ID code: '1SL2' 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' --------------------------------------------------------------------------------- 11 C1' DC P 14 beta 7 12 10 30 C1' DA P 15 beta 26 31 29 51 C1' DG P 16 beta 47 52 50 73 C1' DT P 17 beta 69 74 72 93 C1' DG P 18 beta 89 94 92 115 C1' DC P 19 beta 111 116 114 134 C1' DC P 20 beta 130 135 133 153 C1' DT P 21 beta 149 154 152 172 C1' 2DA P 22 beta 169 173 171 194 C1' TTD T 5 beta 190 195 193 234 C1' DA T 6 beta 230 235 233 255 C1' DG T 7 beta 251 256 254 277 C1' DG T 8 beta 273 278 276 299 C1' DC T 9 beta 295 300 298 318 C1' DA T 10 beta 314 319 317 339 C1' DC T 11 beta 335 340 338 358 C1' DT T 12 beta 354 359 357 378 C1' DG T 13 beta 374 379 377 400 C1' DG T 14 beta 396 401 399 6329 C1' DAD A4004 beta 6326 6330 6328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' DC P 14 11 8 29 C2' DA P 15 30 27 50 C2' DG P 16 51 48 72 C2' DT P 17 73 70 92 C2' DG P 18 93 90 114 C2' DC P 19 115 112 133 C2' DC P 20 134 131 152 C2' DT P 21 153 150 171 C2' 2DA P 22 172 170 193 C2' TTD T 5 194 233 C2' DA T 6 234 231 254 C2' DG T 7 255 252 276 C2' DG T 8 277 274 298 C2' DC T 9 299 296 317 C2' DA T 10 318 315 338 C2' DC T 11 339 336 357 C2' DT T 12 358 355 377 C2' DG T 13 378 375 399 C2' DG T 14 400 397 6328 C2' DAD A4004 6329 6327 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DC P 14 OK 6 9 10 27 C3' DA P 15 OK 25 28 29 48 C3' DG P 16 OK 46 49 50 70 C3' DT P 17 OK 68 71 72 90 C3' DG P 18 OK 88 91 92 112 C3' DC P 19 OK 110 113 114 131 C3' DC P 20 OK 129 132 133 150 C3' DT P 21 OK 148 151 152 170 C3' 2DA P 22 168 171 222 C3' TTD T 5 221 223 231 C3' DA T 6 OK 229 232 233 252 C3' DG T 7 OK 250 253 254 274 C3' DG T 8 OK 272 275 276 296 C3' DC T 9 OK 294 297 298 315 C3' DA T 10 OK 313 316 317 336 C3' DC T 11 OK 334 337 338 355 C3' DT T 12 OK 353 356 357 375 C3' DG T 13 OK 373 376 377 397 C3' DG T 14 OK 395 398 399 6327 C3' DAD A4004 6325 6328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DC P 14 OK 8 5 7 25 C4' DA P 15 OK 27 24 26 46 C4' DG P 16 OK 48 45 47 68 C4' DT P 17 OK 70 67 69 88 C4' DG P 18 OK 90 87 89 110 C4' DC P 19 OK 112 109 111 129 C4' DC P 20 OK 131 128 130 148 C4' DT P 21 OK 150 147 149 168 C4' 2DA P 22 OK 170 167 169 221 C4' TTD T 5 222 229 C4' DA T 6 OK 231 228 230 250 C4' DG T 7 OK 252 249 251 272 C4' DG T 8 OK 274 271 273 294 C4' DC T 9 OK 296 293 295 313 C4' DA T 10 OK 315 312 314 334 C4' DC T 11 OK 336 333 335 353 C4' DT T 12 OK 355 352 354 373 C4' DG T 13 OK 375 372 374 395 C4' DG T 14 OK 397 394 396 6325 C4' DAD A4004 OK 6327 6324 6326 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' DC P 14 4 6 24 C5' DA P 15 23 25 45 C5' DG P 16 44 46 67 C5' DT P 17 66 68 87 C5' DG P 18 86 88 109 C5' DC P 19 108 110 128 C5' DC P 20 127 129 147 C5' DT P 21 146 148 167 C5' 2DA P 22 166 168 188 C5' TTD T 5 187 228 C5' DA T 6 227 229 249 C5' DG T 7 248 250 271 C5' DG T 8 270 272 293 C5' DC T 9 292 294 312 C5' DA T 10 311 313 333 C5' DC T 11 332 334 352 C5' DT T 12 351 353 372 C5' DG T 13 371 373 394 C5' DG T 14 393 395 6324 C5' DAD A4004 6323 6325 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DC P 14 OK OK 2 3 4 20 P DA P 15 distorted distorted 9 21 22 23 41 P DG P 16 distorted distorted 28 42 43 44 63 P DT P 17 distorted distorted 49 64 65 66 83 P DG P 18 distorted distorted 71 84 85 86 105 P DC P 19 distorted distorted 91 106 107 108 124 P DC P 20 distorted distorted 113 125 126 127 143 P DT P 21 distorted distorted 132 144 145 146 163 P 2DA P 22 distorted distorted 151 164 165 166 184 P TTD T 5 distorted distorted 185 186 187 224 P DA T 6 distorted distorted 223 225 226 227 245 P DG T 7 distorted distorted 232 246 247 248 267 P DG T 8 distorted distorted 253 268 269 270 289 P DC T 9 distorted distorted 275 290 291 292 308 P DA T 10 distorted distorted 297 309 310 311 329 P DC T 11 distorted distorted 316 330 331 332 348 P DT T 12 distorted distorted 337 349 350 351 368 P DG T 13 distorted distorted 356 369 370 371 390 P DG T 14 distorted distorted 376 391 392 393 ---------------------------------------------------------------------------------