ID code: '1FYL' 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' --------------------------------------------------------------------------------- 8 C1' A C 1 beta 4 9 7 29 C1' G C 2 beta 25 30 28 51 C1' G C 3 beta 47 52 50 73 C1' A C 4 beta 69 74 72 94 C1' A C 5 beta 90 95 93 115 C1' C C 6 beta 111 116 114 134 C1' G C 7 beta 130 135 133 156 C1' T C 8 beta 152 157 155 176 C1' T C 9 beta 172 177 175 196 C1' C C 10 beta 192 197 195 215 C1' C C 11 beta 211 216 214 234 C1' U C 12 beta 230 235 233 251 C1' A E 1 beta 247 252 250 272 C1' G E 2 beta 268 273 271 294 C1' G E 3 beta 290 295 293 316 C1' A E 4 beta 312 317 315 337 C1' A E 5 beta 333 338 336 358 C1' C E 6 beta 354 359 357 377 C1' G E 7 beta 373 378 376 399 C1' T E 8 beta 395 400 398 419 C1' T E 9 beta 415 420 418 439 C1' C E 10 beta 435 440 438 458 C1' C E 11 beta 454 459 457 477 C1' U E 12 beta 473 478 476 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A C 1 8 5 28 C2' G C 2 29 26 50 C2' G C 3 51 48 72 C2' A C 4 73 70 93 C2' A C 5 94 91 114 C2' C C 6 115 112 133 C2' G C 7 134 131 155 C2' T C 8 156 153 175 C2' T C 9 176 173 195 C2' C C 10 196 193 214 C2' C C 11 215 212 233 C2' U C 12 234 231 250 C2' A E 1 251 248 271 C2' G E 2 272 269 293 C2' G E 3 294 291 315 C2' A E 4 316 313 336 C2' A E 5 337 334 357 C2' C E 6 358 355 376 C2' G E 7 377 374 398 C2' T E 8 399 396 418 C2' T E 9 419 416 438 C2' C E 10 439 436 457 C2' C E 11 458 455 476 C2' U E 12 477 474 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A C 1 OK 3 6 7 26 C3' G C 2 OK 24 27 28 48 C3' G C 3 OK 46 49 50 70 C3' A C 4 OK 68 71 72 91 C3' A C 5 OK 89 92 93 112 C3' C C 6 OK 110 113 114 131 C3' G C 7 OK 129 132 133 153 C3' T C 8 OK 151 154 155 173 C3' T C 9 OK 171 174 175 193 C3' C C 10 OK 191 194 195 212 C3' C C 11 OK 210 213 214 231 C3' U C 12 OK 229 232 233 248 C3' A E 1 OK 246 249 250 269 C3' G E 2 OK 267 270 271 291 C3' G E 3 OK 289 292 293 313 C3' A E 4 OK 311 314 315 334 C3' A E 5 OK 332 335 336 355 C3' C E 6 OK 353 356 357 374 C3' G E 7 OK 372 375 376 396 C3' T E 8 OK 394 397 398 416 C3' T E 9 OK 414 417 418 436 C3' C E 10 OK 434 437 438 455 C3' C E 11 OK 453 456 457 474 C3' U E 12 OK 472 475 476 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A C 1 OK 5 2 4 24 C4' G C 2 OK 26 23 25 46 C4' G C 3 OK 48 45 47 68 C4' A C 4 OK 70 67 69 89 C4' A C 5 OK 91 88 90 110 C4' C C 6 OK 112 109 111 129 C4' G C 7 OK 131 128 130 151 C4' T C 8 OK 153 150 152 171 C4' T C 9 OK 173 170 172 191 C4' C C 10 OK 193 190 192 210 C4' C C 11 OK 212 209 211 229 C4' U C 12 OK 231 228 230 246 C4' A E 1 OK 248 245 247 267 C4' G E 2 OK 269 266 268 289 C4' G E 3 OK 291 288 290 311 C4' A E 4 OK 313 310 312 332 C4' A E 5 OK 334 331 333 353 C4' C E 6 OK 355 352 354 372 C4' G E 7 OK 374 371 373 394 C4' T E 8 OK 396 393 395 414 C4' T E 9 OK 416 413 415 434 C4' C E 10 OK 436 433 435 453 C4' C E 11 OK 455 452 454 472 C4' U E 12 OK 474 471 473 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A C 1 1 3 23 C5' G C 2 22 24 45 C5' G C 3 44 46 67 C5' A C 4 66 68 88 C5' A C 5 87 89 109 C5' C C 6 108 110 128 C5' G C 7 127 129 150 C5' T C 8 149 151 170 C5' T C 9 169 171 190 C5' C C 10 189 191 209 C5' C C 11 208 210 228 C5' U C 12 227 229 245 C5' A E 1 244 246 266 C5' G E 2 265 267 288 C5' G E 3 287 289 310 C5' A E 4 309 311 331 C5' A E 5 330 332 352 C5' C E 6 351 353 371 C5' G E 7 370 372 393 C5' T E 8 392 394 413 C5' T E 9 412 414 433 C5' C E 10 432 434 452 C5' C E 11 451 453 471 C5' U E 12 470 472 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P G C 2 distorted distorted 6 20 21 22 41 P G C 3 distorted distorted 27 42 43 44 63 P A C 4 distorted distorted 49 64 65 66 84 P A C 5 distorted distorted 71 85 86 87 105 P C C 6 distorted distorted 92 106 107 108 124 P G C 7 distorted distorted 113 125 126 127 146 P T C 8 distorted distorted 132 147 148 149 166 P T C 9 distorted distorted 154 167 168 169 186 P C C 10 distorted distorted 174 187 188 189 205 P C C 11 distorted distorted 194 206 207 208 224 P U C 12 distorted distorted 213 225 226 227 262 P G E 2 distorted distorted 249 263 264 265 284 P G E 3 distorted distorted 270 285 286 287 306 P A E 4 distorted distorted 292 307 308 309 327 P A E 5 distorted distorted 314 328 329 330 348 P C E 6 distorted distorted 335 349 350 351 367 P G E 7 distorted distorted 356 368 369 370 389 P T E 8 distorted distorted 375 390 391 392 409 P T E 9 distorted distorted 397 410 411 412 429 P C E 10 distorted distorted 417 430 431 432 448 P C E 11 distorted distorted 437 449 450 451 467 P U E 12 distorted distorted 456 468 469 470 ---------------------------------------------------------------------------------