ID code: '1Z31' 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' --------------------------------------------------------------------------------- 13 C1' G A 257 alpha beta 8 31 14 11 48 C1' A A 258 alpha beta 43 65 49 46 81 C1' G A 259 alpha beta 76 99 82 79 115 C1' G A 260 alpha beta 110 133 116 113 149 C1' U A 261 alpha beta 144 164 150 147 179 C1' C A 262 alpha beta 174 194 180 177 210 C1' G A 263 alpha beta 205 228 211 208 244 C1' G A 264 alpha beta 239 262 245 242 278 C1' C A 265 alpha beta 273 293 279 276 309 C1' C A 266 alpha beta 304 324 310 307 340 C1' C A 267 alpha beta 335 355 341 338 371 C1' G A 268 alpha beta 366 389 372 369 405 C1' A A 269 alpha beta 400 422 406 403 438 C1' C A 270 alpha beta 433 453 439 436 469 C1' U A 271 alpha beta 464 484 470 467 499 C1' U A 272 alpha beta 494 514 500 497 529 C1' C A 284 alpha beta 524 544 530 527 560 C1' G A 285 alpha beta 555 578 561 558 594 C1' G A 286 alpha beta 589 612 595 592 628 C1' U A 287 alpha beta 623 643 629 626 658 C1' C A 288 alpha beta 653 673 659 656 689 C1' A A 289 alpha beta 684 706 690 687 722 C1' C A 290 alpha beta 717 737 723 720 753 C1' U A 291 alpha beta 748 768 754 751 783 C1' G A 292 alpha beta 778 801 784 781 817 C1' C A 293 alpha beta 812 832 818 815 848 C1' C A 294 alpha beta 843 863 849 846 879 C1' A A 295 alpha beta 874 896 880 877 912 C1' C A 296 alpha beta 907 927 913 910 943 C1' C A 297 alpha beta 938 958 944 941 974 C1' U A 298 alpha beta 969 989 975 972 1004 C1' C A 299 alpha beta 999 1020 1005 1002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 257 OK OK 13 9 29 12 46 C2' A A 258 OK OK 48 44 63 47 79 C2' G A 259 OK OK 81 77 97 80 113 C2' G A 260 OK OK 115 111 131 114 147 C2' U A 261 OK OK 149 145 162 148 177 C2' C A 262 OK OK 179 175 192 178 208 C2' G A 263 OK OK 210 206 226 209 242 C2' G A 264 OK OK 244 240 260 243 276 C2' C A 265 OK OK 278 274 291 277 307 C2' C A 266 OK OK 309 305 322 308 338 C2' C A 267 OK OK 340 336 353 339 369 C2' G A 268 OK OK 371 367 387 370 403 C2' A A 269 OK OK 405 401 420 404 436 C2' C A 270 OK OK 438 434 451 437 467 C2' U A 271 OK OK 469 465 482 468 497 C2' U A 272 OK OK 499 495 512 498 527 C2' C A 284 OK OK 529 525 542 528 558 C2' G A 285 OK OK 560 556 576 559 592 C2' G A 286 OK OK 594 590 610 593 626 C2' U A 287 OK OK 628 624 641 627 656 C2' C A 288 OK OK 658 654 671 657 687 C2' A A 289 OK OK 689 685 704 688 720 C2' C A 290 OK OK 722 718 735 721 751 C2' U A 291 OK OK 753 749 766 752 781 C2' G A 292 OK OK 783 779 799 782 815 C2' C A 293 OK OK 817 813 830 816 846 C2' C A 294 OK OK 848 844 861 847 877 C2' A A 295 OK OK 879 875 894 878 910 C2' C A 296 OK OK 912 908 925 911 941 C2' C A 297 OK OK 943 939 956 942 972 C2' U A 298 OK OK 974 970 987 973 1002 C2' C A 299 OK OK 1004 1000 1018 1003 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 257 OK OK 7 28 10 11 44 C3' A A 258 OK OK 42 62 45 46 77 C3' G A 259 OK OK 75 96 78 79 111 C3' G A 260 OK OK 109 130 112 113 145 C3' U A 261 OK OK 143 161 146 147 175 C3' C A 262 OK OK 173 191 176 177 206 C3' G A 263 OK OK 204 225 207 208 240 C3' G A 264 OK OK 238 259 241 242 274 C3' C A 265 OK OK 272 290 275 276 305 C3' C A 266 OK OK 303 321 306 307 336 C3' C A 267 OK OK 334 352 337 338 367 C3' G A 268 OK OK 365 386 368 369 401 C3' A A 269 OK OK 399 419 402 403 434 C3' C A 270 OK OK 432 450 435 436 465 C3' U A 271 OK OK 463 481 466 467 495 C3' U A 272 OK OK 493 511 496 497 525 C3' C A 284 OK OK 523 541 526 527 556 C3' G A 285 OK OK 554 575 557 558 590 C3' G A 286 OK OK 588 609 591 592 624 C3' U A 287 OK OK 622 640 625 626 654 C3' C A 288 OK OK 652 670 655 656 685 C3' A A 289 OK OK 683 703 686 687 718 C3' C A 290 OK OK 716 734 719 720 749 C3' U A 291 OK OK 747 765 750 751 779 C3' G A 292 OK OK 777 798 780 781 813 C3' C A 293 OK OK 811 829 814 815 844 C3' C A 294 OK OK 842 860 845 846 875 C3' A A 295 OK OK 873 893 876 877 908 C3' C A 296 OK OK 906 924 909 910 939 C3' C A 297 OK OK 937 955 940 941 970 C3' U A 298 OK OK 968 986 971 972 1000 C3' C A 299 OK OK 998 1016 1001 1002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 257 OK OK 9 27 6 8 42 C4' A A 