ID code: '5KQE' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' U A 4 alpha beta 106 126 112 109 141 C1' G A 5 alpha beta 136 159 142 139 175 C1' U A 6 alpha beta 170 190 176 173 205 C1' A A 7 alpha beta 200 222 206 203 238 C1' C A 8 alpha beta 233 253 239 236 269 C1' U A 9 alpha beta 264 284 270 267 299 C1' U A 10 alpha beta 294 314 300 297 329 C1' A A 11 alpha beta 324 346 330 327 362 C1' A A 12 alpha beta 357 379 363 360 395 C1' C A 13 alpha beta 390 410 396 393 426 C1' G A 14 alpha beta 421 444 427 424 460 C1' U A 15 alpha beta 455 475 461 458 490 C1' U A 16 alpha beta 485 505 491 488 520 C1' U A 17 alpha beta 515 535 521 518 550 C1' G A 18 alpha beta 545 568 551 548 584 C1' C A 19 alpha beta 579 599 585 582 615 C1' U A 20 alpha beta 610 630 616 613 645 C1' U A 21 alpha beta 640 660 646 643 675 C1' C A 22 alpha beta 670 690 676 673 706 C1' G A 23 alpha beta 701 724 707 704 740 C1' G A 24 alpha beta 735 758 741 738 774 C1' C A 25 alpha beta 769 789 775 772 805 C1' A A 26 alpha beta 800 822 806 803 838 C1' A A 27 alpha beta 833 855 839 836 871 C1' A A 28 alpha beta 866 888 872 869 904 C1' C A 29 alpha beta 899 919 905 902 935 C1' U A 30 alpha beta 930 950 936 933 965 C1' A A 31 alpha beta 960 982 966 963 998 C1' C A 32 alpha beta 993 1013 999 996 1029 C1' A A 33 alpha beta 1024 1046 1030 1027 1062 C1' U A 34 alpha beta 1057 1077 1063 1060 1092 C1' C A 35 alpha beta 1087 1107 1093 1090 1123 C1' C A 36 alpha beta 1118 1139 1124 1121 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 41 C2' G A 2 OK OK 43 39 59 42 75 C2' G A 3 OK OK 77 73 93 76 109 C2' U A 4 OK OK 111 107 124 110 139 C2' G A 5 OK OK 141 137 157 140 173 C2' U A 6 OK OK 175 171 188 174 203 C2' A A 7 OK OK 205 201 220 204 236 C2' C A 8 OK OK 238 234 251 237 267 C2' U A 9 OK OK 269 265 282 268 297 C2' U A 10 OK OK 299 295 312 298 327 C2' A A 11 OK OK 329 325 344 328 360 C2' A A 12 OK OK 362 358 377 361 393 C2' C A 13 OK OK 395 391 408 394 424 C2' G A 14 OK OK 426 422 442 425 458 C2' U A 15 OK OK 460 456 473 459 488 C2' U A 16 OK OK 490 486 503 489 518 C2' U A 17 OK OK 520 516 533 519 548 C2' G A 18 OK OK 550 546 566 549 582 C2' C A 19 OK OK 584 580 597 583 613 C2' U A 20 OK OK 615 611 628 614 643 C2' U A 21 OK OK 645 641 658 644 673 C2' C A 22 OK OK 675 671 688 674 704 C2' G A 23 OK OK 706 702 722 705 738 C2' G A 24 OK OK 740 736 756 739 772 C2' C A 25 OK OK 774 770 787 773 803 C2' A A 26 OK OK 805 801 820 804 836 C2' A A 27 OK OK 838 834 853 837 869 C2' A A 28 OK OK 871 867 886 870 902 C2' C A 29 OK OK 904 900 917 903 933 C2' U A 30 OK OK 935 931 948 934 963 C2' A A 31 OK OK 965 961 980 964 996 C2' C A 32 OK OK 998 994 1011 997 1027 C2' A A 33 OK OK 1029 1025 1044 1028 1060 C2' U A 34 OK OK 1062 1058 1075 1061 1090 C2' C A 35 OK OK 1092 1088 1105 1091 1121 C2' C A 36 OK OK 1123 1119 1137 1122 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' G