ID code: '1SL1' 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 22 169 171 179 C1' TTD T 5 beta 175 180 178 219 C1' DA T 6 beta 215 220 218 240 C1' DG T 7 beta 236 241 239 262 C1' DG T 8 beta 258 263 261 284 C1' DC T 9 beta 280 285 283 303 C1' DA T 10 beta 299 304 302 324 C1' DC T 11 beta 320 325 323 343 C1' DT T 12 beta 339 344 342 363 C1' DG T 13 beta 359 364 362 385 C1' DG T 14 beta 381 386 384 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 22 172 170 178 C2' TTD T 5 179 218 C2' DA T 6 219 216 239 C2' DG T 7 240 237 261 C2' DG T 8 262 259 283 C2' DC T 9 284 281 302 C2' DA T 10 303 300 323 C2' DC T 11 324 321 342 C2' DT T 12 343 340 362 C2' DG T 13 363 360 384 C2' DG T 14 385 382 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 22 168 171 207 C3' TTD T 5 206 208 216 C3' DA T 6 OK 214 217 218 237 C3' DG T 7 OK 235 238 239 259 C3' DG T 8 OK 257 260 261 281 C3' DC T 9 OK 279 282 283 300 C3' DA T 10 OK 298 301 302 321 C3' DC T 11 OK 319 322 323 340 C3' DT T 12 OK 338 341 342 360 C3' DG T 13 OK 358 361 362 382 C3' DG T 14 OK 380 383 384 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 170 167 169 206 C4' TTD T 5 207 214 C4' DA T 6 OK 216 213 215 235 C4' DG T 7 OK 237 234 236 257 C4' DG T 8 OK 259 256 258 279 C4' DC T 9 OK 281 278 280 298 C4' DA T 10 OK 300 297 299 319 C4' DC T 11 OK 321 318 320 338 C4' DT T 12 OK 340 337 339 358 C4' DG T 13 OK 360 357 359 380 C4' DG T 14 OK 382 379 381 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 22 166 168 213 C5' DA T 6 212 214 234 C5' DG T 7 233 235 256 C5' DG T 8 255 257 278 C5' DC T 9 277 279 297 C5' DA T 10 296 298 318 C5' DC T 11 317 319 337 C5' DT T 12 336 338 357 C5' DG T 13 356 358 379 C5' DG T 14 378 380 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DC P 14 distorted distorted 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 151 164 165 166 209 P DA T 6 distorted distorted 208 210 211 212 230 P DG T 7 distorted distorted 217 231 232 233 252 P DG T 8 distorted distorted 238 253 254 255 274 P DC T 9 distorted distorted 260 275 276 277 293 P DA T 10 distorted distorted 282 294 295 296 314 P DC T 11 distorted distorted 301 315 316 317 333 P DT T 12 distorted distorted 322 334 335 336 353 P DG T 13 distorted distorted 341 354 355 356 375 P DG T 14 distorted distorted 361 376 377 378 ---------------------------------------------------------------------------------