ID code: '3CRX' 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' --------------------------------------------------------------------------------- 5140 C1' A C 2 beta 5136 5141 5139 5161 C1' T C 3 beta 5157 5162 5160 5181 C1' A C 4 beta 5177 5182 5180 5202 C1' A C 5 beta 5198 5203 5201 5223 C1' G C 6 beta 5219 5224 5222 5245 C1' T C 7 beta 5241 5246 5244 5265 C1' T C 8 beta 5261 5266 5264 5285 C1' C C 9 beta 5281 5286 5284 5304 C1' G C 10 beta 5300 5305 5303 5326 C1' T C 11 beta 5322 5327 5325 5346 C1' A C 12 beta 5342 5347 5345 5367 C1' T C 13 beta 5363 5368 5366 5387 C1' A C 14 beta 5383 5388 5386 5408 C1' G C 15 beta 5404 5409 5407 5430 C1' C C 16 beta 5426 5431 5429 5449 C1' A C 17 beta 5445 5450 5448 5470 C1' T C 18 beta 5466 5471 5469 6185 C1' A D 19 beta 6181 6186 6184 6206 C1' T D 20 beta 6202 6207 6205 6226 C1' G D 21 beta 6222 6227 6225 6248 C1' C D 22 beta 6244 6249 6247 6267 C1' T D 23 beta 6263 6268 6266 6287 C1' A D 24 beta 6283 6288 6286 6308 C1' T D 25 beta 6304 6309 6307 6328 C1' A D 26 beta 6324 6329 6327 6349 C1' C D 27 beta 6345 6350 6348 6368 C1' G D 28 beta 6364 6369 6367 6390 C1' A D 29 beta 6386 6391 6389 6411 C1' A D 30 beta 6407 6412 6410 6432 C1' C D 31 beta 6428 6433 6431 6451 C1' T D 32 beta 6447 6452 6450 6471 C1' T D 33 beta 6467 6472 6470 6491 C1' A D 34 beta 6487 6492 6490 6512 C1' T D 35 beta 6508 6513 6511 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5139 C2' A C 2 5140 5137 5160 C2' T C 3 5161 5158 5180 C2' A C 4 5181 5178 5201 C2' A C 5 5202 5199 5222 C2' G C 6 5223 5220 5244 C2' T C 7 5245 5242 5264 C2' T C 8 5265 5262 5284 C2' C C 9 5285 5282 5303 C2' G C 10 5304 5301 5325 C2' T C 11 5326 5323 5345 C2' A C 12 5346 5343 5366 C2' T C 13 5367 5364 5386 C2' A C 14 5387 5384 5407 C2' G C 15 5408 5405 5429 C2' C C 16 5430 5427 5448 C2' A C 17 5449 5446 5469 C2' T C 18 5470 5467 6184 C2' A D 19 6185 6182 6205 C2' T D 20 6206 6203 6225 C2' G D 21 6226 6223 6247 C2' C D 22 6248 6245 6266 C2' T D 23 6267 6264 6286 C2' A D 24 6287 6284 6307 C2' T D 25 6308 6305 6327 C2' A D 26 6328 6325 6348 C2' C D 27 6349 6346 6367 C2' G D 28 6368 6365 6389 C2' A D 29 6390 6387 6410 C2' A D 30 6411 6408 6431 C2' C D 31 6432 6429 6450 C2' T D 32 6451 6448 6470 C2' T D 33 6471 6468 6490 C2' A D 34 6491 6488 6511 C2' T D 35 6512 6509 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5137 C3' A C 2 OK 5135 5138 5139 5158 C3' T C 3 OK 5156 5159 5160 5178 C3' A C 4 OK 5176 5179 5180 5199 C3' A C 5 OK 5197 5200 5201 5220 C3' G C 6 OK 5218 5221 5222 5242 C3' T C 7 OK 5240 5243 5244 5262 C3' T C 8 OK 5260 5263 5264 5282 C3' C C 9 OK 5280 5283 5284 5301 C3' G C 10 OK 5299 5302 5303 5323 C3' T C 11 OK 5321 5324 5325 5343 C3' A C 12 OK 5341 5344 5345 5364 C3' T C 13 OK 5362 5365 5366 5384 C3' A C 14 OK 5382 5385 5386 5405 C3' G C 15 OK 5403 5406 5407 5427 C3' C C 16 OK 5425 5428 5429 5446 C3' A C 17 OK 5444 5447 5448 5467 C3' T C 18 OK 5465 5468 5469 6182 C3' A D 19 OK 6180 6183 6184 6203 C3' T D 20 OK 6201 6204 6205 6223 C3' G D 21 OK 6221 6224 6225 6245 C3' C D 22 OK 6243 6246 6247 6264 C3' T D 23 OK 6262 6265 6266 6284 C3' A D 24 OK 6282 6285 6286 6305 C3' T D 25 OK 6303 6306 6307 6325 C3' A D 26 OK 6323 6326 6327 6346 C3' C D 27 OK 6344 6347 6348 6365 C3' G D 28 OK 6363 6366 6367 6387 C3' A D 29 OK 6385 6388 6389 6408 C3' A D 30 OK 6406 6409 6410 6429 C3' C D 31 OK 6427 6430 6431 6448 C3' T D 32 OK 6446 6449 6450 6468 C3' T D 33 OK 6466 6469 6470 6488 C3' A D 34 OK 6486 6489 6490 6509 C3' T D 35 OK 6507 6510 6511 