ID code: '1LPW' 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 103 126 109 106 139 C1' PSU A 5 alpha beta 145 154 135 140 172 C1' A A 6 alpha beta 167 189 173 170 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' U A 8 alpha beta 234 254 240 237 269 C1' A A 9 alpha beta 264 287 270 267 301 C1' U B 1 alpha beta 296 316 302 299 332 C1' A B 2 alpha beta 327 349 333 330 365 C1' C B 3 alpha beta 360 380 366 363 396 C1' U B 4 alpha beta 391 411 397 394 426 C1' A B 5 alpha beta 421 443 427 424 459 C1' A B 6 alpha beta 454 476 460 457 492 C1' C B 7 alpha beta 487 507 493 490 523 C1' A B 8 alpha beta 518 540 524 521 556 C1' C B 9 alpha beta 551 571 557 554 587 C1' C B 10 alpha beta 582 603 588 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' PSU A 5 OK OK 139 142 155 141 170 C2' A A 6 OK OK 172 168 187 171 203 C2' G A 7 OK OK 205 201 221 204 237 C2' U A 8 OK OK 239 235 252 238 267 C2' A A 9 OK OK 269 265 285 268 299 C2' U B 1 OK OK 301 297 314 300 330 C2' A B 2 OK OK 332 328 347 331 363 C2' C B 3 OK OK 365 361 378 364 394 C2' U B 4 OK OK 396 392 409 395 424 C2' A B 5 OK OK 426 422 441 425 457 C2' A B 6 OK OK 459 455 474 458 490 C2' C B 7 OK OK 492 488 505 491 521 C2' A B 8 OK OK 523 519 538 522 554 C2' C B 9 OK OK 556 552 569 555 585 C2' C B 10 OK OK 587 583 601 586 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 102 123 105 106 142 C3' PSU A 5 OK OK 143 157 144 140 168 C3' A A 6 OK OK 166 186 169 170 201 C3' G A 7 OK OK 199 220 202 203 235 C3' U A 8 OK OK 233 251 236 237 265 C3' A A 9 OK OK 263 283 266 267 297 C3' U B 1 OK OK 295 313 298 299 328 C3' A B 2 OK OK 326 346 329 330 361 C3' C B 3 OK OK 359 377 362 363 392 C3' U B 4 OK OK 390 408 393 394 422 C3' A B 5 OK OK 420 440 423 424 455 C3' A B 6 OK OK 453 473 456 457 488 C3' C B 7 OK OK 486 504 489 490 519 C3' A B 8 OK OK 517 537 520 521 552 C3' C B 9 OK OK 550 568 553 554 583 C3' C B 10 OK OK 581 599 584 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 104 122 101 103 143 C4' PSU A 5 OK OK 142 158 146 145 166 C4' A A 6 OK OK 168 185 165 167 199 C4' G A 7 OK OK 201 219 198 200 233 C4' U A 8 OK OK 235 250 232 234 263 C4' A A 9 OK OK 265 282 262 264 295 C4' U B 1 OK OK 297 312 294 296 326 C4' A B 2 OK OK 328 345 325 327 359 C4' C B 3 OK OK 361 376 358 360 390 C4' U B 4 OK OK 392 407 389 391 420 C4' A B 5 OK OK 422 439 419 421 453 C4' A B 6 OK OK 455 472 452 454 486 C4' C B 7 OK OK 488 503 485 487 517 C4' A B 8 OK OK 519 536 516 518 550 C4' C B 9 OK OK 552 567 549 551 581 C4' C B 10 OK OK 583 598 580 582 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 100 120 121 102 146 C5' PSU A 5 OK OK 147 159 160 143 165 C5' A A 6 OK OK 164 183 184 166 198 C5' G A 7 OK OK 197 217 218 199 232 C5' U A 8 OK OK 231 248 249 233 262 C5' A A 9 OK OK 261 280 281 263 294 C5' U B 1 OK OK 293 310 311 295 325 C5' A B 2 OK OK 324 343 344 326 358 C5' C B 3 OK OK 357 374 375 359 389 C5' U B 4 OK OK 388 405 406 390 419 C5' A B 5 OK OK 418 437 438 420 452 C5' A B 6 OK OK 451 470 471 453 485 C5' C B 7 OK OK 484 501 502 486 516 C5' A B 8 OK OK 515 534 535 517 549 C5' C B 9 OK OK 548 565 566 550 580 C5' C B 10 OK OK 579 596 597 581 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 99 100 148 P PSU A 5 distorted distorted 105 149 150 147 161 P A A 6 distorted distorted 144 162 163 164 194 P G A 7 distorted distorted 169 195 196 197 228 P U A 8 distorted distorted 202 229 230 231 258 P A A 9 distorted distorted 236 259 260 261 321 P A B 2 distorted distorted 298 322 323 324 354 P C B 3 distorted distorted 329 355 356 357 385 P U B 4 distorted distorted 362 386 387 388 415 P A B 5 distorted distorted 393 416 417 418 448 P A B 6 distorted distorted 423 449 450 451 481 P C B 7 distorted distorted 456 482 483 484 512 P A B 8 distorted distorted 489 513 514 515 545 P C B 9 distorted distorted 520 546 547 548 576 P C B 10 distorted distorted 553 577 578 579 ---------------------------------------------------------------------------------