ID code: '1O3S' 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 B -2 beta 4 9 7 29 C1' A B -1 beta 25 30 28 50 C1' A B 1 beta 46 51 49 71 C1' A B 2 beta 67 72 70 92 C1' A B 3 beta 88 93 91 113 C1' T B 4 beta 109 114 112 133 C1' G B 5 beta 129 134 132 155 C1' C B 6 beta 151 156 154 174 C1' G B 7 beta 170 175 173 196 C1' A B 8 beta 192 197 195 217 C1' T B 9 beta 213 218 216 238 C1' A C 9 beta 234 239 237 259 C1' T C 8 beta 255 260 258 279 C1' C C 7 beta 275 280 278 298 C1' G C 6 beta 294 299 297 320 C1' C C 5 beta 316 321 319 339 C1' A C 4 beta 335 340 338 360 C1' T C 3 beta 356 361 359 380 C1' T C 2 beta 376 381 379 400 C1' T C 1 beta 396 401 399 420 C1' T C -1 beta 416 421 419 440 C1' T C -2 beta 436 441 439 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A B -2 8 5 28 C2' A B -1 29 26 49 C2' A B 1 50 47 70 C2' A B 2 71 68 91 C2' A B 3 92 89 112 C2' T B 4 113 110 132 C2' G B 5 133 130 154 C2' C B 6 155 152 173 C2' G B 7 174 171 195 C2' A B 8 196 193 216 C2' T B 9 217 214 237 C2' A C 9 238 235 258 C2' T C 8 259 256 278 C2' C C 7 279 276 297 C2' G C 6 298 295 319 C2' C C 5 320 317 338 C2' A C 4 339 336 359 C2' T C 3 360 357 379 C2' T C 2 380 377 399 C2' T C 1 400 397 419 C2' T C -1 420 417 439 C2' T C -2 440 437 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A B -2 OK 3 6 7 26 C3' A B -1 OK 24 27 28 47 C3' A B 1 OK 45 48 49 68 C3' A B 2 OK 66 69 70 89 C3' A B 3 OK 87 90 91 110 C3' T B 4 OK 108 111 112 130 C3' G B 5 OK 128 131 132 152 C3' C B 6 OK 150 153 154 171 C3' G B 7 OK 169 172 173 193 C3' A B 8 OK 191 194 195 214 C3' T B 9 OK 212 215 216 235 C3' A C 9 OK 233 236 237 256 C3' T C 8 OK 254 257 258 276 C3' C C 7 OK 274 277 278 295 C3' G C 6 OK 293 296 297 317 C3' C C 5 OK 315 318 319 336 C3' A C 4 OK 334 337 338 357 C3' T C 3 OK 355 358 359 377 C3' T C 2 OK 375 378 379 397 C3' T C 1 OK 395 398 399 417 C3' T C -1 OK 415 418 419 437 C3' T C -2 OK 435 438 439 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A B -2 OK 5 2 4 24 C4' A B -1 OK 26 23 25 45 C4' A B 1 OK 47 44 46 66 C4' A B 2 OK 68 65 67 87 C4' A B 3 OK 89 86 88 108 C4' T B 4 OK 110 107 109 128 C4' G B 5 OK 130 127 129 150 C4' C B 6 OK 152 149 151 169 C4' G B 7 OK 171 168 170 191 C4' A B 8 OK 193 190 192 212 C4' T B 9 OK 214 211 213 233 C4' A C 9 OK 235 232 234 254 C4' T C 8 OK 256 253 255 274 C4' C C 7 OK 276 273 275 293 C4' G C 6 OK 295 292 294 315 C4' C C 5 OK 317 314 316 334 C4' A C 4 OK 336 333 335 355 C4' T C 3 OK 357 354 356 375 C4' T C 2 OK 377 374 376 395 C4' T C 1 OK 397 394 396 415 C4' T C -1 OK 417 414 416 435 C4' T C -2 OK 437 434 436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A B -2 1 3 23 C5' A B -1 22 24 44 C5' A B 1 43 45 65 C5' A B 2 64 66 86 C5' A B 3 85 87 107 C5' T B 4 106 108 127 C5' G B 5 126 128 149 C5' C B 6 148 150 168 C5' G B 7 167 169 190 C5' A B 8 189 191 211 C5' T B 9 210 212 232 C5' A C 9 231 233 253 C5' T C 8 252 254 273 C5' C C 7 272 274 292 C5' G C 6 291 293 314 C5' C C 5 313 315 333 C5' A C 4 332 334 354 C5' T C 3 353 355 374 C5' T C 2 373 375 394 C5' T C 1 393 395 414 C5' T C -1 413 415 434 C5' T C -2 433 435 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P A B -1 distorted distorted 6 20 21 22 40 P A B 1 distorted distorted 27 41 42 43 61 P A B 2 distorted distorted 48 62 63 64 82 P A B 3 distorted distorted 69 83 84 85 103 P T B 4 distorted distorted 90 104 105 106 123 P G B 5 distorted distorted 111 124 125 126 145 P C B 6 distorted distorted 131 146 147 148 164 P G B 7 distorted distorted 153 165 166 167 186 P A B 8 distorted distorted 172 187 188 189 207 P T B 9 distorted distorted 194 208 209 210 228 P A C 9 distorted distorted 229 230 231 249 P T C 8 distorted distorted 236 250 251 252 269 P C C 7 distorted distorted 257 270 271 272 288 P G C 6 distorted distorted 277 289 290 291 310 P C C 5 distorted distorted 296 311 312 313 329 P A C 4 distorted distorted 318 330 331 332 350 P T C 3 distorted distorted 337 351 352 353 370 P T C 2 distorted distorted 358 371 372 373 390 P T C 1 distorted distorted 378 391 392 393 410 P T C -1 distorted distorted 398 411 412 413 430 P T C -2 distorted distorted 418 431 432 433 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