258 OK OK 44 61 41 43 75 C4' G A 259 OK OK 77 95 74 76 109 C4' G A 260 OK OK 111 129 108 110 143 C4' U A 261 OK OK 145 160 142 144 173 C4' C A 262 OK OK 175 190 172 174 204 C4' G A 263 OK OK 206 224 203 205 238 C4' G A 264 OK OK 240 258 237 239 272 C4' C A 265 OK OK 274 289 271 273 303 C4' C A 266 OK OK 305 320 302 304 334 C4' C A 267 OK OK 336 351 333 335 365 C4' G A 268 OK OK 367 385 364 366 399 C4' A A 269 OK OK 401 418 398 400 432 C4' C A 270 OK OK 434 449 431 433 463 C4' U A 271 OK OK 465 480 462 464 493 C4' U A 272 OK OK 495 510 492 494 523 C4' C A 284 OK OK 525 540 522 524 554 C4' G A 285 OK OK 556 574 553 555 588 C4' G A 286 OK OK 590 608 587 589 622 C4' U A 287 OK OK 624 639 621 623 652 C4' C A 288 OK OK 654 669 651 653 683 C4' A A 289 OK OK 685 702 682 684 716 C4' C A 290 OK OK 718 733 715 717 747 C4' U A 291 OK OK 749 764 746 748 777 C4' G A 292 OK OK 779 797 776 778 811 C4' C A 293 OK OK 813 828 810 812 842 C4' C A 294 OK OK 844 859 841 843 873 C4' A A 295 OK OK 875 892 872 874 906 C4' C A 296 OK OK 908 923 905 907 937 C4' C A 297 OK OK 939 954 936 938 968 C4' U A 298 OK OK 970 985 967 969 998 C4' C A 299 OK OK 1000 1015 997 999 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 257 OK OK 5 25 26 7 41 C5' A A 258 OK OK 40 59 60 42 74 C5' G A 259 OK OK 73 93 94 75 108 C5' G A 260 OK OK 107 127 128 109 142 C5' U A 261 OK OK 141 158 159 143 172 C5' C A 262 OK OK 171 188 189 173 203 C5' G A 263 OK OK 202 222 223 204 237 C5' G A 264 OK OK 236 256 257 238 271 C5' C A 265 OK OK 270 287 288 272 302 C5' C A 266 OK OK 301 318 319 303 333 C5' C A 267 OK OK 332 349 350 334 364 C5' G A 268 OK OK 363 383 384 365 398 C5' A A 269 OK OK 397 416 417 399 431 C5' C A 270 OK OK 430 447 448 432 462 C5' U A 271 OK OK 461 478 479 463 492 C5' U A 272 OK OK 491 508 509 493 522 C5' C A 284 OK OK 521 538 539 523 553 C5' G A 285 OK OK 552 572 573 554 587 C5' G A 286 OK OK 586 606 607 588 621 C5' U A 287 OK OK 620 637 638 622 651 C5' C A 288 OK OK 650 667 668 652 682 C5' A A 289 OK OK 681 700 701 683 715 C5' C A 290 OK OK 714 731 732 716 746 C5' U A 291 OK OK 745 762 763 747 776 C5' G A 292 OK OK 775 795 796 777 810 C5' C A 293 OK OK 809 826 827 811 841 C5' C A 294 OK OK 840 857 858 842 872 C5' A A 295 OK OK 871 890 891 873 905 C5' C A 296 OK OK 904 921 922 906 936 C5' C A 297 OK OK 935 952 953 937 967 C5' U A 298 OK OK 966 983 984 968 997 C5' C A 299 OK OK 996 1013 1014 998 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 257 OK OK 3 4 5 37 P A A 258 distorted distorted 10 38 39 40 70 P G A 259 distorted distorted 45 71 72 73 104 P G A 260 distorted distorted 78 105 106 107 138 P U A 261 distorted distorted 112 139 140 141 168 P C A 262 distorted distorted 146 169 170 171 199 P G A 263 distorted distorted 176 200 201 202 233 P G A 264 distorted distorted 207 234 235 236 267 P C A 265 distorted distorted 241 268 269 270 298 P C A 266 distorted distorted 275 299 300 301 329 P C A 267 distorted distorted 306 330 331 332 360 P G A 268 distorted distorted 337 361 362 363 394 P A A 269 distorted distorted 368 395 396 397 427 P C A 270 distorted distorted 402 428 429 430 458 P U A 271 distorted distorted 435 459 460 461 488 P U A 272 distorted distorted 466 489 490 491 518 P C A 284 distorted distorted 496 519 520 521 549 P G A 285 distorted distorted 526 550 551 552 583 P G A 286 distorted distorted 557 584 585 586 617 P U A 287 distorted distorted 591 618 619 620 647 P C A 288 distorted distorted 625 648 649 650 678 P A A 289 distorted distorted 655 679 680 681 711 P C A 290 distorted distorted 686 712 713 714 742 P U A 291 distorted distorted 719 743 744 745 772 P G A 292 distorted distorted 750 773 774 775 806 P C A 293 distorted distorted 780 807 808 809 837 P C A 294 distorted distorted 814 838 839 840 868 P A A 295 distorted distorted 845 869 870 871 901 P C A 296 distorted distorted 876 902 903 904 932 P C A 297 distorted distorted 909 933 934 935 963 P U A 298 distorted distorted 940 964 965 966 993 P C A 299 distorted distorted 971 994 995 996 ---------------------------------------------------------------------------------