ID code: '2DD3' 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' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' A A 6 alpha beta 170 192 176 173 208 C1' G A 7 alpha beta 203 226 209 206 242 C1' G A 8 alpha beta 237 260 243 240 276 C1' C A 9 alpha beta 271 291 277 274 307 C1' U A 10 alpha beta 302 323 308 305 336 C1' G B 11 alpha beta 331 354 337 334 371 C1' C B 12 alpha beta 366 386 372 369 402 C1' C B 13 alpha beta 397 417 403 400 433 C1' G B 14 alpha beta 428 451 434 431 467 C1' A B 15 alpha beta 462 484 468 465 500 C1' A B 16 alpha beta 495 517 501 498 533 C1' G B 17 alpha beta 528 551 534 531 567 C1' C B 18 alpha beta 562 582 568 565 598 C1' C B 19 alpha beta 593 613 599 596 627 C1' P5P B 20 alpha beta 633 642 626 628 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' A A 5 OK OK 142 138 157 141 173 C2' A A 6 OK OK 175 171 190 174 206 C2' G A 7 OK OK 208 204 224 207 240 C2' G A 8 OK OK 242 238 258 241 274 C2' C A 9 OK OK 276 272 289 275 305 C2' U A 10 OK OK 307 303 321 306 334 C2' G B 11 OK OK 336 332 352 335 369 C2' C B 12 OK OK 371 367 384 370 400 C2' C B 13 OK OK 402 398 415 401 431 C2' G B 14 OK OK 433 429 449 432 465 C2' A B 15 OK OK 467 463 482 466 498 C2' A B 16 OK OK 500 496 515 499 531 C2' G B 17 OK OK 533 529 549 532 565 C2' C B 18 OK OK 567 563 580 566 596 C2' C B 19 OK OK 598 594 611 597 628 C2' P5P B 20 OK OK 627 630 643 629 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' A A 5 OK OK 136 156 139 140 171 C3' A A 6 OK OK 169 189 172 173 204 C3' G A 7 OK OK 202 223 205 206 238 C3' G A 8 OK OK 236 257 239 240 272 C3' C A 9 OK OK 270 288 273 274 303 C3' U A 10 OK OK 301 319 304 305 332 C3' G B 11 OK OK 330 351 333 334 367 C3' C B 12 OK OK 365 383 368 369 398 C3' C B 13 OK OK 396 414 399 400 429 C3' G B 14 OK OK 427 448 430 431 463 C3' A B 15 OK OK 461 481 464 465 496 C3' A B 16 OK OK 494 514 497 498 529 C3' G B 17 OK OK 527 548 530 531 563 C3' C B 18 OK OK 561 579 564 565 594 C3' C B 19 OK OK 592 610 595 596 630 C3' P5P B 20 OK OK 632 645 631 628 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' A A 5 OK OK 138 155 135 137 169 C4' A A 6 OK OK 171 188 168 170 202 C4' G A 7 OK OK 204 222 201 203 236 C4' G A 8 OK OK 238 256 235 237 270 C4' C A 9 OK OK 272 287 269 271 301 C4' U A 10 OK OK 303 318 300 302 330 C4' G B 11 OK OK 332 350 329 331 365 C4' C B 12 OK OK 367 382 364 366 396 C4' C B 13 OK OK 398 413 395 397 427 C4' G B 14 OK OK 429 447 426 428 461 C4' A B 15 OK OK 463 480 460 462 494 C4' A B 16 OK OK 496 513 493 495 527 C4' G B 17 OK OK 529 547 526 528 561 C4' C B 18 OK OK 563 578 560 562 592 C4' C B 19 OK OK 594 609 591 593 632 C4' P5P B 20 OK OK 630 647 634 633 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' A A 5 OK OK 134 153 154 136 168 C5' A A 6 OK OK 167 186 187 169 201 C5' G A 7 OK OK 200 220 221 202 235 C5' G A 8 OK OK 234 254 255 236 269 C5' C A 9 OK OK 268 285 286 270 300 C5' U A 10 OK OK 299 316 317 301 329 C5' G B 11 OK OK 328 348 349 330 364 C5' C B 12 OK OK 363 380 381 365 395 C5' C B 13 OK OK 394 411 412 396 426 C5' G B 14 OK OK 425 445 446 427 460 C5' A B 15 OK OK 459 478 479 461 493 C5' A B 16 OK OK 492 511 512 494 526 C5' G B 17 OK OK 525 545 546 527 560 C5' C B 18 OK OK 559 576 577 561 591 C5' C B 19 OK OK 590 607 608 592 634 C5' P5P B 20 OK OK 635 648 649 632 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P A A 5 distorted distorted 105 132 133 134 164 P A A 6 distorted distorted 139 165 166 167 197 P G A 7 distorted distorted 172 198 199 200 231 P G A 8 distorted distorted 205 232 233 234 265 P C A 9 distorted distorted 239 266 267 268 296 P U A 10 distorted distorted 273 297 298 299 360 P C B 12 distorted distorted 333 361 362 363 391 P C B 13 distorted distorted 368 392 393 394 422 P G B 14 distorted distorted 399 423 424 425 456 P A B 15 distorted distorted 430 457 458 459 489 P A B 16 distorted distorted 464 490 491 492 522 P G B 17 distorted distorted 497 523 524 525 556 P C B 18 distorted distorted 530 557 558 559 587 P C B 19 distorted distorted 564 588 589 590 636 P P5P B 20 distorted distorted 595 637 638 635 ---------------------------------------------------------------------------------