ID code: '2LPS' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' C A 4 alpha beta 106 126 112 109 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' A A 8 alpha beta 232 254 238 235 270 C1' U A 9 alpha beta 265 285 271 268 300 C1' G A 10 alpha beta 295 318 301 298 334 C1' C A 11 alpha beta 329 349 335 332 365 C1' G A 12 alpha beta 360 383 366 363 399 C1' A A 13 alpha beta 394 416 400 397 432 C1' U A 14 alpha beta 427 447 433 430 462 C1' G A 15 alpha beta 457 480 463 460 496 C1' A A 16 alpha beta 491 513 497 494 529 C1' A A 17 alpha beta 524 546 530 527 562 C1' A A 18 alpha beta 557 579 563 560 595 C1' G A 19 alpha beta 590 613 596 593 629 C1' U A 20 alpha beta 624 644 630 627 659 C1' C A 21 alpha beta 654 674 660 657 690 C1' G A 22 alpha beta 685 708 691 688 724 C1' C A 23 alpha beta 719 739 725 722 755 C1' A A 24 alpha beta 750 772 756 753 788 C1' C A 25 alpha beta 783 803 789 786 819 C1' G A 26 alpha beta 814 837 820 817 853 C1' U A 27 alpha beta 848 868 854 851 883 C1' A A 28 alpha beta 878 900 884 881 916 C1' C A 29 alpha beta 911 931 917 914 947 C1' G A 30 alpha beta 942 965 948 945 981 C1' G A 31 alpha beta 976 999 982 979 1015 C1' U A 32 alpha beta 1010 1030 1016 1013 1045 C1' U A 33 alpha beta 1040 1060 1046 1043 1075 C1' C A 34 alpha beta 1070 1091 1076 1073 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' C A 4 OK OK 111 107 124 110 140 C2' C A 5 OK OK 142 138 155 141 171 C2' G A 6 OK OK 173 169 189 172 205 C2' U A 7 OK OK 207 203 220 206 235 C2' A A 8 OK OK 237 233 252 236 268 C2' U A 9 OK OK 270 266 283 269 298 C2' G A 10 OK OK 300 296 316 299 332 C2' C A 11 OK OK 334 330 347 333 363 C2' G A 12 OK OK 365 361 381 364 397 C2' A A 13 OK OK 399 395 414 398 430 C2' U A 14 OK OK 432 428 445 431 460 C2' G A 15 OK OK 462 458 478 461 494 C2' A A 16 OK OK 496 492 511 495 527 C2' A A 17 OK OK 529 525 544 528 560 C2' A A 18 OK OK 562 558 577 561 593 C2' G A 19 OK OK 595 591 611 594 627 C2' U A 20 OK OK 629 625 642 628 657 C2' C A 21 OK OK 659 655 672 658 688 C2' G A 22 OK OK 690 686 706 689 722 C2' C A 23 OK OK 724 720 737 723 753 C2' A A 24 OK OK 755 751 770 754 786 C2' C A 25 OK OK 788 784 801 787 817 C2' G A 26 OK OK 819 815 835 818 851 C2' U A 27 OK OK 853 849 866 852 881 C2' A A 28 OK OK 883 879 898 882 914 C2' C A 29 OK OK 916 912 929 915 945 C2' G A 30 OK OK 947 943 963 946 979 C2' G A 31 OK OK 981 977 997 980 1013 C2' U A 32 OK OK 1015 1011 1028 1014 1043 C2' U A 33 OK OK 1045 1041 1058 1044 1073 C2' C A 34 OK OK 1075 1071 1089 1074 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' C A 4 OK OK 105 123 108 109 138 C3' C A 5 OK OK 136 154 139 140 169 C3' G A 6 OK OK 167 188 170 171 203 C3' U A 7 OK OK 201 219 204 205 233 C3' A A 8 OK OK 231 251 234 235 266 C3' U A 9 OK OK 264 282 267 268 296 C3' G A 10 OK OK 294 315 297 298 330 C3' C A 11 OK OK 328 346 331 332 361 C3' G A 12 OK OK 359 380 362 363 395 C3' A A 13 OK OK 393 413 396 397 428 C3' U A 14 OK OK 426 444 429 430 458 C3' G A 15 OK OK 456 477 459 460 492 C3' A A 16 OK OK 490 510 493 494 525 C3' A A 17 OK OK 523 543 526 527 558 C3' A A 18 OK OK 556 576 559 560 591 C3' G A 19 OK OK 589 610 592 593 625 C3' U A 20 OK OK 623 641 626 627 655 C3' C A 21 OK OK 653 671 656 657 686 C3' G A 22 OK OK 684 705 687 688 720 C3' C A 23 OK OK 718 736 721 722 751 C3' A A 24 OK OK 749 769 752 753 784 C3' C A 25 OK OK 782 800 785 786 815 C3' G A 26 OK OK 813 834 816 817 849 C3' U A 27 OK OK 847 865 850 851 879 C3' A A 28 OK OK 877 897 880 881 912 C3' C A 29 OK OK 910 928 913 914 943 C3' G A 30 OK OK 941 962 944 945 977 C3' G A 31 OK OK 975 996 978 979 1011 C3' U A 32 OK OK 1009 1027 1012 1013 1041 C3' U A 33 OK OK 1039 1057 1042 1043 1071 C3' C A 34 OK OK 1069 1087 1072 1073 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' C A 4 OK OK 107 122 104 106 136 C4' C A 5 OK OK 138 153 135 137 167 C4' G A 6 OK OK 169 187 166 168 201 C4' U A 7 OK OK 203 