ID code: '3KYL' 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' --------------------------------------------------------------------------------- 4993 C1' C E 1 beta 4988 4994 4991 5013 C1' U E 2 beta 5008 5014 5011 5033 C1' G E 3 beta 5028 5034 5031 5056 C1' A E 4 beta 5051 5057 5054 5078 C1' C E 5 beta 5073 5079 5076 5098 C1' C E 6 beta 5093 5099 5096 5118 C1' U E 7 beta 5113 5119 5116 5138 C1' G E 8 beta 5133 5139 5136 5161 C1' A E 9 beta 5156 5162 5159 5183 C1' C E 10 beta 5178 5184 5181 5202 C1' DT E 11 beta 5198 5203 5201 5222 C1' DT E 12 beta 5218 5223 5221 5242 C1' DC E 13 beta 5238 5243 5241 5261 C1' DG E 14 beta 5257 5262 5260 5283 C1' DG E 15 beta 5279 5284 5282 5305 C1' DT E 16 beta 5301 5306 5304 5325 C1' DC E 17 beta 5321 5326 5324 5344 C1' DA E 18 beta 5340 5345 5343 5365 C1' DG E 19 beta 5361 5366 5364 5387 C1' DG E 20 beta 5383 5388 5386 5409 C1' DT E 21 beta 5405 5410 5408 5429 C1' DC E 22 beta 5425 5430 5428 5448 C1' DA E 23 beta 5444 5449 5447 5469 C1' DG E 24 beta 5465 5470 5468 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4991 C2' C E 1 OK 4993 4989 4992 5011 C2' U E 2 OK 5013 5009 5012 5031 C2' G E 3 OK 5033 5029 5032 5054 C2' A E 4 OK 5056 5052 5055 5076 C2' C E 5 OK 5078 5074 5077 5096 C2' C E 6 OK 5098 5094 5097 5116 C2' U E 7 OK 5118 5114 5117 5136 C2' G E 8 OK 5138 5134 5137 5159 C2' A E 9 OK 5161 5157 5160 5181 C2' C E 10 OK 5183 5179 5182 5201 C2' DT E 11 5202 5199 5221 C2' DT E 12 5222 5219 5241 C2' DC E 13 5242 5239 5260 C2' DG E 14 5261 5258 5282 C2' DG E 15 5283 5280 5304 C2' DT E 16 5305 5302 5324 C2' DC E 17 5325 5322 5343 C2' DA E 18 5344 5341 5364 C2' DG E 19 5365 5362 5386 C2' DG E 20 5387 5384 5408 C2' DT E 21 5409 5406 5428 C2' DC E 22 5429 5426 5447 C2' DA E 23 5448 5445 5468 C2' DG E 24 5469 5466 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4989 C3' C E 1 OK 4987 4990 4991 5009 C3' U E 2 OK 5007 5010 5011 5029 C3' G E 3 OK 5027 5030 5031 5052 C3' A E 4 OK 5050 5053 5054 5074 C3' C E 5 OK 5072 5075 5076 5094 C3' C E 6 OK 5092 5095 5096 5114 C3' U E 7 OK 5112 5115 5116 5134 C3' G E 8 OK 5132 5135 5136 5157 C3' A E 9 OK 5155 5158 5159 5179 C3' C E 10 OK 5177 5180 5181 5199 C3' DT E 11 OK 5197 5200 5201 5219 C3' DT E 12 OK 5217 5220 5221 5239 C3' DC E 13 OK 5237 5240 5241 5258 C3' DG E 14 OK 5256 5259 5260 5280 C3' DG E 15 OK 5278 5281 5282 5302 C3' DT E 16 OK 5300 5303 5304 5322 C3' DC E 17 OK 5320 5323 5324 5341 C3' DA E 18 OK 5339 5342 5343 5362 C3' DG E 19 OK 5360 5363 5364 5384 C3' DG E 20 OK 5382 5385 5386 5406 C3' DT E 21 OK 5404 5407 5408 5426 C3' DC E 22 OK 5424 5427 5428 5445 C3' DA E 23 OK 5443 5446 5447 5466 C3' DG E 24 OK 5464 5467 5468 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4987 C4' C E 1 OK 4989 4986 4988 5007 C4' U E 2 OK 5009 5006 5008 5027 C4' G E 3 OK 5029 