A 3 OK OK 71 92 74 75 107 C3' U A 4 OK OK 105 123 108 109 137 C3' G A 5 OK OK 135 156 138 139 171 C3' U A 6 OK OK 169 187 172 173 201 C3' A A 7 OK OK 199 219 202 203 234 C3' C A 8 OK OK 232 250 235 236 265 C3' U A 9 OK OK 263 281 266 267 295 C3' U A 10 OK OK 293 311 296 297 325 C3' A A 11 OK OK 323 343 326 327 358 C3' A A 12 OK OK 356 376 359 360 391 C3' C A 13 OK OK 389 407 392 393 422 C3' G A 14 OK OK 420 441 423 424 456 C3' U A 15 OK OK 454 472 457 458 486 C3' U A 16 OK OK 484 502 487 488 516 C3' U A 17 OK OK 514 532 517 518 546 C3' G A 18 OK OK 544 565 547 548 580 C3' C A 19 OK OK 578 596 581 582 611 C3' U A 20 OK OK 609 627 612 613 641 C3' U A 21 OK OK 639 657 642 643 671 C3' C A 22 OK OK 669 687 672 673 702 C3' G A 23 OK OK 700 721 703 704 736 C3' G A 24 OK OK 734 755 737 738 770 C3' C A 25 OK OK 768 786 771 772 801 C3' A A 26 OK OK 799 819 802 803 834 C3' A A 27 OK OK 832 852 835 836 867 C3' A A 28 OK OK 865 885 868 869 900 C3' C A 29 OK OK 898 916 901 902 931 C3' U A 30 OK OK 929 947 932 933 961 C3' A A 31 OK OK 959 979 962 963 994 C3' C A 32 OK OK 992 1010 995 996 1025 C3' A A 33 OK OK 1023 1043 1026 1027 1058 C3' U A 34 OK OK 1056 1074 1059 1060 1088 C3' C A 35 OK OK 1086 1104 1089 1090 1119 C3' C A 36 OK OK 1117 1135 1120 1121 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' G A 3 OK OK 73 91 70 72 105 C4' U A 4 OK OK 107 122 104 106 135 C4' G A 5 OK OK 137 155 134 136 169 C4' U A 6 OK OK 171 186 168 170 199 C4' A A 7 OK OK 201 218 198 200 232 C4' C A 8 OK OK 234 249 231 233 263 C4' U A 9 OK OK 265 280 262 264 293 C4' U A 10 OK OK 295 310 292 294 323 C4' A A 11 OK OK 325 342 322 324 356 C4' A A 12 OK OK 358 375 355 357 389 C4' C A 13 OK OK 391 406 388 390 420 C4' G A 14 OK OK 422 440 419 421 454 C4' U A 15 OK OK 456 471 453 455 484 C4' U A 16 OK OK 486 501 483 485 514 C4' U A 17 OK OK 516 531 513 515 544 C4' G A 18 OK OK 546 564 543 545 578 C4' C A 19 OK OK 580 595 577 579 609 C4' U A 20 OK OK 611 626 608 610 639 C4' U A 21 OK OK 641 656 638 640 669 C4' C A 22 OK OK 671 686 668 670 700 C4' G A 23 OK OK 702 720 699 701 734 C4' G A 24 OK OK 736 754 733 735 768 C4' C A 25 OK OK 770 785 767 769 799 C4' A A 26 OK OK 801 818 798 800 832 C4' A A 27 OK OK 834 851 831 833 865 C4' A A 28 OK OK 867 884 864 866 898 C4' C A 29 OK OK 900 915 897 899 929 C4' U A 30 OK OK 931 946 928 930 959 C4' A A 31 OK OK 961 978 958 960 992 C4' C A 32 OK OK 994 1009 991 993 1023 C4' A A 33 OK OK 1025 1042 1022 1024 1056 C4' U A 34 OK OK 1058 1073 1055 1057 1086 C4' C A 35 OK OK 1088 1103 1085 1087 1117 C4' C A 36 OK OK 1119 1134 1116 1118 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 36 C5' G A 2 OK OK 35 55 56 37 70 C5' G A 3 OK OK 69 89 90 71 104 C5' U A 4 OK OK 103 120 121 105 134 C5' G A 5 OK OK 133 153 154 135 168 C5' U A 6 OK OK 167 184 185 169 198 C5' A A 7 OK OK 197 216 217 199 231 C5' C A 8 OK OK 230 247 