ID code: '5E3H' 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' --------------------------------------------------------------------------------- 4977 C1' C B 1 beta 4972 4978 4975 4997 C1' G B 2 beta 4992 4998 4995 5020 C1' A B 3 beta 5015 5021 5018 5042 C1' C B 4 beta 5037 5043 5040 5062 C1' G B 5 beta 5057 5063 5060 5085 C1' C B 6 beta 5080 5086 5083 5105 C1' U B 7 beta 5100 5106 5103 5125 C1' A B 8 beta 5120 5126 5123 5147 C1' G B 9 beta 5142 5148 5145 5170 C1' C B 10 beta 5165 5171 5168 5190 C1' G B 11 beta 5185 5191 5188 5213 C1' U B 12 beta 5208 5214 5211 5234 C1' A C 3 beta 5229 5235 5232 5256 C1' C C 4 beta 5251 5257 5254 5276 C1' G C 5 beta 5271 5277 5274 5299 C1' C C 6 beta 5294 5300 5297 5319 C1' U C 7 beta 5314 5320 5317 5339 C1' A C 8 beta 5334 5340 5337 5361 C1' G C 9 beta 5356 5362 5359 5384 C1' C C 10 beta 5379 5385 5382 5404 C1' G C 11 beta 5399 5405 5402 5427 C1' U C 12 beta 5422 5428 5425 5447 C1' C C 13 beta 5442 5448 5445 5467 C1' G C 14 beta 5462 5468 5465 5506 C1' ADP A1006 beta 5501 5507 5504 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4975 C2' C B 1 OK 4977 4973 4976 4995 C2' G B 2 OK 4997 4993 4996 5018 C2' A B 3 OK 5020 5016 5019 5040 C2' C B 4 OK 5042 5038 5041 5060 C2' G B 5 OK 5062 5058 5061 5083 C2' C B 6 OK 5085 5081 5084 5103 C2' U B 7 OK 5105 5101 5104 5123 C2' A B 8 OK 5125 5121 5124 5145 C2' G B 9 OK 5147 5143 5146 5168 C2' C B 10 OK 5170 5166 5169 5188 C2' G B 11 OK 5190 5186 5189 5211 C2' U B 12 OK 5213 5209 5212 5232 C2' A C 3 OK 5234 5230 5233 5254 C2' C C 4 OK 5256 5252 5255 5274 C2' G C 5 OK 5276 5272 5275 5297 C2' C C 6 OK 5299 5295 5298 5317 C2' U C 7 OK 5319 5315 5318 5337 C2' A C 8 OK 5339 5335 5338 5359 C2' G C 9 OK 5361 5357 5360 5382 C2' C C 10 OK 5384 5380 5383 5402 C2' G C 11 OK 5404 5400 5403 5425 C2' U C 12 OK 5427 5423 5426 5445 C2' C C 13 OK 5447 5443 5446 5465 C2' G C 14 OK 5467 5463 5466 5504 C2' ADP A1006 OK 5506 5502 5505 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4973 C3' C B 1 OK 4971 4974 4975 4993 C3' G B 2 OK 4991 4994 4995 5016 C3' A B 3 OK 5014 5017 5018 5038 C3' C B 4 OK 5036 5039 5040 5058 C3' G B 5 OK 5056 5059 5060 5081 C3' C B 6 OK 5079 5082 5083 5101 C3' U B 7 OK 5099 5102 5103 5121 C3' A B 8 OK 5119 5122 5123 5143 C3' G B 9 OK 5141 5144 5145 5166 C3' C B 10 OK 5164 5167 5168 5186 C3' G B 11 OK 5184 5187 5188 5209 C3' U B 12 OK 5207 5210 5211 5230 C3' A C 3 OK 5228 5231 5232 5252 C3' C C 4 OK 5250 5253 5254 5272 C3' G C 5 OK 5270 5273 5274 5295 C3' C C 6 OK 5293 5296 5297 5315 C3' U C 7 OK 5313 5316 5317 5335 C3' A C 8 OK 5333 5336 5337 5357 C3' G C 9 OK 5355 5358 5359 5380 C3' C C 10 OK 5378 5381 5382 5400 C3' G C 11 OK 5398 5401 5402 5423 C3' U C 12 OK 5421 5424 5425 5443 C3' C C 13 OK 5441 5444 5445 5463 C3' G C 14 OK 5461 5464 5465 5502 C3' ADP A1006 OK 5500 5503 5504 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4971 