ID code: '176D' 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' --------------------------------------------------------------------------------- 212 C1' G B 7 alpha beta 207 230 213 210 247 C1' A B 8 alpha beta 242 264 248 245 280 C1' G B 9 alpha beta 275 298 281 278 314 C1' U B 10 alpha beta 309 329 315 312 344 C1' U B 11 alpha beta 339 359 345 342 374 C1' C B 12 alpha beta 369 390 375 372 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 9 C2' GPN A 1 8 29 30 45 C2' APN A 2 44 63 64 78 C2' APN A 3 77 96 97 111 C2' CPN A 4 110 127 128 142 C2' TPN A 5 141 159 160 176 C2' CPN A 6 175 192 193 210 C2' G B 7 OK OK 212 208 228 211 245 C2' A B 8 OK OK 247 243 262 246 278 C2' G B 9 OK OK 280 276 296 279 312 C2' U B 10 OK OK 314 310 327 313 342 C2' U B 11 OK OK 344 340 357 343 372 C2' C B 12 OK OK 374 370 388 373 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' GPN A 1 9 44 C3' APN A 2 45 77 C3' APN A 3 78 110 C3' CPN A 4 111 141 C3' TPN A 5 142 175 C3' CPN A 6 176 208 C3' G B 7 OK OK 206 227 209 210 243 C3' A B 8 OK OK 241 261 244 245 276 C3' G B 9 OK OK 274 295 277 278 310 C3' U B 10 OK OK 308 326 311 312 340 C3' U B 11 OK OK 338 356 341 342 370 C3' C B 12 OK OK 368 386 371 372 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 206 C4' G B 7 OK OK 208 226 205 207 241 C4' A B 8 OK OK 243 260 240 242 274 C4' G B 9 OK OK 276 294 273 275 308 C4' U B 10 OK OK 310 325 307 309 338 C4' U B 11 OK OK 340 355 337 339 368 C4' C B 12 OK OK 370 385 367 369 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4 C5' GPN A 1 25 26 40 C5' APN A 2 59 60 73 C5' APN A 3 92 93 106 C5' CPN A 4 123 124 137 C5' TPN A 5 155 156 170 C5' CPN A 6 188 189 205 C5' G B 7 OK OK 204 224 225 206 240 C5' A B 8 OK OK 239 258 259 241 273 C5' G B 9 OK OK 272 292 293 274 307 C5' U B 10 OK OK 306 323 324 308 337 C5' U B 11 OK OK 336 353 354 338 367 C5' C B 12 OK OK 366 383 384 368 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 201 P G B 7 distorted distorted 202 203 204 236 P A B 8 distorted distorted 209 237 238 239 269 P G B 9 distorted distorted 244 270 271 272 303 P U B 10 distorted distorted 277 304 305 306 333 P U B 11 distorted distorted 311 334 335 336 363 P C B 12 distorted distorted 341 364 365 366 ---------------------------------------------------------------------------------