ID code: '5LR3' 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 beta 4 10 7 33 C1' CBV A 2 beta 28 34 31 54 C1' C A 3 beta 49 55 52 74 C1' G A 4 beta 69 75 72 97 C1' G A 5 beta 92 98 95 120 C1' A A 6 beta 115 121 118 142 C1' U A 7 beta 137 143 140 162 C1' G A 8 beta 157 163 160 185 C1' G A 9 beta 180 186 183 208 C1' C A 10 beta 203 209 206 226 C1' G B 1 beta 221 227 224 250 C1' CBV B 2 beta 245 251 248 271 C1' C B 3 beta 266 272 269 291 C1' G B 4 beta 286 292 289 314 C1' G B 5 beta 309 315 312 337 C1' A B 6 beta 332 338 335 359 C1' U B 7 beta 354 360 357 379 C1' G B 8 beta 374 380 377 402 C1' G B 9 beta 397 403 400 425 C1' C B 10 beta 420 426 423 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 31 C2' CBV A 2 OK 33 29 32 52 C2' C A 3 OK 54 50 53 72 C2' G A 4 OK 74 70 73 95 C2' G A 5 OK 97 93 96 118 C2' A A 6 OK 120 116 119 140 C2' U A 7 OK 142 138 141 160 C2' G A 8 OK 162 158 161 183 C2' G A 9 OK 185 181 184 206 C2' C A 10 OK 208 204 207 224 C2' G B 1 OK 226 222 225 248 C2' CBV B 2 OK 250 246 249 269 C2' C B 3 OK 271 267 270 289 C2' G B 4 OK 291 287 290 312 C2' G B 5 OK 314 310 313 335 C2' A B 6 OK 337 333 336 357 C2' U B 7 OK 359 355 358 377 C2' G B 8 OK 379 375 378 400 C2' G B 9 OK 402 398 401 423 C2' C B 10 OK 425 421 424 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 29 C3' CBV A 2 OK 27 30 31 50 C3' C A 3 OK 48 51 52 70 C3' G A 4 OK 68 71 72 93 C3' G A 5 OK 91 94 95 116 C3' A A 6 OK 114 117 118 138 C3' U A 7 OK 136 139 140 158 C3' G A 8 OK 156 159 160 181 C3' G A 9 OK 179 182 183 204 C3' C A 10 OK 202 205 206 222 C3' G B 1 OK 220 223 224 246 C3' CBV B 2 OK 244 247 248 267 C3' C B 3 OK 265 268 269 287 C3' G B 4 OK 285 288 289 310 C3' G B 5 OK 308 311 312 333 C3' A B 6 OK 331 334 335 355 C3' U B 7 OK 353 356 357 375 C3' G B 8 OK 373 376 377 398 C3' G B 9 OK 396 399 400 421 C3' C B 10 OK 419 422 423 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 27 C4' CBV A 2 OK 29 26 28 48 C4' C A 3 OK 50 47 49 68 C4' G A 4 OK 70 67 69 91 C4' G A 5 OK 93 90 92 114 C4' A A 6 OK 116 113 115 136 C4' U A 7 OK 138 135 137 156 C4' G A 8 OK 158 155 157 179 C4' G A 9 OK 181 178 180 202 C4' C A 10 OK 204 201 203 220 C4' G B 1 OK 222 219 221 244 C4' CBV B 2 OK 246 243 245 265 C4' C B 3 OK 267 264 266 285 C4' G B 4 OK 287 284 286 308 C4' G B 5 OK 310 307 309 331 C4' A B 6 OK 333 330 332 353 C4' U B 7 OK 355 352 354 373 C4' G B 8 OK 375 372 374 396 C4' G B 9 OK 398 395 397 419 C4' C B 10 OK 421 418 420 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 26 C5' CBV A 2 25 27 47 C5' C A 3 46 48 67 C5' G A 4 66 68 90 C5' G A 5 89 91 113 C5' A A 6 112 114 135 C5' U A 7 134 136 155 C5' G A 8 154 156 178 C5' G A 9 177 179 201 C5' C A 10 200 202 219 C5' G B 1 218 220 243 C5' CBV B 2 242 244 264 C5' C B 3 263 265 284 C5' G B 4 283 285 307 C5' G B 5 306 308 330 C5' A B 6 329 331 352 C5' U B 7 351 353 372 C5' G B 8 371 373 395 C5' G B 9 394 396 418 C5' C B 10 417 419 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 22 P CBV A 2 distorted distorted 6 23 24 25 43 P C A 3 distorted distorted 30 44 45 46 63 P G A 4 distorted distorted 51 64 65 66 86 P G A 5 distorted distorted 71 87 88 89 109 P A A 6 distorted distorted 94 110 111 112 131 P U A 7 distorted distorted 117 132 133 134 151 P G A 8 distorted distorted 139 152 153 154 174 P G A 9 distorted distorted 159 175 176 177 197 P C A 10 distorted distorted 182 198 199 200 239 P CBV B 2 distorted distorted 223 240 241 242 260 P C B 3 distorted distorted 247 261 262 263 280 P G B 4 distorted distorted 268 281 282 283 303 P G B 5 distorted distorted 288 304 305 306 326 P A B 6 distorted distorted 311 327 328 329 348 P U B 7 distorted distorted 334 349 350 351 368 P G B 8 distorted distorted 356 369 370 371 391 P G B 9 distorted distorted 376 392 393 394 414 P C B 10 distorted distorted 399 415 416 417 ---------------------------------------------------------------------------------