ID code: '2LA5' 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 44 C1' C A 2 alpha beta 39 59 45 42 75 C1' U A 3 alpha beta 70 90 76 73 105 C1' G A 4 alpha beta 100 123 106 103 139 C1' C A 5 alpha beta 134 154 140 137 170 C1' G A 6 alpha beta 165 188 171 168 204 C1' G A 7 alpha beta 199 222 205 202 238 C1' U A 8 alpha beta 233 253 239 236 268 C1' G A 9 alpha beta 263 286 269 266 302 C1' U A 10 alpha beta 297 317 303 300 332 C1' G A 11 alpha beta 327 350 333 330 366 C1' G A 12 alpha beta 361 384 367 364 400 C1' A A 13 alpha beta 395 417 401 398 433 C1' A A 14 alpha beta 428 450 434 431 466 C1' G A 15 alpha beta 461 484 467 464 500 C1' G A 16 alpha beta 495 518 501 498 534 C1' A A 17 alpha beta 529 551 535 532 567 C1' G A 18 alpha beta 562 585 568 565 601 C1' U A 19 alpha beta 596 616 602 599 631 C1' G A 20 alpha beta 626 649 632 629 665 C1' G A 21 alpha beta 660 683 666 663 699 C1' C A 22 alpha beta 694 714 700 697 730 C1' U A 23 alpha beta 725 745 731 728 760 C1' G A 24 alpha beta 755 778 761 758 794 C1' G A 25 alpha beta 789 812 795 792 828 C1' G A 26 alpha beta 823 846 829 826 862 C1' U A 27 alpha beta 857 877 863 860 892 C1' U A 28 alpha beta 887 907 893 890 922 C1' G A 29 alpha beta 917 940 923 920 956 C1' C A 30 alpha beta 951 971 957 954 987 C1' G A 31 alpha beta 982 1005 988 985 1021 C1' C A 32 alpha beta 1016 1036 1022 1019 1052 C1' A A 33 alpha beta 1047 1069 1053 1050 1085 C1' G A 34 alpha beta 1080 1103 1086 1083 1119 C1' C A 35 alpha beta 1114 1134 1120 1117 1150 C1' G A 36 alpha beta 1145 1169 1151 1148 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 42 C2' C A 2 OK OK 44 40 57 43 73 C2' U A 3 OK OK 75 71 88 74 103 C2' G A 4 OK OK 105 101 121 104 137 C2' C A 5 OK OK 139 135 152 138 168 C2' G A 6 OK OK 170 166 186 169 202 C2' G A 7 OK OK 204 200 220 203 236 C2' U A 8 OK OK 238 234 251 237 266 C2' G A 9 OK OK 268 264 284 267 300 C2' U A 10 OK OK 302 298 315 301 330 C2' G A 11 OK OK 332 328 348 331 364 C2' G A 12 OK OK 366 362 382 365 398 C2' A A 13 OK OK 400 396 415 399 431 C2' A A 14 OK OK 433 429 448 432 464 C2' G A 15 OK OK 466 462 482 465 498 C2' G A 16 OK OK 500 496 516 499 532 C2' A A 17 OK OK 534 530 549 533 565 C2' G A 18 OK OK 567 563 583 566 599 C2' U A 19 OK OK 601 597 614 600 629 C2' G A 20 OK OK 631 627 647 630 663 C2' G A 21 OK OK 665 661 681 664 697 C2' C A 22 OK OK 699 695 712 698 728 C2' U A 23 OK OK 730 726 743 729 758 C2' G A 24 OK OK 760 756 776 759 792 C2' G A 25 OK OK 794 790 810 793 826 C2' G A 26 OK OK 828 824 844 827 860 C2' U A 27 OK OK 862 858 875 861 890 C2' U A 28 OK OK 892 888 905 891 920 C2' G A 29 OK OK 922 918 938 921 954 C2' C A 30 OK OK 956 952 969 955 985 C2' G A 31 OK OK 987 983 1003 986 1019 C2' C A 32 OK OK 1021 1017 1034 1020 1050 C2' A A 33 OK OK 1052 1048 1067 1051 1083 C2' G A 34 OK OK 1085 1081 1101 1084 1117 C2' C A 35 OK OK 1119 1115 1132 1118 1148 C2' G A 36 OK OK 1150 1146 1167 