5026 5028 5050 C4' A E 4 OK 5052 5049 5051 5072 C4' C E 5 OK 5074 5071 5073 5092 C4' C E 6 OK 5094 5091 5093 5112 C4' U E 7 OK 5114 5111 5113 5132 C4' G E 8 OK 5134 5131 5133 5155 C4' A E 9 OK 5157 5154 5156 5177 C4' C E 10 OK 5179 5176 5178 5197 C4' DT E 11 OK 5199 5196 5198 5217 C4' DT E 12 OK 5219 5216 5218 5237 C4' DC E 13 OK 5239 5236 5238 5256 C4' DG E 14 OK 5258 5255 5257 5278 C4' DG E 15 OK 5280 5277 5279 5300 C4' DT E 16 OK 5302 5299 5301 5320 C4' DC E 17 OK 5322 5319 5321 5339 C4' DA E 18 OK 5341 5338 5340 5360 C4' DG E 19 OK 5362 5359 5361 5382 C4' DG E 20 OK 5384 5381 5383 5404 C4' DT E 21 OK 5406 5403 5405 5424 C4' DC E 22 OK 5426 5423 5425 5443 C4' DA E 23 OK 5445 5442 5444 5464 C4' DG E 24 OK 5466 5463 5465 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4986 C5' C E 1 4985 4987 5006 C5' U E 2 5005 5007 5026 C5' G E 3 5025 5027 5049 C5' A E 4 5048 5050 5071 C5' C E 5 5070 5072 5091 C5' C E 6 5090 5092 5111 C5' U E 7 5110 5112 5131 C5' G E 8 5130 5132 5154 C5' A E 9 5153 5155 5176 C5' C E 10 5175 5177 5196 C5' DT E 11 5195 5197 5216 C5' DT E 12 5215 5217 5236 C5' DC E 13 5235 5237 5255 C5' DG E 14 5254 5256 5277 C5' DG E 15 5276 5278 5299 C5' DT E 16 5298 5300 5319 C5' DC E 17 5318 5320 5338 C5' DA E 18 5337 5339 5359 C5' DG E 19 5358 5360 5381 C5' DG E 20 5380 5382 5403 C5' DT E 21 5402 5404 5423 C5' DC E 22 5422 5424 5442 C5' DA E 23 5441 5443 5463 C5' DG E 24 5462 5464 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5002 P U E 2 distorted distorted 4990 5003 5004 5005 5022 P G E 3 distorted distorted 5010 5023 5024 5025 5045 P A E 4 distorted distorted 5030 5046 5047 5048 5067 P C E 5 distorted distorted 5053 5068 5069 5070 5087 P C E 6 distorted distorted 5075 5088 5089 5090 5107 P U E 7 distorted distorted 5095 5108 5109 5110 5127 P G E 8 distorted distorted 5115 5128 5129 5130 5150 P A E 9 distorted distorted 5135 5151 5152 5153 5172 P C E 10 distorted distorted 5158 5173 5174 5175 5192 P DT E 11 distorted distorted 5180 5193 5194 5195 5212 P DT E 12 distorted distorted 5200 5213 5214 5215 5232 P DC E 13 distorted distorted 5220 5233 5234 5235 5251 P DG E 14 distorted distorted 5240 5252 5253 5254 5273 P DG E 15 distorted distorted 5259 5274 5275 5276 5295 P DT E 16 distorted distorted 5281 5296 5297 5298 5315 P DC E 17 distorted distorted 5303 5316 5317 5318 5334 P DA E 18 distorted distorted 5323 5335 5336 5337 5355 P DG E 19 distorted distorted 5342 5356 5357 5358 5377 P DG E 20 distorted distorted 5363 5378 5379 5380 5399 P DT E 21 distorted distorted 5385 5400 5401 5402 5419 P DC E 22 distorted distorted 5407 5420 5421 5422 5438 P DA E 23 distorted distorted 5427 5439 5440 5441 5459 P DG E 24 distorted distorted 5446 5460 5461 5462 ---------------------------------------------------------------------------------