ID code: '1I9K' 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' U A 1 alpha beta 4 24 10 7 40 C1' C A 2 alpha beta 35 55 41 38 71 C1' C A 3 alpha beta 66 86 72 69 102 C1' C A 4 alpha beta 97 117 103 100 133 C1' C A 5 alpha beta 128 148 134 131 164 C1' C A 6 alpha beta 159 180 165 162 194 C1' U B 1 alpha beta 189 209 195 192 225 C1' C B 2 alpha beta 220 240 226 223 256 C1' C B 3 alpha beta 251 271 257 254 287 C1' C B 4 alpha beta 282 302 288 285 318 C1' C B 5 alpha beta 313 333 319 316 349 C1' C B 6 alpha beta 344 365 350 347 379 C1' U C 1 alpha beta 374 394 380 377 410 C1' C C 2 alpha beta 405 425 411 408 441 C1' C C 3 alpha beta 436 456 442 439 472 C1' C C 4 alpha beta 467 487 473 470 503 C1' C C 5 alpha beta 498 518 504 501 534 C1' C C 6 alpha beta 529 550 535 532 564 C1' U D 1 alpha beta 559 579 565 562 595 C1' C D 2 alpha beta 590 610 596 593 626 C1' C D 3 alpha beta 621 641 627 624 657 C1' C D 4 alpha beta 652 672 658 655 688 C1' C D 5 alpha beta 683 703 689 686 719 C1' C D 6 alpha beta 714 735 720 717 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK OK 9 5 22 8 38 C2' C A 2 OK OK 40 36 53 39 69 C2' C A 3 OK OK 71 67 84 70 100 C2' C A 4 OK OK 102 98 115 101 131 C2' C A 5 OK OK 133 129 146 132 162 C2' C A 6 OK OK 164 160 178 163 192 C2' U B 1 OK OK 194 190 207 193 223 C2' C B 2 OK OK 225 221 238 224 254 C2' C B 3 OK OK 256 252 269 255 285 C2' C B 4 OK OK 287 283 300 286 316 C2' C B 5 OK OK 318 314 331 317 347 C2' C B 6 OK OK 349 345 363 348 377 C2' U C 1 OK OK 379 375 392 378 408 C2' C C 2 OK OK 410 406 423 409 439 C2' C C 3 OK OK 441 437 454 440 470 C2' C C 4 OK OK 472 468 485 471 501 C2' C C 5 OK OK 503 499 516 502 532 C2' C C 6 OK OK 534 530 548 533 562 C2' U D 1 OK OK 564 560 577 563 593 C2' C D 2 OK OK 595 591 608 594 624 C2' C D 3 OK OK 626 622 639 625 655 C2' C D 4 OK OK 657 653 670 656 686 C2' C D 5 OK OK 688 684 701 687 717 C2' C D 6 OK OK 719 715 733 718 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK OK 3 21 6 7 36 C3' C A 2 OK OK 34 52 37 38 67 C3' C A 3 OK OK 65 83 68 69 98 C3' C A 4 OK OK 96 114 99 100 129 C3' C A 5 OK OK 127 145 130 131 160 C3' C A 6 OK OK 158 176 161 162 190 C3' U B 1 OK OK 188 206 191 192 221 C3' C B 2 OK OK 219 237 222 223 252 C3' C B 3 OK OK 250 268 253 254 283 C3' C B 4 OK OK 281 299 284 285 314 C3' C B 5 OK OK 312 330 315 316 345 C3' C B 6 OK OK 343 361 346 347 375 C3' U C 1 OK OK 373 391 376 377 406 C3' C C 2 OK OK 404 422 407 408 437 C3' C C 3 OK OK 435 453 438 439 468 C3' C C 4 OK OK 466 484 469 470 499 C3' C C 5 OK OK 497 515 500 501 530 C3' C C 6 OK OK 528 546 531 532 560 C3' U D 1 OK OK 558 576 561 562 591 C3' C D 2 OK OK 589 607 592 593 622 C3' C D 3 OK OK 620 638 623 624 653 C3' C D 4 OK OK 651 669 654 655 684 C3' C D 5 OK OK 682 700 685 686 715 C3' C D 6 OK OK 713 731 716 717 