C4' C B 1 OK 4973 4970 4972 4991 C4' G B 2 OK 4993 4990 4992 5014 C4' A B 3 OK 5016 5013 5015 5036 C4' C B 4 OK 5038 5035 5037 5056 C4' G B 5 OK 5058 5055 5057 5079 C4' C B 6 OK 5081 5078 5080 5099 C4' U B 7 OK 5101 5098 5100 5119 C4' A B 8 OK 5121 5118 5120 5141 C4' G B 9 OK 5143 5140 5142 5164 C4' C B 10 OK 5166 5163 5165 5184 C4' G B 11 OK 5186 5183 5185 5207 C4' U B 12 OK 5209 5206 5208 5228 C4' A C 3 OK 5230 5227 5229 5250 C4' C C 4 OK 5252 5249 5251 5270 C4' G C 5 OK 5272 5269 5271 5293 C4' C C 6 OK 5295 5292 5294 5313 C4' U C 7 OK 5315 5312 5314 5333 C4' A C 8 OK 5335 5332 5334 5355 C4' G C 9 OK 5357 5354 5356 5378 C4' C C 10 OK 5380 5377 5379 5398 C4' G C 11 OK 5400 5397 5399 5421 C4' U C 12 OK 5423 5420 5422 5441 C4' C C 13 OK 5443 5440 5442 5461 C4' G C 14 OK 5463 5460 5462 5500 C4' ADP A1006 OK 5502 5499 5501 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4970 C5' C B 1 4969 4971 4990 C5' G B 2 4989 4991 5013 C5' A B 3 5012 5014 5035 C5' C B 4 5034 5036 5055 C5' G B 5 5054 5056 5078 C5' C B 6 5077 5079 5098 C5' U B 7 5097 5099 5118 C5' A B 8 5117 5119 5140 C5' G B 9 5139 5141 5163 C5' C B 10 5162 5164 5183 C5' G B 11 5182 5184 5206 C5' U B 12 5205 5207 5227 C5' A C 3 5226 5228 5249 C5' C C 4 5248 5250 5269 C5' G C 5 5268 5270 5292 C5' C C 6 5291 5293 5312 C5' U C 7 5311 5313 5332 C5' A C 8 5331 5333 5354 C5' G C 9 5353 5355 5377 C5' C C 10 5376 5378 5397 C5' G C 11 5396 5398 5420 C5' U C 12 5419 5421 5440 C5' C C 13 5439 5441 5460 C5' G C 14 5459 5461 5499 C5' ADP A1006 5498 5500 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4986 P G B 2 distorted distorted 4974 4987 4988 4989 5009 P A B 3 distorted distorted 4994 5010 5011 5012 5031 P C B 4 distorted distorted 5017 5032 5033 5034 5051 P G B 5 distorted distorted 5039 5052 5053 5054 5074 P C B 6 distorted distorted 5059 5075 5076 5077 5094 P U B 7 distorted distorted 5082 5095 5096 5097 5114 P A B 8 distorted distorted 5102 5115 5116 5117 5136 P G B 9 distorted distorted 5122 5137 5138 5139 5159 P C B 10 distorted distorted 5144 5160 5161 5162 5179 P G B 11 distorted distorted 5167 5180 5181 5182 5202 P U B 12 distorted distorted 5187 5203 5204 5205 5223 P A C 3 distorted distorted 5224 5225 5226 5245 P C C 4 distorted distorted 5231 5246 5247 5248 5265 P G C 5 distorted distorted 5253 5266 5267 5268 5288 P C C 6 distorted distorted 5273 5289 5290 5291 5308 P U C 7 distorted distorted 5296 5309 5310 5311 5328 P A C 8 distorted distorted 5316 5329 5330 5331 5350 P G C 9 distorted distorted 5336 5351 5352 5353 5373 P C C 10 distorted distorted 5358 5374 5375 5376 5393 P G C 11 distorted distorted 5381 5394 5395 5396 5416 P U C 12 distorted distorted 5401 5417 5418 5419 5436 P C C 13 distorted distorted 5424 5437 5438 5439 5456 P G C 14 distorted distorted 5444 5457 5458 5459 ---------------------------------------------------------------------------------