ID code: '2LJJ' 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 290 alpha beta 8 31 14 11 48 C1' G A 291 alpha beta 43 66 49 46 82 C1' C A 292 alpha beta 77 97 83 80 113 C1' C A 293 alpha beta 108 128 114 111 144 C1' U A 294 alpha beta 139 159 145 142 174 C1' C A 295 alpha beta 169 189 175 172 205 C1' A A 296 alpha beta 200 222 206 203 238 C1' G A 297 alpha beta 233 256 239 236 272 C1' C A 298 alpha beta 267 287 273 270 303 C1' A A 299 alpha beta 298 320 304 301 336 C1' C A 300 alpha beta 331 351 337 334 367 C1' U A 301 alpha beta 362 382 368 365 397 C1' A A 302 alpha beta 392 414 398 395 430 C1' C A 303 alpha beta 425 445 431 428 461 C1' C A 304 alpha beta 456 476 462 459 492 C1' C A 305 alpha beta 487 507 493 490 523 C1' C A 306 alpha beta 518 538 524 521 554 C1' A A 307 alpha beta 549 571 555 552 587 C1' G A 308 alpha beta 582 605 588 585 621 C1' U A 309 alpha beta 616 636 622 619 651 C1' G A 310 alpha beta 646 669 652 649 685 C1' U A 311 alpha beta 680 700 686 683 715 C1' A A 312 alpha beta 710 732 716 713 748 C1' G A 313 alpha beta 743 766 749 746 782 C1' G A 314 alpha beta 777 800 783 780 816 C1' U A 315 alpha beta 811 831 817 814 846 C1' C A 316 alpha beta 841 862 847 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 290 OK OK 13 9 29 12 46 C2' G A 291 OK OK 48 44 64 47 80 C2' C A 292 OK OK 82 78 95 81 111 C2' C A 293 OK OK 113 109 126 112 142 C2' U A 294 OK OK 144 140 157 143 172 C2' C A 295 OK OK 174 170 187 173 203 C2' A A 296 OK OK 205 201 220 204 236 C2' G A 297 OK OK 238 234 254 237 270 C2' C A 298 OK OK 272 268 285 271 301 C2' A A 299 OK OK 303 299 318 302 334 C2' C A 300 OK OK 336 332 349 335 365 C2' U A 301 OK OK 367 363 380 366 395 C2' A A 302 OK OK 397 393 412 396 428 C2' C A 303 OK OK 430 426 443 429 459 C2' C A 304 OK OK 461 457 474 460 490 C2' C A 305 OK OK 492 488 505 491 521 C2' C A 306 OK OK 523 519 536 522 552 C2' A A 307 OK OK 554 550 569 553 585 C2' G A 308 OK OK 587 583 603 586 619 C2' U A 309 OK OK 621 617 634 620 649 C2' G A 310 OK OK 651 647 667 650 683 C2' U A 311 OK OK 685 681 698 684 713 C2' A A 312 OK OK 715 711 730 714 746 C2' G A 313 OK OK 748 744 764 747 780 C2' G A 314 OK OK 782 778 798 781 814 C2' U A 315 OK OK 816 812 829 815 844 C2' C A 316 OK OK 846 842 860 845 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 290 OK OK 7 28 10 11 44 C3' G A 291 OK OK 42 63 45 46 78 C3' C A 292 OK OK 76 94 79 80 109 C3' C A 293 OK OK 107 125 110 111 140 C3' U A 294 OK OK 138 156 141 142 170 C3' C A 295 OK OK 168 186 171 172 201 C3' A A 296 OK OK 199 219 202 203 234 C3' G A 297 OK OK 232 253 235 236 268 C3' C A 298 OK OK 266 284 269 270 299 C3' A A 299 OK OK 297 317 300 301 332 C3' C A 300 OK OK 330 348 333 334 363 C3' U A 301 OK OK 361 379 364 365 393 C3' A A 302 OK OK 391 411 394 395 426 C3' C A 303 OK OK 424 442 427 428 457 C3' C A 304 OK OK 455 473 458 459 488 C3' C A 305 OK OK 486 504 489 490 519 C3' C A 306 OK OK 517 535 520 521 550 C3' A A 307 OK OK 548 568 551 552 583 C3' G A 308 OK OK 581 602 584 585 617 C3' U A 309 OK OK 615 633 618 619 647 C3' G A 310 OK OK 645 666 648 649 681 C3' U A 311 OK OK 679 697 682 683 711 C3' A A 312 OK OK 709 729 712 713 744 C3' G A 313 OK OK 742 763 745 746 778 C3' G A 314 OK OK 776 797 779 780 812 C3' U A 315 OK OK 810 828 813 814 842 C3' C A 316 OK OK 840 858 843 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 290 OK OK 9 27 6 8 42 C4' G A 291 OK OK 44 62 41 43 76 C4' C A 292 OK