ID code: '1XSN' 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' --------------------------------------------------------------------------------- 8 C1' DC T 1 beta 4 9 7 27 C1' DG T 2 beta 23 28 26 49 C1' DG T 3 beta 45 50 48 71 C1' DC T 4 beta 67 72 70 90 C1' DA T 5 beta 86 91 89 111 C1' DA T 6 beta 107 112 110 132 C1' DT T 7 beta 128 133 131 152 C1' DA T 8 beta 148 153 151 173 C1' DC T 9 beta 169 174 172 192 C1' DT T 10 beta 188 193 191 212 C1' DG T 11 beta 208 213 211 232 C1' DC P 1 beta 228 233 231 251 C1' DA P 2 beta 247 252 250 272 C1' DG P 3 beta 268 273 271 294 C1' DT P 4 beta 290 295 293 314 C1' DA P 5 beta 310 315 313 342 C1' 2DT P 6 beta 341 329 338 356 C1' DG D 1 beta 352 357 355 378 C1' DC D 2 beta 374 379 377 397 C1' DC D 3 beta 393 398 396 416 C1' DG D 4 beta 412 417 415 2962 C1' D3T A 579 beta 2961 2963 2972 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DC T 1 8 5 26 C2' DG T 2 27 24 48 C2' DG T 3 49 46 70 C2' DC T 4 71 68 89 C2' DA T 5 90 87 110 C2' DA T 6 111 108 131 C2' DT T 7 132 129 151 C2' DA T 8 152 149 172 C2' DC T 9 173 170 191 C2' DT T 10 192 189 211 C2' DG T 11 212 209 231 C2' DC P 1 232 229 250 C2' DA P 2 251 248 271 C2' DG P 3 272 269 293 C2' DT P 4 294 291 313 C2' DA P 5 314 311 338 C2' 2DT P 6 342 343 355 C2' DG D 1 356 353 377 C2' DC D 2 378 375 396 C2' DC D 3 397 394 415 C2' DG D 4 416 413 2972 C2' D3T A 579 2962 2973 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC T 1 OK 3 6 7 24 C3' DG T 2 OK 22 25 26 46 C3' DG T 3 OK 44 47 48 68 C3' DC T 4 OK 66 69 70 87 C3' DA T 5 OK 85 88 89 108 C3' DA T 6 OK 106 109 110 129 C3' DT T 7 OK 127 130 131 149 C3' DA T 8 OK 147 150 151 170 C3' DC T 9 OK 168 171 172 189 C3' DT T 10 OK 187 190 191 209 C3' DG T 11 OK 207 210 211 229 C3' DC P 1 OK 227 230 231 248 C3' DA P 2 OK 246 249 250 269 C3' DG P 3 OK 267 270 271 291 C3' DT P 4 OK 289 292 293 311 C3' DA P 5 OK 309 312 313 343 C3' 2DT P 6 340 338 353 C3' DG D 1 OK 351 354 355 375 C3' DC D 2 OK 373 376 377 394 C3' DC D 3 OK 392 395 396 413 C3' DG D 4 OK 411 414 415 2973 C3' D3T A 579 2960 2972 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC T 1 OK 5 2 4 22 C4' DG T 2 OK 24 21 23 44 C4' DG T 3 OK 46 43 45 66 C4' DC T 4 OK 68 65 67 85 C4' DA T 5 OK 87 84 86 106 C4' DA T 6 OK 108 105 107 127 C4' DT T 7 OK 129 126 128 147 C4' DA T 8 OK 149 146 148 168 C4' DC T 9 OK 170 167 169 187 C4' DT T 10 OK 189 186 188 207 C4' DG T 11 OK 209 206 208 227 C4' DC P 1 OK 229 226 228 246 C4' DA P 2 OK 248 245 247 267 C4' DG P 3 OK 269 266 268 289 C4' DT P 4 OK 291 288 290 309 C4' DA P 5 OK 311 308 310 340 C4' 2DT P 6 OK 343 339 341 351 C4' DG D 1 OK 353 350 352 373 C4' DC D 2 OK 375 372 374 392 C4' DC D 3 OK 394 391 393 411 C4' DG D 4 OK 413 410 412 2960 C4' D3T A 579 OK 2973 2959 2961 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC T 1 1 3 21 C5' DG T 2 20 22 43 C5' DG T 3 42 44 65 C5' DC T 4 64 66 84 C5' DA T 5 83 85 105 C5' DA T 6 104 106 126 C5' DT T 7 125 127 146 C5' DA T 8 145 147 167 C5' DC T 9 166 168 186 C5' DT T 10 185 187 206 C5' DG T 11 205 207 226 C5' DC P 1 225 227 245 C5' DA P 2 244 246 266 C5' DG P 3 265 267 288 C5' DT P 4 287 289 308 C5' DA P 5 307 309 339 C5' 2DT P 6 328 340 350 C5' DG D 1 349 351 372 C5' DC D 2 371 373 391 C5' DC D 3 390 392 410 C5' DG D 4 409 411 2959 C5' D3T A 579 2958 2960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P DG T 2 distorted distorted 6 18 19 20 39 P DG T 3 distorted distorted 25 40 41 42 61 P DC T 4 distorted distorted 47 62 63 64 80 P DA T 5 distorted distorted 69 81 82 83 101 P DA T 6 distorted distorted 88 102 103 104 122 P DT T 7 distorted distorted 109 123 124 125 142 P DA T 8 distorted distorted 130 143 144 145 163 P DC T 9 distorted distorted 150 164 165 166 182 P DT T 10 distorted distorted 171 183 184 185 202 P DG T 11 distorted distorted 190 203 204 205 241 P DA P 2 distorted distorted 230 242 243 244 262 P DG P 3 distorted distorted 249 263 264 265 284 P DT P 4 distorted distorted 270 285 286 287 304 P DA P 5 distorted distorted 292 305 306 307 325 P 2DT P 6 distorted distorted 312 326 327 328 346 P DG D 1 OK OK 347 348 349 368 P DC D 2 distorted distorted 354 369 370 371 387 P DC D 3 distorted distorted 376 388 389 390 406 P DG D 4 distorted distorted 395 407 408 409 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