1149 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' U A 3 OK OK 69 87 72 73 101 C3' G A 4 OK OK 99 120 102 103 135 C3' C A 5 OK OK 133 151 136 137 166 C3' G A 6 OK OK 164 185 167 168 200 C3' G A 7 OK OK 198 219 201 202 234 C3' U A 8 OK OK 232 250 235 236 264 C3' G A 9 OK OK 262 283 265 266 298 C3' U A 10 OK OK 296 314 299 300 328 C3' G A 11 OK OK 326 347 329 330 362 C3' G A 12 OK OK 360 381 363 364 396 C3' A A 13 OK OK 394 414 397 398 429 C3' A A 14 OK OK 427 447 430 431 462 C3' G A 15 OK OK 460 481 463 464 496 C3' G A 16 OK OK 494 515 497 498 530 C3' A A 17 OK OK 528 548 531 532 563 C3' G A 18 OK OK 561 582 564 565 597 C3' U A 19 OK OK 595 613 598 599 627 C3' G A 20 OK OK 625 646 628 629 661 C3' G A 21 OK OK 659 680 662 663 695 C3' C A 22 OK OK 693 711 696 697 726 C3' U A 23 OK OK 724 742 727 728 756 C3' G A 24 OK OK 754 775 757 758 790 C3' G A 25 OK OK 788 809 791 792 824 C3' G A 26 OK OK 822 843 825 826 858 C3' U A 27 OK OK 856 874 859 860 888 C3' U A 28 OK OK 886 904 889 890 918 C3' G A 29 OK OK 916 937 919 920 952 C3' C A 30 OK OK 950 968 953 954 983 C3' G A 31 OK OK 981 1002 984 985 1017 C3' C A 32 OK OK 1015 1033 1018 1019 1048 C3' A A 33 OK OK 1046 1066 1049 1050 1081 C3' G A 34 OK OK 1079 1100 1082 1083 1115 C3' C A 35 OK OK 1113 1131 1116 1117 1146 C3' G A 36 OK OK 1144 1165 1147 1148 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' U A 3 OK OK 71 86 68 70 99 C4' G A 4 OK OK 101 119 98 100 133 C4' C A 5 OK OK 135 150 132 134 164 C4' G A 6 OK OK 166 184 163 165 198 C4' G A 7 OK OK 200 218 197 199 232 C4' U A 8 OK OK 234 249 231 233 262 C4' G A 9 OK OK 264 282 261 263 296 C4' U A 10 OK OK 298 313 295 297 326 C4' G A 11 OK OK 328 346 325 327 360 C4' G A 12 OK OK 362 380 359 361 394 C4' A A 13 OK OK 396 413 393 395 427 C4' A A 14 OK OK 429 446 426 428 460 C4' G A 15 OK OK 462 480 459 461 494 C4' G A 16 OK OK 496 514 493 495 528 C4' A A 17 OK OK 530 547 527 529 561 C4' G A 18 OK OK 563 581 560 562 595 C4' U A 19 OK OK 597 612 594 596 625 C4' G A 20 OK OK 627 645 624 626 659 C4' G A 21 OK OK 661 679 658 660 693 C4' C A 22 OK OK 695 710 692 694 724 C4' U A 23 OK OK 726 741 723 725 754 C4' G A 24 OK OK 756 774 753 755 788 C4' G A 25 OK OK 790 808 787 789 822 C4' G A 26 OK OK 824 842 821 823 856 C4' U A 27 OK OK 858 873 855 857 886 C4' U A 28 OK OK 888 903 885 887 916 C4' G A 29 OK OK 918 936 915 917 950 C4' C A 30 OK OK 952 967 949 951 981 C4' G A 31 OK OK 983 1001 980 982 1015 C4' C A 32 OK OK 1017 1032 1014 1016 1046 C4' A A 33 OK OK 1048 1065 1045 1047 1079 C4' G A 34 OK OK 1081 1099 1078 1080 1113 C4' C A 35 OK OK 1115 1130 1112 1114 1144 C4' G A 36 OK OK 1146 1164 1143 1145 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 37 C5' C A 2 OK OK 36 53 54 38 68 C5' U A 3 OK OK 67 84 85 69 98 C5' G A 4 OK OK 97 117 118 99 132 C5' C A 5 OK OK 131 148 149 133 163 C5' G A 6 OK OK 162 182 183 164 197 C5' G A 7 OK OK 196 216 217 198 