ID code: '1SZY' 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 1 alpha beta 8 31 14 11 48 C1' G A 2 alpha beta 43 66 49 46 82 C1' C A 3 alpha beta 77 97 83 80 113 C1' A A 4 alpha beta 108 130 114 111 146 C1' G A 5 alpha beta 141 164 147 144 180 C1' G A 6 alpha beta 175 198 181 178 214 C1' G A 7 alpha beta 209 232 215 212 248 C1' C A 8 alpha beta 243 263 249 246 279 C1' U A 9 alpha beta 274 294 280 277 309 C1' C A 10 alpha beta 304 324 310 307 340 C1' A A 11 alpha beta 335 357 341 338 373 C1' U A 12 alpha beta 368 388 374 371 403 C1' A A 13 alpha beta 398 420 404 401 436 C1' A A 14 alpha beta 431 453 437 434 469 C1' C A 15 alpha beta 464 484 470 467 500 C1' C A 16 alpha beta 495 515 501 498 531 C1' C A 17 alpha beta 526 546 532 529 562 C1' U A 18 alpha beta 557 577 563 560 592 C1' G A 19 alpha beta 587 610 593 590 626 C1' C A 20 alpha beta 621 641 627 624 657 C1' C A 21 alpha beta 652 673 658 655 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 29 12 46 C2' G A 2 OK OK 48 44 64 47 80 C2' C A 3 OK OK 82 78 95 81 111 C2' A A 4 OK OK 113 109 128 112 144 C2' G A 5 OK OK 146 142 162 145 178 C2' G A 6 OK OK 180 176 196 179 212 C2' G A 7 OK OK 214 210 230 213 246 C2' C A 8 OK OK 248 244 261 247 277 C2' U A 9 OK OK 279 275 292 278 307 C2' C A 10 OK OK 309 305 322 308 338 C2' A A 11 OK OK 340 336 355 339 371 C2' U A 12 OK OK 373 369 386 372 401 C2' A A 13 OK OK 403 399 418 402 434 C2' A A 14 OK OK 436 432 451 435 467 C2' C A 15 OK OK 469 465 482 468 498 C2' C A 16 OK OK 500 496 513 499 529 C2' C A 17 OK OK 531 527 544 530 560 C2' U A 18 OK OK 562 558 575 561 590 C2' G A 19 OK OK 592 588 608 591 624 C2' C A 20 OK OK 626 622 639 625 655 C2' C A 21 OK OK 657 653 671 656 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' G A 2 OK OK 42 63 45 46 78 C3' C A 3 OK OK 76 94 79 80 109 C3' A A 4 OK OK 107 127 110 111 142 C3' G A 5 OK OK 140 161 143 144 176 C3' G A 6 OK OK 174 195 177 178 210 C3' G A 7 OK OK 208 229 211 212 244 C3' C A 8 OK OK 242 260 245 246 275 C3' U A 9 OK OK 273 291 276 277 305 C3' C A 10 OK OK 303 321 306 307 336 C3' A A 11 OK OK 334 354 337 338 369 C3' U A 12 OK OK 367 385 370 371 399 C3' A A 13 OK OK 397 417 400 401 432 C3' A A 14 OK OK 430 450 433 434 465 C3' C A 15 OK OK 463 481 466 467 496 C3' C A 16 OK OK 494 512 497 498 527 C3' C A 17 OK OK 525 543 528 529 558 C3' U A 18 OK OK 556 574 559 560 588 C3' G A 19 OK OK 586 607 589 590 622 C3' C A 20 OK OK 620 638 623 624 653 C3' C A 21 OK OK 651 669 654 655 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' G A 2 OK OK 44 62 41 43 76 C4' C A 3 OK OK 78 93 75 77 107 C4' A A 4 OK OK 109 126 106 108 140 C4' G A 5 OK OK 142 160 139 141 174 C4' G A 6 OK OK 176 194 173 175 208 C4' G A 7 OK OK 210 228 207 209 242 C4' C A 8 OK OK 244 259 241 243 273 C4' U A 9 OK OK 275 290 272 274 303 C4' C A 10 OK OK 305 320 302 304 334 C4' A A 11 OK OK 336 353 333 335 367 C4' U A 12 OK OK 369 384 366 368 397 C4' A A 13 OK OK 399 416 396 398 430 C4' A A 14 OK OK 432 449 429 431 463 C4' C A 15 OK OK 465 480 462 464 494 C4' C A 16 OK OK 496 511 493 495 525 C4' C A 17 OK OK 527 542 524 526 556 C4' U A 18 OK OK 558 573 555 557 586 C4' G A 19 OK OK 588 606 585 587 620 C4' C A 20 OK OK 622 637 619 621 651 C4' C A 21 OK OK 653 668 650 652 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' G A 2 OK OK 40 60 61 42 75 C5' C A 3 OK OK 74 91 92 76 106 C5' A A 4 OK OK 105 124 125 107 139 C5' G A 5 OK OK 138 158 159 140 173 C5' G A 6 OK OK 172 192 193 174 207 C5' G A 7 OK OK 206 226 227 208 241 C5' C A 8 OK OK 240 257 258 242 272 C5' U A 9 OK OK 271 288 289 273 302 C5' C A 10 OK OK 301 318 319 303 333 C5' A A 11 OK OK 332 351 352 334 366 C5' U A 12 OK OK 365 382 383 367 396 C5' A A 13 OK OK 395 414 415 397 429 C5' A A 14 OK OK 428 447 448 430 462 C5' C A 15 OK OK 461 478 479 463 493 C5' C A 16 OK OK 492 509 510 494 524 C5' C A 17 OK OK 523 540 541 525 555 C5' U A 18 OK OK 554 571 572 556 585 C5' G A 19 OK OK 584 604 605 586 619 C5' C A 20 OK OK 618 635 636 620 650 C5' C A 21 OK OK 649 666 667 651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 OK OK 3 4 5 37 P G A 2 distorted distorted 10 38 39 40 71 P C A 3 distorted distorted 45 72 73 74 102 P A A 4 distorted distorted 79 103 104 105 135 P G A 5 distorted distorted 110 136 137 138 169 P G A 6 distorted distorted 143 170 171 172 203 P G A 7 distorted distorted 177 204 205 206 237 P C A 8 distorted distorted 211 238 239 240 268 P U A 9 distorted distorted 245 269 270 271 298 P C A 10 distorted distorted 276 299 300 301 329 P A A 11 distorted distorted 306 330 331 332 362 P U A 12 distorted distorted 337 363 364 365 392 P A A 13 distorted distorted 370 393 394 395 425 P A A 14 distorted distorted 400 426 427 428 458 P C A 15 distorted distorted 433 459 460 461 489 P C A 16 distorted distorted 466 490 491 492 520 P C A 17 distorted distorted 497 521 522 523 551 P U A 18 distorted distorted 528 552 553 554 581 P G A 19 distorted distorted 559 582 583 584 615 P C A 20 distorted distorted 589 616 617 618 646 P C A 21 distorted distorted 623 647 648 649 ---------------------------------------------------------------------------------