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK OK 5 20 2 4 34 C4' C A 2 OK OK 36 51 33 35 65 C4' C A 3 OK OK 67 82 64 66 96 C4' C A 4 OK OK 98 113 95 97 127 C4' C A 5 OK OK 129 144 126 128 158 C4' C A 6 OK OK 160 175 157 159 188 C4' U B 1 OK OK 190 205 187 189 219 C4' C B 2 OK OK 221 236 218 220 250 C4' C B 3 OK OK 252 267 249 251 281 C4' C B 4 OK OK 283 298 280 282 312 C4' C B 5 OK OK 314 329 311 313 343 C4' C B 6 OK OK 345 360 342 344 373 C4' U C 1 OK OK 375 390 372 374 404 C4' C C 2 OK OK 406 421 403 405 435 C4' C C 3 OK OK 437 452 434 436 466 C4' C C 4 OK OK 468 483 465 467 497 C4' C C 5 OK OK 499 514 496 498 528 C4' C C 6 OK OK 530 545 527 529 558 C4' U D 1 OK OK 560 575 557 559 589 C4' C D 2 OK OK 591 606 588 590 620 C4' C D 3 OK OK 622 637 619 621 651 C4' C D 4 OK OK 653 668 650 652 682 C4' C D 5 OK OK 684 699 681 683 713 C4' C D 6 OK OK 715 730 712 714 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 OK OK 1 18 19 3 33 C5' C A 2 OK OK 32 49 50 34 64 C5' C A 3 OK OK 63 80 81 65 95 C5' C A 4 OK OK 94 111 112 96 126 C5' C A 5 OK OK 125 142 143 127 157 C5' C A 6 OK OK 156 173 174 158 187 C5' U B 1 OK OK 186 203 204 188 218 C5' C B 2 OK OK 217 234 235 219 249 C5' C B 3 OK OK 248 265 266 250 280 C5' C B 4 OK OK 279 296 297 281 311 C5' C B 5 OK OK 310 327 328 312 342 C5' C B 6 OK OK 341 358 359 343 372 C5' U C 1 OK OK 371 388 389 373 403 C5' C C 2 OK OK 402 419 420 404 434 C5' C C 3 OK OK 433 450 451 435 465 C5' C C 4 OK OK 464 481 482 466 496 C5' C C 5 OK OK 495 512 513 497 527 C5' C C 6 OK OK 526 543 544 528 557 C5' U D 1 OK OK 556 573 574 558 588 C5' C D 2 OK OK 587 604 605 589 619 C5' C D 3 OK OK 618 635 636 620 650 C5' C D 4 OK OK 649 666 667 651 681 C5' C D 5 OK OK 680 697 698 682 712 C5' C D 6 OK OK 711 728 729 713 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P C A 2 distorted distorted 6 30 31 32 60 P C A 3 distorted distorted 37 61 62 63 91 P C A 4 distorted distorted 68 92 93 94 122 P C A 5 distorted distorted 99 123 124 125 153 P C A 6 distorted distorted 130 154 155 156 214 P C B 2 distorted distorted 191 215 216 217 245 P C B 3 distorted distorted 222 246 247 248 276 P C B 4 distorted distorted 253 277 278 279 307 P C B 5 distorted distorted 284 308 309 310 338 P C B 6 distorted distorted 315 339 340 341 399 P C C 2 distorted distorted 376 400 401 402 430 P C C 3 distorted distorted 407 431 432 433 461 P C C 4 distorted distorted 438 462 463 464 492 P C C 5 distorted distorted 469 493 494 495 523 P C C 6 distorted distorted 500 524 525 526 584 P C D 2 distorted distorted 561 585 586 587 615 P C D 3 distorted distorted 592 616 617 618 646 P C D 4 distorted distorted 623 647 648 649 677 P C D 5 distorted distorted 654 678 679 680 708 P C D 6 distorted distorted 685 709 710 711 ---------------------------------------------------------------------------------