ID code: '2DD1' 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' G A 5 alpha beta 137 160 143 140 176 C1' A A 6 alpha beta 171 193 177 174 209 C1' G A 7 alpha beta 204 227 210 207 243 C1' G A 8 alpha beta 238 261 244 241 277 C1' C A 9 alpha beta 272 292 278 275 308 C1' U A 10 alpha beta 303 324 309 306 337 C1' G B 11 alpha beta 332 355 338 335 372 C1' C B 12 alpha beta 367 387 373 370 403 C1' C B 13 alpha beta 398 418 404 401 434 C1' G B 14 alpha beta 429 452 435 432 468 C1' A B 15 alpha beta 463 485 469 466 501 C1' A B 16 alpha beta 496 518 502 499 534 C1' A B 17 alpha beta 529 551 535 532 567 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' G A 5 OK OK 142 138 158 141 174 C2' A A 6 OK OK 176 172 191 175 207 C2' G A 7 OK OK 209 205 225 208 241 C2' G A 8 OK OK 243 239 259 242 275 C2' C A 9 OK OK 277 273 290 276 306 C2' U A 10 OK OK 308 304 322 307 335 C2' G B 11 OK OK 337 333 353 336 370 C2' C B 12 OK OK 372 368 385 371 401 C2' C B 13 OK OK 403 399 416 402 432 C2' G B 14 OK OK 434 430 450 433 466 C2' A B 15 OK OK 468 464 483 467 499 C2' A B 16 OK OK 501 497 516 500 532 C2' A B 17 OK OK 534 530 549 533 565 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' G A 5 OK OK 136 157 139 140 172 C3' A A 6 OK OK 170 190 173 174 205 C3' G A 7 OK OK 203 224 206 207 239 C3' G A 8 OK OK 237 258 240 241 273 C3' C A 9 OK OK 271 289 274 275 304 C3' U A 10 OK OK 302 320 305 306 333 C3' G B 11 OK OK 331 352 334 335 368 C3' C B 12 OK OK 366 384 369 370 399 C3' C B 13 OK OK 397 415 400 401 430 C3' G B 14 OK OK 428 449 431 432 464 C3' A B 15 OK OK 462 482 465 466 497 C3' A B 16 OK OK 495 515 498 499 530 C3' A B 17 OK OK 528 548 531 532 563 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' G A 5 OK OK 138 156 135 137 170 C4' A A 6 OK OK 172 189 169 171 203 C4' G A 7 OK OK 205 223 202 204 237 C4' G A 8 OK OK 239 257 236 238 271 C4' C A 9 OK OK 273 288 270 272 302 C4' U A 10 OK OK 304 319 301 303 331 C4' G B 11 OK OK 333 351 330 332 366 C4' C B 12 OK OK 368 383 365 367 397 C4' C B 13 OK OK 399 414 396 398 428 C4' G B 14 OK OK 430 448 427 429 462 C4' A B 15 OK OK 464 481 461 463 495 C4' A B 16 OK OK 497 514 494 496 528 C4' A B 17 OK OK 530 547 527 529 561 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' G A 5 OK OK 134 154 155 136 169 C5' A A 6 OK OK 168 187 188 170 202 C5' G A 7 OK OK 201 221 222 203 236 C5' G A 8 OK OK 235 255 256 237 270 C5' C A 9 OK OK 269 286 287 271 301 C5' U A 10 OK OK 300 317 318 302 330 C5' G B 11 OK OK 329 349 350 331 365 C5' C B 12 OK OK 364 381 382 366 396 C5' C B 13 OK OK 395 412 413 397 427 C5' G B 14 OK OK 426 446 447 428 461 C5' A B 15 OK OK 460 479 480 462 494 C5' A B 16 OK OK 493 512 513 495 527 C5' A B 17 OK OK 526 545 546 528 560 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 G A 5 distorted distorted 105 132 133 134 165 P A A 6 distorted distorted 139 166 167 168 198 P G A 7 distorted distorted 173 199 200 201 232 P G A 8 distorted distorted 206 233 234 235 266 P C A 9 distorted distorted 240 267 268 269 297 P U A 10 distorted distorted 274 298 299 300 361 P C B 12 distorted distorted 334 362 363 364 392 P C B 13 distorted distorted 369 393 394 395 423 P G B 14 distorted distorted 400 424 425 426 457 P A B 15 distorted distorted 431 458 459 460 490 P A B 16 distorted distorted 465 491 492 493 523 P A B 17 distorted distorted 498 524 525 526 556 P C B 18 distorted distorted 531 557 558 559 587 P C B 19 distorted distorted 564 588 589 590 636 P P5P B 20 distorted distorted 595 637 638 635 ---------------------------------------------------------------------------------