ID code: '1HS3' 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' U A 5 alpha beta 134 154 140 137 169 C1' A A 6 alpha beta 164 186 170 167 202 C1' A A 7 alpha beta 197 219 203 200 235 C1' U A 8 alpha beta 230 250 236 233 265 C1' U A 9 alpha beta 260 280 266 263 295 C1' C A 10 alpha beta 290 310 296 293 326 C1' G A 11 alpha beta 321 344 327 324 360 C1' C A 12 alpha beta 355 375 361 358 391 C1' A A 13 alpha beta 386 409 392 389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 5 OK OK 139 135 152 138 167 C2' A A 6 OK OK 169 165 184 168 200 C2' A A 7 OK OK 202 198 217 201 233 C2' U A 8 OK OK 235 231 248 234 263 C2' U A 9 OK OK 265 261 278 264 293 C2' C A 10 OK OK 295 291 308 294 324 C2' G A 11 OK OK 326 322 342 325 358 C2' C A 12 OK OK 360 356 373 359 389 C2' A A 13 OK OK 391 387 407 390 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 5 OK OK 133 151 136 137 165 C3' A A 6 OK OK 163 183 166 167 198 C3' A A 7 OK OK 196 216 199 200 231 C3' U A 8 OK OK 229 247 232 233 261 C3' U A 9 OK OK 259 277 262 263 291 C3' C A 10 OK OK 289 307 292 293 322 C3' G A 11 OK OK 320 341 323 324 356 C3' C A 12 OK OK 354 372 357 358 387 C3' A A 13 OK OK 385 405 388 389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 5 OK OK 135 150 132 134 163 C4' A A 6 OK OK 165 182 162 164 196 C4' A A 7 OK OK 198 215 195 197 229 C4' U A 8 OK OK 231 246 228 230 259 C4' U A 9 OK OK 261 276 258 260 289 C4' C A 10 OK OK 291 306 288 290 320 C4' G A 11 OK OK 322 340 319 321 354 C4' C A 12 OK OK 356 371 353 355 385 C4' A A 13 OK OK 387 404 384 386 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 5 OK OK 131 148 149 133 162 C5' A A 6 OK OK 161 180 181 163 195 C5' A A 7 OK OK 194 213 214 196 228 C5' U A 8 OK OK 227 244 245 229 258 C5' U A 9 OK OK 257 274 275 259 288 C5' C A 10 OK OK 287 304 305 289 319 C5' G A 11 OK OK 318 338 339 320 353 C5' C A 12 OK OK 352 369 370 354 384 C5' A A 13 OK OK 383 402 403 385 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 5 distorted distorted 106 129 130 131 158 P A A 6 distorted distorted 136 159 160 161 191 P A A 7 distorted distorted 166 192 193 194 224 P U A 8 distorted distorted 199 225 226 227 254 P U A 9 distorted distorted 232 255 256 257 284 P C A 10 distorted distorted 262 285 286 287 315 P G A 11 distorted distorted 292 316 317 318 349 P C A 12 distorted distorted 323 350 351 352 380 P A A 13 distorted distorted 357 381 382 383 ---------------------------------------------------------------------------------