OK 78 93 75 77 107 C4' C A 293 OK OK 109 124 106 108 138 C4' U A 294 OK OK 140 155 137 139 168 C4' C A 295 OK OK 170 185 167 169 199 C4' A A 296 OK OK 201 218 198 200 232 C4' G A 297 OK OK 234 252 231 233 266 C4' C A 298 OK OK 268 283 265 267 297 C4' A A 299 OK OK 299 316 296 298 330 C4' C A 300 OK OK 332 347 329 331 361 C4' U A 301 OK OK 363 378 360 362 391 C4' A A 302 OK OK 393 410 390 392 424 C4' C A 303 OK OK 426 441 423 425 455 C4' C A 304 OK OK 457 472 454 456 486 C4' C A 305 OK OK 488 503 485 487 517 C4' C A 306 OK OK 519 534 516 518 548 C4' A A 307 OK OK 550 567 547 549 581 C4' G A 308 OK OK 583 601 580 582 615 C4' U A 309 OK OK 617 632 614 616 645 C4' G A 310 OK OK 647 665 644 646 679 C4' U A 311 OK OK 681 696 678 680 709 C4' A A 312 OK OK 711 728 708 710 742 C4' G A 313 OK OK 744 762 741 743 776 C4' G A 314 OK OK 778 796 775 777 810 C4' U A 315 OK OK 812 827 809 811 840 C4' C A 316 OK OK 842 857 839 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 290 OK OK 5 25 26 7 41 C5' G A 291 OK OK 40 60 61 42 75 C5' C A 292 OK OK 74 91 92 76 106 C5' C A 293 OK OK 105 122 123 107 137 C5' U A 294 OK OK 136 153 154 138 167 C5' C A 295 OK OK 166 183 184 168 198 C5' A A 296 OK OK 197 216 217 199 231 C5' G A 297 OK OK 230 250 251 232 265 C5' C A 298 OK OK 264 281 282 266 296 C5' A A 299 OK OK 295 314 315 297 329 C5' C A 300 OK OK 328 345 346 330 360 C5' U A 301 OK OK 359 376 377 361 390 C5' A A 302 OK OK 389 408 409 391 423 C5' C A 303 OK OK 422 439 440 424 454 C5' C A 304 OK OK 453 470 471 455 485 C5' C A 305 OK OK 484 501 502 486 516 C5' C A 306 OK OK 515 532 533 517 547 C5' A A 307 OK OK 546 565 566 548 580 C5' G A 308 OK OK 579 599 600 581 614 C5' U A 309 OK OK 613 630 631 615 644 C5' G A 310 OK OK 643 663 664 645 678 C5' U A 311 OK OK 677 694 695 679 708 C5' A A 312 OK OK 707 726 727 709 741 C5' G A 313 OK OK 740 760 761 742 775 C5' G A 314 OK OK 774 794 795 776 809 C5' U A 315 OK OK 808 825 826 810 839 C5' C A 316 OK OK 838 855 856 840 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 290 distorted distorted 3 4 5 37 P G A 291 distorted distorted 10 38 39 40 71 P C A 292 distorted distorted 45 72 73 74 102 P C A 293 distorted distorted 79 103 104 105 133 P U A 294 distorted distorted 110 134 135 136 163 P C A 295 distorted distorted 141 164 165 166 194 P A A 296 distorted distorted 171 195 196 197 227 P G A 297 distorted distorted 202 228 229 230 261 P C A 298 distorted distorted 235 262 263 264 292 P A A 299 distorted distorted 269 293 294 295 325 P C A 300 distorted distorted 300 326 327 328 356 P U A 301 distorted distorted 333 357 358 359 386 P A A 302 distorted distorted 364 387 388 389 419 P C A 303 distorted distorted 394 420 421 422 450 P C A 304 distorted distorted 427 451 452 453 481 P C A 305 distorted distorted 458 482 483 484 512 P C A 306 distorted distorted 489 513 514 515 543 P A A 307 distorted distorted 520 544 545 546 576 P G A 308 distorted distorted 551 577 578 579 610 P U A 309 distorted distorted 584 611 612 613 640 P G A 310 distorted distorted 618 641 642 643 674 P U A 311 distorted distorted 648 675 676 677 704 P A A 312 distorted distorted 682 705 706 707 737 P G A 313 distorted distorted 712 738 739 740 771 P G A 314 distorted distorted 745 772 773 774 805 P U A 315 distorted distorted 779 806 807 808 835 P C A 316 distorted distorted 813 836 837 838 ---------------------------------------------------------------------------------