218 200 202 231 C4' A A 8 OK OK 233 250 230 232 264 C4' U A 9 OK OK 266 281 263 265 294 C4' G A 10 OK OK 296 314 293 295 328 C4' C A 11 OK OK 330 345 327 329 359 C4' G A 12 OK OK 361 379 358 360 393 C4' A A 13 OK OK 395 412 392 394 426 C4' U A 14 OK OK 428 443 425 427 456 C4' G A 15 OK OK 458 476 455 457 490 C4' A A 16 OK OK 492 509 489 491 523 C4' A A 17 OK OK 525 542 522 524 556 C4' A A 18 OK OK 558 575 555 557 589 C4' G A 19 OK OK 591 609 588 590 623 C4' U A 20 OK OK 625 640 622 624 653 C4' C A 21 OK OK 655 670 652 654 684 C4' G A 22 OK OK 686 704 683 685 718 C4' C A 23 OK OK 720 735 717 719 749 C4' A A 24 OK OK 751 768 748 750 782 C4' C A 25 OK OK 784 799 781 783 813 C4' G A 26 OK OK 815 833 812 814 847 C4' U A 27 OK OK 849 864 846 848 877 C4' A A 28 OK OK 879 896 876 878 910 C4' C A 29 OK OK 912 927 909 911 941 C4' G A 30 OK OK 943 961 940 942 975 C4' G A 31 OK OK 977 995 974 976 1009 C4' U A 32 OK OK 1011 1026 1008 1010 1039 C4' U A 33 OK OK 1041 1056 1038 1040 1069 C4' C A 34 OK OK 1071 1086 1068 1070 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' C A 4 OK OK 103 120 121 105 135 C5' C A 5 OK OK 134 151 152 136 166 C5' G A 6 OK OK 165 185 186 167 200 C5' U A 7 OK OK 199 216 217 201 230 C5' A A 8 OK OK 229 248 249 231 263 C5' U A 9 OK OK 262 279 280 264 293 C5' G A 10 OK OK 292 312 313 294 327 C5' C A 11 OK OK 326 343 344 328 358 C5' G A 12 OK OK 357 377 378 359 392 C5' A A 13 OK OK 391 410 411 393 425 C5' U A 14 OK OK 424 441 442 426 455 C5' G A 15 OK OK 454 474 475 456 489 C5' A A 16 OK OK 488 507 508 490 522 C5' A A 17 OK OK 521 540 541 523 555 C5' A A 18 OK OK 554 573 574 556 588 C5' G A 19 OK OK 587 607 608 589 622 C5' U A 20 OK OK 621 638 639 623 652 C5' C A 21 OK OK 651 668 669 653 683 C5' G A 22 OK OK 682 702 703 684 717 C5' C A 23 OK OK 716 733 734 718 748 C5' A A 24 OK OK 747 766 767 749 781 C5' C A 25 OK OK 780 797 798 782 812 C5' G A 26 OK OK 811 831 832 813 846 C5' U A 27 OK OK 845 862 863 847 876 C5' A A 28 OK OK 875 894 895 877 909 C5' C A 29 OK OK 908 925 926 910 940 C5' G A 30 OK OK 939 959 960 941 974 C5' G A 31 OK OK 973 993 994 975 1008 C5' U A 32 OK OK 1007 1024 1025 1009 1038 C5' U A 33 OK OK 1037 1054 1055 1039 1068 C5' C A 34 OK OK 1067 1084 1085 1069 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P C A 4 distorted distorted 74 101 102 103 131 P C A 5 distorted distorted 108 132 133 134 162 P G A 6 distorted distorted 139 163 164 165 196 P U A 7 distorted distorted 170 197 198 199 226 P A A 8 distorted distorted 204 227 228 229 259 P U A 9 distorted distorted 234 260 261 262 289 P G A 10 distorted distorted 267 290 291 292 323 P C A 11 distorted distorted 297 324 325 326 354 P G A 12 distorted distorted 331 355 356 357 388 P A A 13 distorted distorted 362 389 390 391 421 P U A 14 distorted distorted 396 422 423 424 451 P G A 15 distorted distorted 429 452 453 454 485 P A A 16 distorted distorted 459 486 487 488 518 P A A 17 distorted distorted 493 519 520 521 551 P A A 18 distorted distorted 526 552 553 554 584 P G A 19 distorted distorted 559 585 586 587 618 P U A 20 distorted distorted 592 619 620 621 648 P C A 21 distorted distorted 626 649 650 651 679 P G A 22 distorted distorted 656 680 681 682 713 P C A 23 distorted distorted 687 714 715 716 744 P A A 24 distorted distorted 721 745 746 747 777 P C A 25 distorted distorted 752 778 779 780 808 P G A 26 distorted distorted 785 809 810 811 842 P U A 27 distorted distorted 816 843 844 845 872 P A A 28 distorted distorted 850 873 874 875 905 P C A 29 distorted distorted 880 906 907 908 936 P G A 30 distorted distorted 913 937 938 939 970 P G A 31 distorted distorted 944 971 972 973 1004 P U A 32 distorted distorted 978 1005 1006 1007 1034 P U A 33 distorted distorted 1012 1035 1036 1037 1064 P C A 34 distorted distorted 1042 1065 1066 1067 ---------------------------------------------------------------------------------