ID code: '1LU3' 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' --------------------------------------------------------------------------------- 12 C1' G A 26 beta 7 13 10 35 C1' C A 27 beta 30 36 33 55 C1' C A 28 beta 50 56 53 75 C1' A A 29 beta 70 76 73 97 C1' G A 30 beta 92 98 95 120 C1' A A 31 beta 115 121 118 142 C1' C A 32 beta 137 143 140 162 C1' U A 33 beta 157 163 160 182 C1' G A 34 beta 177 183 180 205 C1' A A 35 beta 200 206 203 227 C1' A A 36 beta 222 228 225 249 C1' G A 37 beta 244 250 247 272 C1' A A 38 beta 267 273 270 291 C1' PSU A 39 beta 297 287 292 314 C1' C A 40 beta 309 315 312 334 C1' U A 41 beta 329 335 332 354 C1' G A 42 beta 349 355 352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 26 OK 12 8 11 33 C2' C A 27 OK 35 31 34 53 C2' C A 28 OK 55 51 54 73 C2' A A 29 OK 75 71 74 95 C2' G A 30 OK 97 93 96 118 C2' A A 31 OK 120 116 119 140 C2' C A 32 OK 142 138 141 160 C2' U A 33 OK 162 158 161 180 C2' G A 34 OK 182 178 181 203 C2' A A 35 OK 205 201 204 225 C2' A A 36 OK 227 223 226 247 C2' G A 37 OK 249 245 248 270 C2' A A 38 OK 272 268 271 292 C2' PSU A 39 OK 291 294 293 312 C2' C A 40 OK 314 310 313 332 C2' U A 41 OK 334 330 333 352 C2' G A 42 OK 354 350 353 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 26 OK 6 9 10 31 C3' C A 27 OK 29 32 33 51 C3' C A 28 OK 49 52 53 71 C3' A A 29 OK 69 72 73 93 C3' G A 30 OK 91 94 95 116 C3' A A 31 OK 114 117 118 138 C3' C A 32 OK 136 139 140 158 C3' U A 33 OK 156 159 160 178 C3' G A 34 OK 176 179 180 201 C3' A A 35 OK 199 202 203 223 C3' A A 36 OK 221 224 225 245 C3' G A 37 OK 243 246 247 268 C3' A A 38 OK 266 269 270 294 C3' PSU A 39 OK 295 296 292 310 C3' C A 40 OK 308 311 312 330 C3' U A 41 OK 328 331 332 350 C3' G A 42 OK 348 351 352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 26 OK 8 5 7 29 C4' C A 27 OK 31 28 30 49 C4' C A 28 OK 51 48 50 69 C4' A A 29 OK 71 68 70 91 C4' G A 30 OK 93 90 92 114 C4' A A 31 OK 116 113 115 136 C4' C A 32 OK 138 135 137 156 C4' U A 33 OK 158 155 157 176 C4' G A 34 OK 178 175 177 199 C4' A A 35 OK 201 198 200 221 C4' A A 36 OK 223 220 222 243 C4' G A 37 OK 245 242 244 266 C4' A A 38 OK 268 265 267 295 C4' PSU A 39 OK 294 298 297 308 C4' C A 40 OK 310 307 309 328 C4' U A 41 OK 330 327 329 348 C4' G A 42 OK 350 347 349 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 26 4 6 28 C5' C A 27 27 29 48 C5' C A 28 47 49 68 C5' A A 29 67 69 90 C5' G A 30 89 91 113 C5' A A 31 112 114 135 C5' C A 32 134 136 155 C5' U A 33 154 156 175 C5' G A 34 174 176 198 C5' A A 35 197 199 220 C5' A A 36 219 221 242 C5' G A 37 241 243 265 C5' A A 38 264 266 298 C5' PSU A 39 299 295 307 C5' C A 40 306 308 327 C5' U A 41 326 328 347 C5' G A 42 346 348 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 26 OK OK 2 3 4 24 P C A 27 distorted distorted 9 25 26 27 44 P C A 28 distorted distorted 32 45 46 47 64 P A A 29 distorted distorted 52 65 66 67 86 P G A 30 distorted distorted 72 87 88 89 109 P A A 31 distorted distorted 94 110 111 112 131 P C A 32 distorted distorted 117 132 133 134 151 P U A 33 distorted distorted 139 152 153 154 171 P G A 34 distorted distorted 159 172 173 174 194 P A A 35 distorted distorted 179 195 196 197 216 P A A 36 distorted distorted 202 217 218 219 238 P G A 37 distorted distorted 224 239 240 241 261 P A A 38 distorted distorted 246 262 263 264 300 P PSU A 39 distorted distorted 269 301 302 299 303 P C A 40 distorted distorted 296 304 305 306 323 P U A 41 distorted distorted 311 324 325 326 343 P G A 42 distorted distorted 331 344 345 346 ---------------------------------------------------------------------------------