ID code: '5TDJ'
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.
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Center Reference for correct naming
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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.
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Author: Peter Slickers (slickers@imb-jena.de)
Biocomputing, IMB Jena, Germany
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Seq No Atom Residue H1' base O4' H1' base C2'
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9 C1' C A 1 beta 4 10 7
29 C1' C A 2 beta 24 30 27
49 C1' G A 3 beta 44 50 47
72 C1' G A 4 beta 67 73 70
95 C1' C A 5 beta 90 96 93
115 C1' G A 6 beta 110 116 113
138 C1' C A 7 beta 133 139 136
158 C1' C A 8 beta 153 159 156
178 C1' G A 9 beta 173 179 176
201 C1' G A 10 beta 196 202 199
222 C1' C B 1 beta 217 223 220
242 C1' C B 2 beta 237 243 240
262 C1' G B 3 beta 257 263 260
285 C1' G B 4 beta 280 286 283
308 C1' C B 5 beta 303 309 306
328 C1' G B 6 beta 323 329 326
351 C1' C B 7 beta 346 352 349
371 C1' C B 8 beta 366 372 369
391 C1' G B 9 beta 386 392 389
414 C1' G B 10 beta 409 415 412
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Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2'
H2'1 H2'2 H2' O2'
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7 C2' C A 1 OK 9 5 8
27 C2' C A 2 OK 29 25 28
47 C2' G A 3 OK 49 45 48
70 C2' G A 4 OK 72 68 71
93 C2' C A 5 OK 95 91 94
113 C2' G A 6 OK 115 111 114
136 C2' C A 7 OK 138 134 137
156 C2' C A 8 OK 158 154 157
176 C2' G A 9 OK 178 174 177
199 C2' G A 10 OK 201 197 200
220 C2' C B 1 OK 222 218 221
240 C2' C B 2 OK 242 238 241
260 C2' G B 3 OK 262 258 261
283 C2' G B 4 OK 285 281 284
306 C2' C B 5 OK 308 304 307
326 C2' G B 6 OK 328 324 327
349 C2' C B 7 OK 351 347 350
369 C2' C B 8 OK 371 367 370
389 C2' G B 9 OK 391 387 390
412 C2' G B 10 OK 414 410 413
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Seq No Atom Residue H3' O3' C4' H3' O3' C2'
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5 C3' C A 1 OK 3 6 7
25 C3' C A 2 OK 23 26 27
45 C3' G A 3 OK 43 46 47
68 C3' G A 4 OK 66 69 70
91 C3' C A 5 OK 89 92 93
111 C3' G A 6 OK 109 112 113
134 C3' C A 7 OK 132 135 136
154 C3' C A 8 OK 152 155 156
174 C3' G A 9 OK 172 175 176
197 C3' G A 10 OK 195 198 199
218 C3' C B 1 OK 216 219 220
238 C3' C B 2 OK 236 239 240
258 C3' G B 3 OK 256 259 260
281 C3' G B 4 OK 279 282 283
304 C3' C B 5 OK 302 305 306
324 C3' G B 6 OK 322 325 326
347 C3' C B 7 OK 345 348 349
367 C3' C B 8 OK 365 368 369
387 C3' G B 9 OK 385 388 389
410 C3' G B 10 OK 408 411 412
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Seq No Atom Residue H4' C5' C3' H4' C5' O4'
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3 C4' C A 1 OK 5 2 4
23 C4' C A 2 OK 25 22 24
43 C4' G A 3 OK 45 42 44
66 C4' G A 4 OK 68 65 67
89 C4' C A 5 OK 91 88 90
109 C4' G A 6 OK 111 108 110
132 C4' C A 7 OK 134 131 133
152 C4' C A 8 OK 154 151 153
172 C4' G A 9 OK 174 171 173
195 C4' G A 10 OK 197 194 196
216 C4' C B 1 OK 218 215 217
236 C4' C B 2 OK 238 235 237
256 C4' G B 3 OK 258 255 257
279 C4' G B 4 OK 281 278 280
302 C4' C B 5 OK 304 301 303
322 C4' G B 6 OK 324 321 323
345 C4' C B 7 OK 347 344 346
365 C4' C B 8 OK 367 364 366
385 C4' G B 9 OK 387 384 386
408 C4' G B 10 OK 410 407 409
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Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4'
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2 C5' C A 1 1 3
22 C5' C A 2 21 23
42 C5' G A 3 41 43
65 C5' G A 4 64 66
88 C5' C A 5 87 89
108 C5' G A 6 107 109
131 C5' C A 7 130 132
151 C5' C A 8 150 152
171 C5' G A 9 170 172
194 C5' G A 10 193 195
215 C5' C B 1 214 216
235 C5' C B 2 234 236
255 C5' G B 3 254 256
278 C5' G B 4 277 279
301 C5' C B 5 300 302
321 C5' G B 6 320 322
344 C5' C B 7 343 345
364 C5' C B 8 363 365
384 C5' G B 9 383 385
407 C5' G B 10 406 408
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Seq No Atom Residue O1P O2P O3' O1P O2P O5'
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18 P C A 2 distorted distorted 6 19 20 21
38 P G A 3 distorted distorted 26 39 40 41
61 P G A 4 distorted distorted 62 63 64
84 P C A 5 distorted distorted 69 85 86 87
104 P G A 6 distorted distorted 105 106 107
127 P C A 7 distorted distorted 112 128 129 130
147 P C A 8 distorted distorted 135 148 149 150
167 P G A 9 distorted distorted 155 168 169 170
190 P G A 10 distorted distorted 175 191 192 193
231 P C B 2 distorted distorted 219 232 233 234
251 P G B 3 distorted distorted 239 252 253 254
274 P G B 4 distorted distorted 275 276 277
297 P C B 5 distorted distorted 282 298 299 300
317 P G B 6 distorted distorted 318 319 320
340 P C B 7 distorted distorted 325 341 342 343
360 P C B 8 distorted distorted 348 361 362 363
380 P G B 9 distorted distorted 368 381 382 383
403 P G B 10 distorted distorted 388 404 405 406
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