ID code: '2A0P' 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' C A 1 beta 4 10 7 33 C1' C A 2 beta 28 34 31 49 C1' S4C A 3 45 54 79 C1' C A 4 beta 74 80 77 102 C1' G A 5 beta 97 103 100 129 C1' G A 6 beta 124 130 127 156 C1' G A 7 beta 151 157 154 183 C1' G A 8 beta 178 184 181 208 C1' C B 9 beta 203 209 206 232 C1' C B 10 beta 227 233 230 248 C1' S4C B 11 244 253 278 C1' C B 12 beta 273 279 276 301 C1' G B 13 beta 296 302 299 328 C1' G B 14 beta 323 329 326 355 C1' G B 15 beta 350 356 353 382 C1' G B 16 beta 377 383 380 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 31 C2' C A 2 OK 33 29 32 54 C2' S4C A 3 distorted OK 49 56 67 55 77 C2' C A 4 OK 79 75 78 100 C2' G A 5 OK 102 98 101 127 C2' G A 6 OK 129 125 128 154 C2' G A 7 OK 156 152 155 181 C2' G A 8 OK 183 179 182 206 C2' C B 9 OK 208 204 207 230 C2' C B 10 OK 232 228 231 253 C2' S4C B 11 distorted OK 248 255 266 254 276 C2' C B 12 OK 278 274 277 299 C2' G B 13 OK 301 297 300 326 C2' G B 14 OK 328 324 327 353 C2' G B 15 OK 355 351 354 380 C2' G B 16 OK 382 378 381 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 29 C3' C A 2 OK 27 30 31 56 C3' S4C A 3 OK 58 57 54 75 C3' C A 4 OK 73 76 77 98 C3' G A 5 OK 96 99 100 125 C3' G A 6 OK 123 126 127 152 C3' G A 7 OK 150 153 154 179 C3' G A 8 OK 177 180 181 204 C3' C B 9 OK 202 205 206 228 C3' C B 10 OK 226 229 230 255 C3' S4C B 11 OK 257 256 253 274 C3' C B 12 OK 272 275 276 297 C3' G B 13 OK 295 298 299 324 C3' G B 14 OK 322 325 326 351 C3' G B 15 OK 349 352 353 378 C3' G B 16 OK 376 379 380 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 27 C4' C A 2 OK 29 26 28 58 C4' S4C A 3 56 61 73 C4' C A 4 OK 75 72 74 96 C4' G A 5 OK 98 95 97 123 C4' G A 6 OK 125 122 124 150 C4' G A 7 OK 152 149 151 177 C4' G A 8 OK 179 176 178 202 C4' C B 9 OK 204 201 203 226 C4' C B 10 OK 228 225 227 257 C4' S4C B 11 255 260 272 C4' C B 12 OK 274 271 273 295 C4' G B 13 OK 297 294 296 322 C4' G B 14 OK 324 321 323 349 C4' G B 15 OK 351 348 350 376 C4' G B 16 OK 378 375 377 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 26 C5' C A 2 25 27 61 C5' S4C A 3 62 58 72 C5' C A 4 71 73 95 C5' G A 5 94 96 122 C5' G A 6 121 123 149 C5' G A 7 148 150 176 C5' G A 8 175 177 201 C5' C B 9 200 202 225 C5' C B 10 224 226 260 C5' S4C B 11 261 257 271 C5' C B 12 270 272 294 C5' G B 13 293 295 321 C5' G B 14 320 322 348 C5' G B 15 347 349 375 C5' G B 16 374 376 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 22 P C A 2 distorted distorted 6 23 24 25 64 P S4C A 3 distorted distorted 30 60 63 62 68 P C A 4 distorted distorted 57 69 70 71 91 P G A 5 distorted distorted 76 92 93 94 118 P G A 6 distorted distorted 99 119 120 121 145 P G A 7 distorted distorted 126 146 147 148 172 P G A 8 distorted distorted 153 173 174 175 221 P C B 10 distorted distorted 205 222 223 224 263 P S4C B 11 distorted distorted 229 259 262 261 267 P C B 12 distorted distorted 256 268 269 270 290 P G B 13 distorted distorted 275 291 292 293 317 P G B 14 distorted distorted 298 318 319 320 344 P G B 15 distorted distorted 325 345 346 347 371 P G B 16 distorted distorted 352 372 373 374 ---------------------------------------------------------------------------------