231 C5' U A 8 OK OK 230 247 248 232 261 C5' G A 9 OK OK 260 280 281 262 295 C5' U A 10 OK OK 294 311 312 296 325 C5' G A 11 OK OK 324 344 345 326 359 C5' G A 12 OK OK 358 378 379 360 393 C5' A A 13 OK OK 392 411 412 394 426 C5' A A 14 OK OK 425 444 445 427 459 C5' G A 15 OK OK 458 478 479 460 493 C5' G A 16 OK OK 492 512 513 494 527 C5' A A 17 OK OK 526 545 546 528 560 C5' G A 18 OK OK 559 579 580 561 594 C5' U A 19 OK OK 593 610 611 595 624 C5' G A 20 OK OK 623 643 644 625 658 C5' G A 21 OK OK 657 677 678 659 692 C5' C A 22 OK OK 691 708 709 693 723 C5' U A 23 OK OK 722 739 740 724 753 C5' G A 24 OK OK 752 772 773 754 787 C5' G A 25 OK OK 786 806 807 788 821 C5' G A 26 OK OK 820 840 841 822 855 C5' U A 27 OK OK 854 871 872 856 885 C5' U A 28 OK OK 884 901 902 886 915 C5' G A 29 OK OK 914 934 935 916 949 C5' C A 30 OK OK 948 965 966 950 980 C5' G A 31 OK OK 979 999 1000 981 1014 C5' C A 32 OK OK 1013 1030 1031 1015 1045 C5' A A 33 OK OK 1044 1063 1064 1046 1078 C5' G A 34 OK OK 1077 1097 1098 1079 1112 C5' C A 35 OK OK 1111 1128 1129 1113 1143 C5' G A 36 OK OK 1142 1162 1163 1144 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P U A 3 distorted distorted 41 65 66 67 94 P G A 4 distorted distorted 72 95 96 97 128 P C A 5 distorted distorted 102 129 130 131 159 P G A 6 distorted distorted 136 160 161 162 193 P G A 7 distorted distorted 167 194 195 196 227 P U A 8 distorted distorted 201 228 229 230 257 P G A 9 distorted distorted 235 258 259 260 291 P U A 10 distorted distorted 265 292 293 294 321 P G A 11 distorted distorted 299 322 323 324 355 P G A 12 distorted distorted 329 356 357 358 389 P A A 13 distorted distorted 363 390 391 392 422 P A A 14 distorted distorted 397 423 424 425 455 P G A 15 distorted distorted 430 456 457 458 489 P G A 16 distorted distorted 463 490 491 492 523 P A A 17 distorted distorted 497 524 525 526 556 P G A 18 distorted distorted 531 557 558 559 590 P U A 19 distorted distorted 564 591 592 593 620 P G A 20 distorted distorted 598 621 622 623 654 P G A 21 distorted distorted 628 655 656 657 688 P C A 22 distorted distorted 662 689 690 691 719 P U A 23 distorted distorted 696 720 721 722 749 P G A 24 distorted distorted 727 750 751 752 783 P G A 25 distorted distorted 757 784 785 786 817 P G A 26 distorted distorted 791 818 819 820 851 P U A 27 distorted distorted 825 852 853 854 881 P U A 28 distorted distorted 859 882 883 884 911 P G A 29 distorted distorted 889 912 913 914 945 P C A 30 distorted distorted 919 946 947 948 976 P G A 31 distorted distorted 953 977 978 979 1010 P C A 32 distorted distorted 984 1011 1012 1013 1041 P A A 33 distorted distorted 1018 1042 1043 1044 1074 P G A 34 distorted distorted 1049 1075 1076 1077 1108 P C A 35 distorted distorted 1082 1109 1110 1111 1139 P G A 36 distorted distorted 1116 1140 1141 1142 ---------------------------------------------------------------------------------