248 232 262 C5' U A 9 OK OK 261 278 279 263 292 C5' U A 10 OK OK 291 308 309 293 322 C5' A A 11 OK OK 321 340 341 323 355 C5' A A 12 OK OK 354 373 374 356 388 C5' C A 13 OK OK 387 404 405 389 419 C5' G A 14 OK OK 418 438 439 420 453 C5' U A 15 OK OK 452 469 470 454 483 C5' U A 16 OK OK 482 499 500 484 513 C5' U A 17 OK OK 512 529 530 514 543 C5' G A 18 OK OK 542 562 563 544 577 C5' C A 19 OK OK 576 593 594 578 608 C5' U A 20 OK OK 607 624 625 609 638 C5' U A 21 OK OK 637 654 655 639 668 C5' C A 22 OK OK 667 684 685 669 699 C5' G A 23 OK OK 698 718 719 700 733 C5' G A 24 OK OK 732 752 753 734 767 C5' C A 25 OK OK 766 783 784 768 798 C5' A A 26 OK OK 797 816 817 799 831 C5' A A 27 OK OK 830 849 850 832 864 C5' A A 28 OK OK 863 882 883 865 897 C5' C A 29 OK OK 896 913 914 898 928 C5' U A 30 OK OK 927 944 945 929 958 C5' A A 31 OK OK 957 976 977 959 991 C5' C A 32 OK OK 990 1007 1008 992 1022 C5' A A 33 OK OK 1021 1040 1041 1023 1055 C5' U A 34 OK OK 1054 1071 1072 1056 1085 C5' C A 35 OK OK 1084 1101 1102 1086 1116 C5' C A 36 OK OK 1115 1132 1133 1117 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P G A 3 distorted distorted 40 67 68 69 100 P U A 4 distorted distorted 74 101 102 103 130 P G A 5 distorted distorted 108 131 132 133 164 P U A 6 distorted distorted 138 165 166 167 194 P A A 7 distorted distorted 172 195 196 197 227 P C A 8 distorted distorted 202 228 229 230 258 P U A 9 distorted distorted 235 259 260 261 288 P U A 10 distorted distorted 266 289 290 291 318 P A A 11 distorted distorted 296 319 320 321 351 P A A 12 distorted distorted 326 352 353 354 384 P C A 13 distorted distorted 359 385 386 387 415 P G A 14 distorted distorted 392 416 417 418 449 P U A 15 distorted distorted 423 450 451 452 479 P U A 16 distorted distorted 457 480 481 482 509 P U A 17 distorted distorted 487 510 511 512 539 P G A 18 distorted distorted 517 540 541 542 573 P C A 19 distorted distorted 547 574 575 576 604 P U A 20 distorted distorted 581 605 606 607 634 P U A 21 distorted distorted 612 635 636 637 664 P C A 22 distorted distorted 642 665 666 667 695 P G A 23 distorted distorted 672 696 697 698 729 P G A 24 distorted distorted 703 730 731 732 763 P C A 25 distorted distorted 737 764 765 766 794 P A A 26 distorted distorted 771 795 796 797 827 P A A 27 distorted distorted 802 828 829 830 860 P A A 28 distorted distorted 835 861 862 863 893 P C A 29 distorted distorted 868 894 895 896 924 P U A 30 distorted distorted 901 925 926 927 954 P A A 31 distorted distorted 932 955 956 957 987 P C A 32 distorted distorted 962 988 989 990 1018 P A A 33 distorted distorted 995 1019 1020 1021 1051 P U A 34 distorted distorted 1026 1052 1053 1054 1081 P C A 35 distorted distorted 1059 1082 1083 1084 1112 P C A 36 distorted distorted 1089 1113 1114 1115 ---------------------------------------------------------------------------------