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5135 C4' A C 2 OK 5137 5134 5136 5156 C4' T C 3 OK 5158 5155 5157 5176 C4' A C 4 OK 5178 5175 5177 5197 C4' A C 5 OK 5199 5196 5198 5218 C4' G C 6 OK 5220 5217 5219 5240 C4' T C 7 OK 5242 5239 5241 5260 C4' T C 8 OK 5262 5259 5261 5280 C4' C C 9 OK 5282 5279 5281 5299 C4' G C 10 OK 5301 5298 5300 5321 C4' T C 11 OK 5323 5320 5322 5341 C4' A C 12 OK 5343 5340 5342 5362 C4' T C 13 OK 5364 5361 5363 5382 C4' A C 14 OK 5384 5381 5383 5403 C4' G C 15 OK 5405 5402 5404 5425 C4' C C 16 OK 5427 5424 5426 5444 C4' A C 17 OK 5446 5443 5445 5465 C4' T C 18 OK 5467 5464 5466 6180 C4' A D 19 OK 6182 6179 6181 6201 C4' T D 20 OK 6203 6200 6202 6221 C4' G D 21 OK 6223 6220 6222 6243 C4' C D 22 OK 6245 6242 6244 6262 C4' T D 23 OK 6264 6261 6263 6282 C4' A D 24 OK 6284 6281 6283 6303 C4' T D 25 OK 6305 6302 6304 6323 C4' A D 26 OK 6325 6322 6324 6344 C4' C D 27 OK 6346 6343 6345 6363 C4' G D 28 OK 6365 6362 6364 6385 C4' A D 29 OK 6387 6384 6386 6406 C4' A D 30 OK 6408 6405 6407 6427 C4' C D 31 OK 6429 6426 6428 6446 C4' T D 32 OK 6448 6445 6447 6466 C4' T D 33 OK 6468 6465 6467 6486 C4' A D 34 OK 6488 6485 6487 6507 C4' T D 35 OK 6509 6506 6508 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5134 C5' A C 2 5133 5135 5155 C5' T C 3 5154 5156 5175 C5' A C 4 5174 5176 5196 C5' A C 5 5195 5197 5217 C5' G C 6 5216 5218 5239 C5' T C 7 5238 5240 5259 C5' T C 8 5258 5260 5279 C5' C C 9 5278 5280 5298 C5' G C 10 5297 5299 5320 C5' T C 11 5319 5321 5340 C5' A C 12 5339 5341 5361 C5' T C 13 5360 5362 5381 C5' A C 14 5380 5382 5402 C5' G C 15 5401 5403 5424 C5' C C 16 5423 5425 5443 C5' A C 17 5442 5444 5464 C5' T C 18 5463 5465 6179 C5' A D 19 6178 6180 6200 C5' T D 20 6199 6201 6220 C5' G D 21 6219 6221 6242 C5' C D 22 6241 6243 6261 C5' T D 23 6260 6262 6281 C5' A D 24 6280 6282 6302 C5' T D 25 6301 6303 6322 C5' A D 26 6321 6323 6343 C5' C D 27 6342 6344 6362 C5' G D 28 6361 6363 6384 C5' A D 29 6383 6385 6405 C5' A D 30 6404 6406 6426 C5' C D 31 6425 6427 6445 C5' T D 32 6444 6446 6465 C5' T D 33 6464 6466 6485 C5' A D 34 6484 6486 6506 C5' T D 35 6505 6507 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5151 P T C 3 OK OK 5138 5152 5153 5154 5171 P A C 4 OK OK 5159 5172 5173 5174 5192 P A C 5 OK OK 5179 5193 5194 5195 5213 P G C 6 OK OK 5200 5214 5215 5216 5235 P T C 7 OK OK 5221 5236 5237 5238 5255 P T C 8 OK OK 5243 5256 5257 5258 5275 P C C 9 OK OK 5263 5276 5277 5278 5294 P G C 10 OK OK 5283 5295 5296 5297 5316 P T C 11 OK OK 5302 5317 5318 5319 5336 P A C 12 OK OK 5324 5337 5338 5339 5357 P T C 13 OK OK 5344 5358 5359 5360 5377 P A C 14 OK OK 5365 5378 5379 5380 5398 P G C 15 OK OK 5385 5399 5400 5401 5420 P C C 16 OK OK 5406 5421 5422 5423 5439 P A C 17 OK OK 5428 5440 5441 5442 5460 P T C 18 OK OK 5447 5461 5462 5463 6196 P T D 20 OK OK 6183 6197 6198 6199 6216 P G D 21 OK OK 6204 6217 6218 6219 6238 P C D 22 OK OK 6224 6239 6240 6241 6257 P T D 23 OK OK 6246 6258 6259 6260 6277 P A D 24 OK OK 6265 6278 6279 6280 6298 P T D 25 OK OK 6285 6299 6300 6301 6318 P A D 26 OK OK 6306 6319 6320 6321 6339 P C D 27 OK OK 6326 6340 6341 6342 6358 P G D 28 OK OK 6347 6359 6360 6361 6380 P A D 29 OK OK 6366 6381 6382 6383 6401 P A D 30 OK OK 6388 6402 6403 6404 6422 P C D 31 OK OK 6409 6423 6424 6425 6441 P T D 32 OK OK 6430 6442 6443 6444 6461 P T D 33 OK OK 6449 6462 6463 6464 6481 P A D 34 OK OK 6469 6482 6483 6484 6502 P T D 35 OK OK 6489 6503 6504 6505 ---------------------------------------------------------------------------------