ID code: '1S2F' 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 907 alpha beta 4 27 10 7 44 C1' G A 908 alpha beta 39 62 45 42 78 C1' G A 909 alpha beta 73 96 79 76 112 C1' G A 910 alpha beta 107 130 113 110 146 C1' A A 911 alpha beta 141 163 147 144 179 C1' G A 912 alpha beta 174 197 180 177 213 C1' U A 913 alpha beta 208 228 214 211 243 C1' G A 914 alpha beta 238 261 244 241 277 C1' G A 915 alpha beta 272 295 278 275 311 C1' U A 916 alpha beta 306 326 312 309 341 C1' U A 917 alpha beta 336 356 342 339 371 C1' U A 918 alpha beta 366 386 372 369 401 C1' G A 919 alpha beta 396 419 402 399 435 C1' U A 920 alpha beta 430 450 436 433 465 C1' A A 921 alpha beta 460 482 466 463 498 C1' U A 922 alpha beta 493 513 499 496 528 C1' C A 923 alpha beta 523 543 529 526 559 C1' C A 924 alpha beta 554 574 560 557 590 C1' U A 925 alpha beta 585 605 591 588 620 C1' U A 926 alpha beta 615 635 621 618 650 C1' C A 927 alpha beta 645 665 651 648 681 C1' C A 928 alpha beta 676 696 682 679 712 C1' C A 929 alpha beta 707 728 713 710 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 907 OK OK 9 5 25 8 42 C2' G A 908 OK OK 44 40 60 43 76 C2' G A 909 OK OK 78 74 94 77 110 C2' G A 910 OK OK 112 108 128 111 144 C2' A A 911 OK OK 146 142 161 145 177 C2' G A 912 OK OK 179 175 195 178 211 C2' U A 913 OK OK 213 209 226 212 241 C2' G A 914 OK OK 243 239 259 242 275 C2' G A 915 OK OK 277 273 293 276 309 C2' U A 916 OK OK 311 307 324 310 339 C2' U A 917 OK OK 341 337 354 340 369 C2' U A 918 OK OK 371 367 384 370 399 C2' G A 919 OK OK 401 397 417 400 433 C2' U A 920 OK OK 435 431 448 434 463 C2' A A 921 OK OK 465 461 480 464 496 C2' U A 922 OK OK 498 494 511 497 526 C2' C A 923 OK OK 528 524 541 527 557 C2' C A 924 OK OK 559 555 572 558 588 C2' U A 925 OK OK 590 586 603 589 618 C2' U A 926 OK OK 620 616 633 619 648 C2' C A 927 OK OK 650 646 663 649 679 C2' C A 928 OK OK 681 677 694 680 710 C2' C A 929 OK OK 712 708 726 711 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 907 OK OK 3 24 6 7 40 C3' G A 908 OK OK 38 59 41 42 74 C3' G A 909 OK OK 72 93 75 76 108 C3' G A 910 OK OK 106 127 109 110 142 C3' A A 911 OK OK 140 160 143 144 175 C3' G A 912 OK OK 173 194 176 177 209 C3' U A 913 OK OK 207 225 210 211 239 C3' G A 914 OK OK 237 258 240 241 273 C3' G A 915 OK OK 271 292 274 275 307 C3' U A 916 OK OK 305 323 308 309 337 C3' U A 917 OK OK 335 353 338 339 367 C3' U A 918 OK OK 365 383 368 369 397 C3' G A 919 OK OK 395 416 398 399 431 C3' U A 920 OK OK 429 447 432 433 461 C3' A A 921 OK OK 459 479 462 463 494 C3' U A 922 OK OK 492 510 495 496 524 C3' C A 923 OK OK 522 540 525 526 555 C3' C A 924 OK OK 553 571 556 557 586 C3' U A 925 OK OK 584 602 587 588 616 C3' U A 926 OK OK 614 632 617 618 646 C3' C A 927 OK OK 644 662 647 648 677 C3' C A 928 OK OK 675 693 678 679 708 C3' C A 929 OK OK 706 724 709 710 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 907 OK OK 5 23 2 4 38 C4' G A 908 OK