ID code: '1YTY' 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' U C 1 beta 4 10 7 29 C1' G C 2 beta 24 30 27 52 C1' C C 3 beta 47 53 50 72 C1' U C 4 beta 67 73 70 92 C1' G C 5 beta 87 93 90 115 C1' U C 6 beta 110 116 113 135 C1' U C 7 beta 130 136 133 155 C1' U C 8 beta 150 156 153 175 C1' U C 9 beta 170 176 173 193 C1' U D 1 beta 188 194 191 213 C1' G D 2 beta 208 214 211 236 C1' C D 3 beta 231 237 234 256 C1' U D 4 beta 251 257 254 276 C1' G D 5 beta 271 277 274 299 C1' U D 6 beta 294 300 297 319 C1' U D 7 beta 314 320 317 339 C1' U D 8 beta 334 340 337 359 C1' U D 9 beta 354 360 357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U C 1 OK 9 5 8 27 C2' G C 2 OK 29 25 28 50 C2' C C 3 OK 52 48 51 70 C2' U C 4 OK 72 68 71 90 C2' G C 5 OK 92 88 91 113 C2' U C 6 OK 115 111 114 133 C2' U C 7 OK 135 131 134 153 C2' U C 8 OK 155 151 154 173 C2' U C 9 OK 175 171 174 191 C2' U D 1 OK 193 189 192 211 C2' G D 2 OK 213 209 212 234 C2' C D 3 OK 236 232 235 254 C2' U D 4 OK 256 252 255 274 C2' G D 5 OK 276 272 275 297 C2' U D 6 OK 299 295 298 317 C2' U D 7 OK 319 315 318 337 C2' U D 8 OK 339 335 338 357 C2' U D 9 OK 359 355 358 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U C 1 OK 3 6 7 25 C3' G C 2 OK 23 26 27 48 C3' C C 3 OK 46 49 50 68 C3' U C 4 OK 66 69 70 88 C3' G C 5 OK 86 89 90 111 C3' U C 6 OK 109 112 113 131 C3' U C 7 OK 129 132 133 151 C3' U C 8 OK 149 152 153 171 C3' U C 9 OK 169 172 173 189 C3' U D 1 OK 187 190 191 209 C3' G D 2 OK 207 210 211 232 C3' C D 3 OK 230 233 234 252 C3' U D 4 OK 250 253 254 272 C3' G D 5 OK 270 273 274 295 C3' U D 6 OK 293 296 297 315 C3' U D 7 OK 313 316 317 335 C3' U D 8 OK 333 336 337 355 C3' U D 9 OK 353 356 357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U C 1 OK 5 2 4 23 C4' G C 2 OK 25 22 24 46 C4' C C 3 OK 48 45 47 66 C4' U C 4 OK 68 65 67 86 C4' G C 5 OK 88 85 87 109 C4' U C 6 OK 111 108 110 129 C4' U C 7 OK 131 128 130 149 C4' U C 8 OK 151 148 150 169 C4' U C 9 OK 171 168 170 187 C4' U D 1 OK 189 186 188 207 C4' G D 2 OK 209 206 208 230 C4' C D 3 OK 232 229 231 250 C4' U D 4 OK 252 249 251 270 C4' G D 5 OK 272 269 271 293 C4' U D 6 OK 295 292 294 313 C4' U D 7 OK 315 312 314 333 C4' U D 8 OK 335 332 334 353 C4' U D 9 OK 355 352 354 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U C 1 1 3 22 C5' G C 2 21 23 45 C5' C C 3 44 46 65 C5' U C 4 64 66 85 C5' G C 5 84 86 108 C5' U C 6 107 109 128 C5' U C 7 127 129 148 C5' U C 8 147 149 168 C5' U C 9 167 169 186 C5' U D 1 185 187 206 C5' G D 2 205 207 229 C5' C D 3 228 230 249 C5' U D 4 248 250 269 C5' G D 5 268 270 292 C5' U D 6 291 293 312 C5' U D 7 311 313 332 C5' U D 8 331 333 352 C5' U D 9 351 353 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G C 2 distorted distorted 6 19 20 21 41 P C C 3 distorted distorted 26 42 43 44 61 P U C 4 distorted distorted 49 62 63 64 81 P G C 5 distorted distorted 69 82 83 84 104 P U C 6 distorted distorted 89 105 106 107 124 P U C 7 distorted distorted 112 125 126 127 144 P U C 8 distorted distorted 132 145 146 147 164 P U C 9 distorted distorted 152 165 166 167 202 P G D 2 distorted distorted 190 203 204 205 225 P C D 3 distorted distorted 210 226 227 228 245 P U D 4 distorted distorted 233 246 247 248 265 P G D 5 distorted distorted 253 266 267 268 288 P U D 6 distorted distorted 273 289 290 291 308 P U D 7 distorted distorted 296 309 310 311 328 P U D 8 distorted distorted 316 329 330 331 348 P U D 9 distorted distorted 336 349 350 351 ---------------------------------------------------------------------------------