 461 474 475 476 493 P A B 9 distorted distorted 481 494 495 496 515 P A B 10 distorted distorted 501 516 517 518 537 P G B 11 distorted distorted 523 538 539 540 560 P U B 12 distorted distorted 545 561 562 563 580 P C B 13 distorted distorted 568 581 582 583 600 P G B 14 distorted distorted 588 601 602 603 623 P G B 15 distorted distorted 608 624 625 626 685 P LCC C 2 OK OK 664 686 687 666 707 P LCC C 3 OK OK 683 708 709 688 710 P LCG C 4 distorted distorted 705 711 729 712 734 P A C 5 distorted distorted 733 735 736 737 756 P C C 6 distorted distorted 742 757 758 759 776 P U C 7 distorted distorted 764 777 778 779 796 P U C 8 distorted distorted 784 797 798 799 816 P A C 9 distorted distorted 804 817 818 819 838 P A C 10 distorted distorted 824 839 840 841 860 P G C 11 distorted distorted 846 861 862 863 883 P U C 12 distorted distorted 868 884 885 886 903 P C C 13 distorted distorted 891 904 905 906 923 P G C 14 distorted distorted 911 924 925 926 946 P G C 15 distorted distorted 931 947 948 949 1008 P LCC D 2 distorted distorted 987 1009 1010 989 1030 P LCC D 3 distorted distorted 1006 1031 1032 1011 1033 P LCG D 4 distorted distorted 1028 1034 1052 1035 1057 P A D 5 distorted distorted 1056 1058 1059 1060 1079 P C D 6 distorted distorted 1065 1080 1081 1082 1099 P U D 7 distorted distorted 1087 1100 1101 1102 1119 P U D 8 distorted distorted 1107 1120 1121 1122 1139 P A D 9 distorted distorted 1127 1140 1141 1142 1161 P A D 10 distorted distorted 1147 1162 1163 1164 1183 P G D 11 distorted distorted 1169 1184 1185 1186 1206 P U D 12 distorted distorted 1191 1207 1208 1209 1226 P C D 13 distorted distorted 1214 1227 1228 1229 1246 P G D 14 distorted distorted 1234 1247 1248 1249 1269 P G D 15 distorted distorted 1254 1270 1271 1272 ---------------------------------------------------------------------------------