OK 40 58 37 39 72 C4' G A 909 OK OK 74 92 71 73 106 C4' G A 910 OK OK 108 126 105 107 140 C4' A A 911 OK OK 142 159 139 141 173 C4' G A 912 OK OK 175 193 172 174 207 C4' U A 913 OK OK 209 224 206 208 237 C4' G A 914 OK OK 239 257 236 238 271 C4' G A 915 OK OK 273 291 270 272 305 C4' U A 916 OK OK 307 322 304 306 335 C4' U A 917 OK OK 337 352 334 336 365 C4' U A 918 OK OK 367 382 364 366 395 C4' G A 919 OK OK 397 415 394 396 429 C4' U A 920 OK OK 431 446 428 430 459 C4' A A 921 OK OK 461 478 458 460 492 C4' U A 922 OK OK 494 509 491 493 522 C4' C A 923 OK OK 524 539 521 523 553 C4' C A 924 OK OK 555 570 552 554 584 C4' U A 925 OK OK 586 601 583 585 614 C4' U A 926 OK OK 616 631 613 615 644 C4' C A 927 OK OK 646 661 643 645 675 C4' C A 928 OK OK 677 692 674 676 706 C4' C A 929 OK OK 708 723 705 707 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 907 OK OK 1 21 22 3 37 C5' G A 908 OK OK 36 56 57 38 71 C5' G A 909 OK OK 70 90 91 72 105 C5' G A 910 OK OK 104 124 125 106 139 C5' A A 911 OK OK 138 157 158 140 172 C5' G A 912 OK OK 171 191 192 173 206 C5' U A 913 OK OK 205 222 223 207 236 C5' G A 914 OK OK 235 255 256 237 270 C5' G A 915 OK OK 269 289 290 271 304 C5' U A 916 OK OK 303 320 321 305 334 C5' U A 917 OK OK 333 350 351 335 364 C5' U A 918 OK OK 363 380 381 365 394 C5' G A 919 OK OK 393 413 414 395 428 C5' U A 920 OK OK 427 444 445 429 458 C5' A A 921 OK OK 457 476 477 459 491 C5' U A 922 OK OK 490 507 508 492 521 C5' C A 923 OK OK 520 537 538 522 552 C5' C A 924 OK OK 551 568 569 553 583 C5' U A 925 OK OK 582 599 600 584 613 C5' U A 926 OK OK 612 629 630 614 643 C5' C A 927 OK OK 642 659 660 644 674 C5' C A 928 OK OK 673 690 691 675 705 C5' C A 929 OK OK 704 721 722 706 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 908 distorted distorted 6 34 35 36 67 P G A 909 distorted distorted 41 68 69 70 101 P G A 910 distorted distorted 75 102 103 104 135 P A A 911 distorted distorted 109 136 137 138 168 P G A 912 distorted distorted 143 169 170 171 202 P U A 913 distorted distorted 176 203 204 205 232 P G A 914 distorted distorted 210 233 234 235 266 P G A 915 distorted distorted 240 267 268 269 300 P U A 916 distorted distorted 274 301 302 303 330 P U A 917 distorted distorted 308 331 332 333 360 P U A 918 distorted distorted 338 361 362 363 390 P G A 919 distorted distorted 368 391 392 393 424 P U A 920 distorted distorted 398 425 426 427 454 P A A 921 distorted distorted 432 455 456 457 487 P U A 922 distorted distorted 462 488 489 490 517 P C A 923 distorted distorted 495 518 519 520 548 P C A 924 distorted distorted 525 549 550 551 579 P U A 925 distorted distorted 556 580 581 582 609 P U A 926 distorted distorted 587 610 611 612 639 P C A 927 distorted distorted 617 640 641 642 670 P C A 928 distorted distorted 647 671 672 673 701 P C A 929 distorted distorted 678 702 703 704 ---------------------------------------------------------------------------------