ID code: '2F87' 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 alpha beta 4 27 10 7 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' C A 3 alpha beta 72 92 78 75 108 C1' U A 4 alpha beta 103 123 109 106 138 C1' G A 5 alpha beta 133 156 139 136 172 C1' A A 6 alpha beta 167 189 173 170 205 C1' A A 7 alpha beta 200 222 206 203 238 C1' G A 8 alpha beta 233 256 239 236 272 C1' G A 9 alpha beta 267 290 273 270 306 C1' G A 10 alpha beta 301 324 307 304 340 C1' C A 11 alpha beta 335 355 341 338 371 C1' C A 12 alpha beta 366 386 372 369 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 25 8 41 C2' G A 2 OK OK 43 39 59 42 75 C2' C A 3 OK OK 77 73 90 76 106 C2' U A 4 OK OK 108 104 121 107 136 C2' G A 5 OK OK 138 134 154 137 170 C2' A A 6 OK OK 172 168 187 171 203 C2' A A 7 OK OK 205 201 220 204 236 C2' G A 8 OK OK 238 234 254 237 270 C2' G A 9 OK OK 272 268 288 271 304 C2' G A 10 OK OK 306 302 322 305 338 C2' C A 11 OK OK 340 336 353 339 369 C2' C A 12 OK OK 371 367 384 370 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' C A 3 OK OK 71 89 74 75 104 C3' U A 4 OK OK 102 120 105 106 134 C3' G A 5 OK OK 132 153 135 136 168 C3' A A 6 OK OK 166 186 169 170 201 C3' A A 7 OK OK 199 219 202 203 234 C3' G A 8 OK OK 232 253 235 236 268 C3' G A 9 OK OK 266 287 269 270 302 C3' G A 10 OK OK 300 321 303 304 336 C3' C A 11 OK OK 334 352 337 338 367 C3' C A 12 OK OK 365 383 368 369 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' C A 3 OK OK 73 88 70 72 102 C4' U A 4 OK OK 104 119 101 103 132 C4' G A 5 OK OK 134 152 131 133 166 C4' A A 6 OK OK 168 185 165 167 199 C4' A A 7 OK OK 201 218 198 200 232 C4' G A 8 OK OK 234 252 231 233 266 C4' G A 9 OK OK 268 286 265 267 300 C4' G A 10 OK OK 302 320 299 301 334 C4' C A 11 OK OK 336 351 333 335 365 C4' C A 12 OK OK 367 382 364 366 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 36 C5' G A 2 OK OK 35 55 56 37 70 C5' C A 3 OK OK 69 86 87 71 101 C5' U A 4 OK OK 100 117 118 102 131 C5' G A 5 OK OK 130 150 151 132 165 C5' A A 6 OK OK 164 183 184 166 198 C5' A A 7 OK OK 197 216 217 199 231 C5' G A 8 OK OK 230 250 251 232 265 C5' G A 9 OK OK 264 284 285 266 299 C5' G A 10 OK OK 298 318 319 300 333 C5' C A 11 OK OK 332 349 350 334 364 C5' C A 12 OK OK 363 380 381 365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P C A 3 distorted distorted 40 67 68 69 97 P U A 4 distorted distorted 74 98 99 100 127 P G A 5 distorted distorted 105 128 129 130 161 P A A 6 distorted distorted 135 162 163 164 194 P A A 7 distorted distorted 169 195 196 197 227 P G A 8 distorted distorted 202 228 229 230 261 P G A 9 distorted distorted 235 262 263 264 295 P G A 10 distorted distorted 269 296 297 298 329 P C A 11 distorted distorted 303 330 331 332 360 P C A 12 distorted distorted 337 361 362 363 ---------------------------------------------------------------------------------