ID code: '1FL8' 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 27 alpha beta 4 24 10 7 40 C1' C A 28 alpha beta 35 55 41 38 71 C1' A A 29 alpha beta 66 88 72 69 104 C1' G A 30 alpha beta 99 122 105 102 138 C1' A A 31 alpha beta 133 155 139 136 171 C1' C A 32 alpha beta 166 186 172 169 202 C1' U A 33 alpha beta 197 217 203 200 232 C1' U8U A 34 alpha beta 238 252 221 234 271 C1' U A 35 alpha beta 266 286 272 269 301 C1' U A 36 alpha beta 296 316 302 299 331 C1' T6A A 37 alpha beta 326 358 332 329 380 C1' A A 38 alpha beta 375 397 381 378 410 C1' PSU A 39 alpha beta 416 425 406 411 443 C1' C A 40 alpha beta 438 458 444 441 474 C1' U A 41 alpha beta 469 489 475 472 504 C1' G A 42 alpha beta 499 522 505 502 538 C1' A A 43 alpha beta 533 556 539 536 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 27 OK OK 9 5 22 8 38 C2' C A 28 OK OK 40 36 53 39 69 C2' A A 29 OK OK 71 67 86 70 102 C2' G A 30 OK OK 104 100 120 103 136 C2' A A 31 OK OK 138 134 153 137 169 C2' C A 32 OK OK 171 167 184 170 200 C2' U A 33 OK OK 202 198 215 201 234 C2' U8U A 34 OK OK 232 236 254 233 269 C2' U A 35 OK OK 271 267 284 270 299 C2' U A 36 OK OK 301 297 314 300 329 C2' T6A A 37 OK OK 331 327 356 330 378 C2' A A 38 OK OK 380 376 395 379 411 C2' PSU A 39 OK OK 410 413 426 412 441 C2' C A 40 OK OK 443 439 456 442 472 C2' U A 41 OK OK 474 470 487 473 502 C2' G A 42 OK OK 504 500 520 503 536 C2' A A 43 OK OK 538 534 554 537 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 27 OK OK 3 21 6 7 36 C3' C A 28 OK OK 34 52 37 38 67 C3' A A 29 OK OK 65 85 68 69 100 C3' G A 30 OK OK 98 119 101 102 134 C3' A A 31 OK OK 132 152 135 136 167 C3' C A 32 OK OK 165 183 168 169 198 C3' U A 33 OK OK 196 214 199 200 236 C3' U8U A 34 OK OK 237 255 235 234 267 C3' U A 35 OK OK 265 283 268 269 297 C3' U A 36 OK OK 295 313 298 299 327 C3' T6A A 37 OK OK 325 355 328 329 376 C3' A A 38 OK OK 374 394 377 378 413 C3' PSU A 39 OK OK 414 428 415 411 439 C3' C A 40 OK OK 437 455 440 441 470 C3' U A 41 OK OK 468 486 471 472 500 C3' G A 42 OK OK 498 519 501 502 534 C3' A A 43 OK OK 532 552 535 536 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 27 OK OK 5 20 2 4 34 C4' C A 28 OK OK 36 51 33 35 65 C4' A A 29 OK OK 67 84 64 66 98 C4' G A 30 OK OK 100 118 97 99 132 C4' A A 31 OK OK 134 151 131 133 165 C4' C A 32 OK OK 167 182 164 166 196 C4' U A 33 OK OK 198 213 195 197 237 C4' U8U A 34 OK OK 236 256 239 238 265 C4' U A 35 OK OK 267 282 264 266 295 C4' U A 36 OK OK 297 312 294 296 325 C4' T6A A 37 OK OK 327 354 324 326 374 C4' A A 38 OK OK 376 393 373 375 414 C4' PSU A 39 OK OK 413 429 417 416 437 C4' C A 40 OK OK 439 454 436 438 468 C4' U A 41 OK OK 470 485 467 469 498 C4' G A 42 OK OK 500 518 497 499 532 C4' A A 43 OK OK 534 551 531 533 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 27 OK OK 1 18 19 3 33 C5' C A 28 OK OK 32 49 50 34 64 C5' A A 29 OK OK 63 82 83 65 97 C5' G A 30 OK OK 96 116 117 98 131 C5' A A 31 OK OK 130 149 150 132 164 C5' C A 32 OK OK 163 180 181 165 195 C5' U A 33 OK OK 194 211 212 196 239 C5' U8U A 34 OK OK 240 257 258 237 264 C5' U A 35 OK OK 263 280 281 265 294 C5' U A 36 OK OK 293 310 311 295 324 C5' T6A A 37 OK OK 323 352 353 325 373 C5' A A 38 OK OK 372 391 392 374 417 C5' PSU A 39 OK OK 418 430 431 414 436 C5' C A 40 OK OK 435 452 453 437 467 C5' U A 41 OK OK 466 483 484 468 497 C5' G A 42 OK OK 496 516 517 498 531 C5' A A 43 OK OK 530 549 550 532 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P C A 28 distorted distorted 6 30 31 32 60 P A A 29 distorted distorted 37 61 62 63 93 P G A 30 distorted distorted 68 94 95 96 127 P A A 31 distorted distorted 101 128 129 130 160 P C A 32 distorted distorted 135 161 162 163 191 P U A 33 distorted distorted 168 192 193 194 241 P U8U A 34 distorted distorted 199 242 243 240 260 P U A 35 distorted distorted 235 261 262 263 290 P U A 36 distorted distorted 268 291 292 293 320 P T6A A 37 distorted distorted 298 321 322 323 369 P A A 38 distorted distorted 328 370 371 372 419 P PSU A 39 distorted distorted 377 420 421 418 432 P C A 40 distorted distorted 415 433 434 435 463 P U A 41 distorted distorted 440 464 465 466 493 P G A 42 distorted distorted 471 494 495 496 527 P A A 43 distorted distorted 501 528 529 530 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