ID code: '3BOY' 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 D 1 beta 4 10 7 29 C1' U D 2 beta 24 30 27 49 C1' U D 3 beta 44 50 47 69 C1' A D 4 beta 64 70 67 91 C1' G D 5 beta 86 92 89 114 C1' U D 6 beta 109 115 112 134 C1' U D 7 beta 129 135 132 154 C1' U D 8 beta 149 155 152 174 C1' U D 9 beta 169 175 172 194 C1' U D 10 beta 189 195 192 214 C1' A D 11 beta 209 215 212 236 C1' G D 12 beta 231 237 234 259 C1' U D 13 beta 254 260 257 279 C1' U D 14 beta 274 280 277 299 C1' U D 15 beta 294 300 297 319 C1' U D 16 beta 314 320 317 339 C1' U D 17 beta 334 340 337 359 C1' A D 18 beta 354 360 357 381 C1' G D 19 beta 376 382 379 404 C1' U D 20 beta 399 405 402 424 C1' U D 21 beta 419 425 422 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U D 1 OK 9 5 8 27 C2' U D 2 OK 29 25 28 47 C2' U D 3 OK 49 45 48 67 C2' A D 4 OK 69 65 68 89 C2' G D 5 OK 91 87 90 112 C2' U D 6 OK 114 110 113 132 C2' U D 7 OK 134 130 133 152 C2' U D 8 OK 154 150 153 172 C2' U D 9 OK 174 170 173 192 C2' U D 10 OK 194 190 193 212 C2' A D 11 OK 214 210 213 234 C2' G D 12 OK 236 232 235 257 C2' U D 13 OK 259 255 258 277 C2' U D 14 OK 279 275 278 297 C2' U D 15 OK 299 295 298 317 C2' U D 16 OK 319 315 318 337 C2' U D 17 OK 339 335 338 357 C2' A D 18 OK 359 355 358 379 C2' G D 19 OK 381 377 380 402 C2' U D 20 OK 404 400 403 422 C2' U D 21 OK 424 420 423 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U D 1 OK 3 6 7 25 C3' U D 2 OK 23 26 27 45 C3' U D 3 OK 43 46 47 65 C3' A D 4 OK 63 66 67 87 C3' G D 5 OK 85 88 89 110 C3' U D 6 OK 108 111 112 130 C3' U D 7 OK 128 131 132 150 C3' U D 8 OK 148 151 152 170 C3' U D 9 OK 168 171 172 190 C3' U D 10 OK 188 191 192 210 C3' A D 11 OK 208 211 212 232 C3' G D 12 OK 230 233 234 255 C3' U D 13 OK 253 256 257 275 C3' U D 14 OK 273 276 277 295 C3' U D 15 OK 293 296 297 315 C3' U D 16 OK 313 316 317 335 C3' U D 17 OK 333 336 337 355 C3' A D 18 OK 353 356 357 377 C3' G D 19 OK 375 378 379 400 C3' U D 20 OK 398 401 402 420 C3' U D 21 OK 418 421 422 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U D 1 OK 5 2 4 23 C4' U D 2 OK 25 22 24 43 C4' U D 3 OK 45 42 44 63 C4' A D 4 OK 65 62 64 85 C4' G D 5 OK 87 84 86 108 C4' U D 6 OK 110 107 109 128 C4' U D 7 OK 130 127 129 148 C4' U D 8 OK 150 147 149 168 C4' U D 9 OK 170 167 169 188 C4' U D 10 OK 190 187 189 208 C4' A D 11 OK 210 207 209 230 C4' G D 12 OK 232 229 231 253 C4' U D 13 OK 255 252 254 273 C4' U D 14 OK 275 272 274 293 C4' U D 15 OK 295 292 294 313 C4' U D 16 OK 315 312 314 333 C4' U D 17 OK 335 332 334 353 C4' A D 18 OK 355 352 354 375 C4' G D 19 OK 377 374 376 398 C4' U D 20 OK 400 397 399 418 C4' U D 21 OK 420 417 419 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U D 1 1 3 22 C5' U D 2 21 23 42 C5' U D 3 41 43 62 C5' A D 4 61 63 84 C5' G D 5 83 85 107 C5' U D 6 106 108 127 C5' U D 7 126 128 147 C5' U D 8 146 148 167 C5' U D 9 166 168 187 C5' U D 10 186 188 207 C5' A D 11 206 208 229 C5' G D 12 228 230 252 C5' U D 13 251 253 272 C5' U D 14 271 273 292 C5' U D 15 291 293 312 C5' U D 16 311 313 332 C5' U D 17 331 333 352 C5' A D 18 351 353 374 C5' G D 19 373 375 397 C5' U D 20 396 398 417 C5' U D 21 416 418 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U D 2 distorted distorted 6 19 20 21 38 P U D 3 distorted distorted 26 39 40 41 58 P A D 4 distorted distorted 46 59 60 61 80 P G D 5 distorted distorted 66 81 82 83 103 P U D 6 distorted distorted 88 104 105 106 123 P U D 7 distorted distorted 111 124 125 126 143 P U D 8 distorted distorted 131 144 145 146 163 P U D 9 distorted distorted 151 164 165 166 183 P U D 10 distorted distorted 171 184 185 186 203 P A D 11 distorted distorted 191 204 205 206 225 P G D 12 distorted distorted 211 226 227 228 248 P U D 13 distorted distorted 233 249 250 251 268 P U D 14 distorted distorted 256 269 270 271 288 P U D 15 distorted distorted 276 289 290 291 308 P U D 16 distorted distorted 296 309 310 311 328 P U D 17 distorted distorted 316 329 330 331 348 P A D 18 distorted distorted 336 349 350 351 370 P G D 19 distorted distorted 356 371 372 373 393 P U D 20 distorted distorted 378 394 395 396 413 P U D 21 distorted distorted 401 414 415 416 433 P U D 22 distorted distorted 421 434 435 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