ID code: '1HS8' 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 44 C1' C A 2 alpha beta 39 59 45 42 75 C1' G A 3 alpha beta 70 93 76 73 109 C1' U A 4 alpha beta 104 124 110 107 139 C1' C A 5 alpha beta 134 154 140 137 170 C1' A A 6 alpha beta 165 187 171 168 203 C1' A A 7 alpha beta 198 220 204 201 236 C1' U A 8 alpha beta 231 251 237 234 266 C1' U A 9 alpha beta 261 281 267 264 296 C1' C A 10 alpha beta 291 311 297 294 327 C1' G A 11 alpha beta 322 345 328 325 361 C1' C A 12 alpha beta 356 376 362 359 392 C1' A A 13 alpha beta 387 410 393 390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 42 C2' C A 2 OK OK 44 40 57 43 73 C2' G A 3 OK OK 75 71 91 74 107 C2' U A 4 OK OK 109 105 122 108 137 C2' C A 5 OK OK 139 135 152 138 168 C2' A A 6 OK OK 170 166 185 169 201 C2' A A 7 OK OK 203 199 218 202 234 C2' U A 8 OK OK 236 232 249 235 264 C2' U A 9 OK OK 266 262 279 265 294 C2' C A 10 OK OK 296 292 309 295 325 C2' G A 11 OK OK 327 323 343 326 359 C2' C A 12 OK OK 361 357 374 360 390 C2' A A 13 OK OK 392 388 408 391 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' G A 3 OK OK 69 90 72 73 105 C3' U A 4 OK OK 103 121 106 107 135 C3' C A 5 OK OK 133 151 136 137 166 C3' A A 6 OK OK 164 184 167 168 199 C3' A A 7 OK OK 197 217 200 201 232 C3' U A 8 OK OK 230 248 233 234 262 C3' U A 9 OK OK 260 278 263 264 292 C3' C A 10 OK OK 290 308 293 294 323 C3' G A 11 OK OK 321 342 324 325 357 C3' C A 12 OK OK 355 373 358 359 388 C3' A A 13 OK OK 386 406 389 390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' G A 3 OK OK 71 89 68 70 103 C4' U A 4 OK OK 105 120 102 104 133 C4' C A 5 OK OK 135 150 132 134 164 C4' A A 6 OK OK 166 183 163 165 197 C4' A A 7 OK OK 199 216 196 198 230 C4' U A 8 OK OK 232 247 229 231 260 C4' U A 9 OK OK 262 277 259 261 290 C4' C A 10 OK OK 292 307 289 291 321 C4' G A 11 OK OK 323 341 320 322 355 C4' C A 12 OK OK 357 372 354 356 386 C4' A A 13 OK OK 388 405 385 387 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 37 C5' C A 2 OK OK 36 53 54 38 68 C5' G A 3 OK OK 67 87 88 69 102 C5' U A 4 OK OK 101 118 119 103 132 C5' C A 5 OK OK 131 148 149 133 163 C5' A A 6 OK OK 162 181 182 164 196 C5' A A 7 OK OK 195 214 215 197 229 C5' U A 8 OK OK 228 245 246 230 259 C5' U A 9 OK OK 258 275 276 260 289 C5' C A 10 OK OK 288 305 306 290 320 C5' G A 11 OK OK 319 339 340 321 354 C5' C A 12 OK OK 353 370 371 355 385 C5' A A 13 OK OK 384 403 404 386 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P G A 3 distorted distorted 41 65 66 67 98 P U A 4 distorted distorted 72 99 100 101 128 P C A 5 distorted distorted 106 129 130 131 159 P A A 6 distorted distorted 136 160 161 162 192 P A A 7 distorted distorted 167 193 194 195 225 P U A 8 distorted distorted 200 226 227 228 255 P U A 9 distorted distorted 233 256 257 258 285 P C A 10 distorted distorted 263 286 287 288 316 P G A 11 distorted distorted 293 317 318 319 350 P C A 12 distorted distorted 324 351 352 353 381 P A A 13 distorted distorted 358 382 383 384 ---------------------------------------------------------------------------------