ID code: '1VOP' 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 1 alpha beta 7 30 13 10 46 C1' A A 2 alpha beta 41 63 47 44 79 C1' C A 3 alpha beta 74 94 80 77 110 C1' U A 4 alpha beta 105 125 111 108 140 C1' G A 5 alpha beta 135 158 141 138 174 C1' G A 6 alpha beta 169 192 175 172 208 C1' G A 7 alpha beta 203 226 209 206 242 C1' G A 8 alpha beta 237 260 243 240 276 C1' C A 9 alpha beta 271 291 277 274 307 C1' G A 10 alpha beta 302 325 308 305 341 C1' G A 11 alpha beta 336 359 342 339 375 C1' U A 12 alpha beta 370 390 376 373 405 C1' C A 13 alpha beta 400 420 406 403 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' A A 2 OK OK 46 42 61 45 77 C2' C A 3 OK OK 79 75 92 78 108 C2' U A 4 OK OK 110 106 123 109 138 C2' G A 5 OK OK 140 136 156 139 172 C2' G A 6 OK OK 174 170 190 173 206 C2' G A 7 OK OK 208 204 224 207 240 C2' G A 8 OK OK 242 238 258 241 274 C2' C A 9 OK OK 276 272 289 275 305 C2' G A 10 OK OK 307 303 323 306 339 C2' G A 11 OK OK 341 337 357 340 373 C2' U A 12 OK OK 375 371 388 374 403 C2' C A 13 OK OK 405 401 418 404 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' A A 2 OK OK 40 60 43 44 75 C3' C A 3 OK OK 73 91 76 77 106 C3' U A 4 OK OK 104 122 107 108 136 C3' G A 5 OK OK 134 155 137 138 170 C3' G A 6 OK OK 168 189 171 172 204 C3' G A 7 OK OK 202 223 205 206 238 C3' G A 8 OK OK 236 257 239 240 272 C3' C A 9 OK OK 270 288 273 274 303 C3' G A 10 OK OK 301 322 304 305 337 C3' G A 11 OK OK 335 356 338 339 371 C3' U A 12 OK OK 369 387 372 373 401 C3' C A 13 OK OK 399 417 402 403 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' A A 2 OK OK 42 59 39 41 73 C4' C A 3 OK OK 75 90 72 74 104 C4' U A 4 OK OK 106 121 103 105 134 C4' G A 5 OK OK 136 154 133 135 168 C4' G A 6 OK OK 170 188 167 169 202 C4' G A 7 OK OK 204 222 201 203 236 C4' G A 8 OK OK 238 256 235 237 270 C4' C A 9 OK OK 272 287 269 271 301 C4' G A 10 OK OK 303 321 300 302 335 C4' G A 11 OK OK 337 355 334 336 369 C4' U A 12 OK OK 371 386 368 370 399 C4' C A 13 OK OK 401 416 398 400 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' A A 2 OK OK 38 57 58 40 72 C5' C A 3 OK OK 71 88 89 73 103 C5' U A 4 OK OK 102 119 120 104 133 C5' G A 5 OK OK 132 152 153 134 167 C5' G A 6 OK OK 166 186 187 168 201 C5' G A 7 OK OK 200 220 221 202 235 C5' G A 8 OK OK 234 254 255 236 269 C5' C A 9 OK OK 268 285 286 270 300 C5' G A 10 OK OK 299 319 320 301 334 C5' G A 11 OK OK 333 353 354 335 368 C5' U A 12 OK OK 367 384 385 369 398 C5' C A 13 OK OK 397 414 415 399 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 OK OK 2 3 4 35 P A A 2 distorted distorted 9 36 37 38 68 P C A 3 distorted distorted 43 69 70 71 99 P U A 4 distorted distorted 76 100 101 102 129 P G A 5 distorted distorted 107 130 131 132 163 P G A 6 distorted distorted 137 164 165 166 197 P G A 7 distorted distorted 171 198 199 200 231 P G A 8 distorted distorted 205 232 233 234 265 P C A 9 distorted distorted 239 266 267 268 296 P G A 10 distorted distorted 273 297 298 299 330 P G A 11 distorted distorted 304 331 332 333 364 P U A 12 distorted distorted 338 365 366 367 394 P C A 13 distorted distorted 372 395 396 397 ---------------------------------------------------------------------------------