ID code: '5JBJ' 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' --------------------------------------------------------------------------------- 5040 C1' G X 1 beta 5035 5041 5038 5063 C1' G X 2 beta 5058 5064 5061 5086 C1' U X 3 beta 5081 5087 5084 5106 C1' A X 4 beta 5101 5107 5104 5128 C1' G X 5 beta 5123 5129 5126 5151 C1' C X 6 beta 5146 5152 5149 5171 C1' G X 7 beta 5166 5172 5169 5194 C1' C X 8 beta 5189 5195 5192 5214 C1' U X 9 beta 5209 5215 5212 5234 C1' A X 10 beta 5229 5235 5232 5256 C1' C X 11 beta 5251 5257 5254 5276 C1' C X 12 beta 5271 5277 5274 5297 C1' G Y 13 beta 5292 5298 5295 5320 C1' G Y 14 beta 5315 5321 5318 5343 C1' U Y 15 beta 5338 5344 5341 5363 C1' A Y 16 beta 5358 5364 5361 5385 C1' G Y 17 beta 5380 5386 5383 5408 C1' C Y 18 beta 5403 5409 5406 5428 C1' G Y 19 beta 5423 5429 5426 5451 C1' C Y 20 beta 5446 5452 5449 5471 C1' U Y 21 beta 5466 5472 5469 5491 C1' A Y 22 beta 5486 5492 5489 5513 C1' C Y 23 beta 5508 5514 5511 5533 C1' C Y 24 beta 5528 5534 5531 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5038 C2' G X 1 OK 5040 5036 5039 5061 C2' G X 2 OK 5063 5059 5062 5084 C2' U X 3 OK 5086 5082 5085 5104 C2' A X 4 OK 5106 5102 5105 5126 C2' G X 5 OK 5128 5124 5127 5149 C2' C X 6 OK 5151 5147 5150 5169 C2' G X 7 OK 5171 5167 5170 5192 C2' C X 8 OK 5194 5190 5193 5212 C2' U X 9 OK 5214 5210 5213 5232 C2' A X 10 OK 5234 5230 5233 5254 C2' C X 11 OK 5256 5252 5255 5274 C2' C X 12 OK 5276 5272 5275 5295 C2' G Y 13 OK 5297 5293 5296 5318 C2' G Y 14 OK 5320 5316 5319 5341 C2' U Y 15 OK 5343 5339 5342 5361 C2' A Y 16 OK 5363 5359 5362 5383 C2' G Y 17 OK 5385 5381 5384 5406 C2' C Y 18 OK 5408 5404 5407 5426 C2' G Y 19 OK 5428 5424 5427 5449 C2' C Y 20 OK 5451 5447 5450 5469 C2' U Y 21 OK 5471 5467 5470 5489 C2' A Y 22 OK 5491 5487 5490 5511 C2' C Y 23 OK 5513 5509 5512 5531 C2' C Y 24 OK 5533 5529 5532 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5036 C3' G X 1 OK 5034 5037 5038 5059 C3' G X 2 OK 5057 5060 5061 5082 C3' U X 3 OK 5080 5083 5084 5102 C3' A X 4 OK 5100 5103 5104 5124 C3' G X 5 OK 5122 5125 5126 5147 C3' C X 6 OK 5145 5148 5149 5167 C3' G X 7 OK 5165 5168 5169 5190 C3' C X 8 OK 5188 5191 5192 5210 C3' U X 9 OK 5208 5211 5212 5230 C3' A X 10 OK 5228 5231 5232 5252 C3' C X 11 OK 5250 5253 5254 5272 C3' C X 12 OK 5270 5273 5274 5293 C3' G Y 13 OK 5291 5294 5295 5316 C3' G Y 14 OK 5314 5317 5318 5339 C3' U Y 15 OK 5337 5340 5341 5359 C3' A Y 16 OK 5357 5360 5361 5381 C3' G Y 17 OK 5379 5382 5383 5404 C3' C Y 18 OK 5402 5405 5406 5424 C3' G Y 19 OK 5422 5425 5426 5447 C3' C Y 20 OK 5445 5448 5449 5467 C3' U Y 21 OK 5465 5468 5469 5487 C3' A Y 22 OK 5485 5488 5489 5509 C3' C Y 23 OK 5507 5510 5511 5529 C3' C Y 24 OK 5527 5530 5531 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5034 C4' G X 1 OK 5036 5033 5035 5057 C4' G X 2 OK 5059 5056 5058 5080 C4' U X 3 OK 5082 5079 5081 5100 C4' A X 4 OK 5102 5099 5101 5122 C4' G X 5 OK 5124 5121 5123 5145 C4' C X 6 OK 5147 5144 5146 5165 C4' G X 7 OK 5167 5164 5166 5188 C4' C X 8 OK 5190 5187 5189 5208 C4' U X 9 OK 5210 5207 5209 5228 C4' A X 10 OK 5230 5227 5229 5250 C4' C X 11 OK 5252 5249 5251 5270 C4' C X 12 OK 5272 5269 5271 5291 C4' G Y 13 OK 5293 5290 5292 5314 C4' G Y 14 OK 5316 5313 5315 5337 C4' U Y 15 OK 5339 5336 5338 5357 C4' A Y 16 OK 5359 5356 5358 5379 C4' G Y 17 OK 5381 5378 5380 5402 C4' C Y 18 OK 5404 5401 5403 5422 C4' G Y 19 OK 5424 5421 5423 5445 C4' C Y 20 OK 5447 5444 5446 5465 C4' U Y 21 OK 5467 5464 5466 5485 C4' A Y 22 OK 5487 5484 5486 5507 C4' C Y 23 OK 5509 5506 5508 5527 C4' C Y 24 OK 5529 5526 5528 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5033 C5' G X 1 5032 5034 5056 C5' G X 2 5055 5057 5079 C5' U X 3 5078 5080 5099 C5' A X 4 5098 5100 5121 C5' G X 5 5120 5122 5144 C5' C X 6 5143 5145 5164 C5' G X 7 5163 5165 5187 C5' C X 8 5186 5188 5207 C5' U X 9 5206 5208 5227 C5' A X 10 5226 5228 5249 C5' C X 11 5248 5250 5269 C5' C X 12 5268 5270 5290 C5' G Y 13 5289 5291 5313 C5' G Y 14 5312 5314 5336 C5' U Y 15 5335 5337 5356 C5' A Y 16 5355 5357 5378 C5' G Y 17 5377 5379 5401 C5' C Y 18 5400 5402 5421 C5' G Y 19 5420 5422 5444 C5' C Y 20 5443 5445 5464 C5' U Y 21 5463 5465 5484 C5' A Y 22 5483 5485 5506 C5' C Y 23 5505 5507 5526 C5' C Y 24 5525 5527 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5029 P G X 1 distorted distorted 5030 5031 5032 5052 P G X 2 distorted distorted 5037 5053 5054 5055 5075 P U X 3 distorted distorted 5060 5076 5077 5078 5095 P A X 4 distorted distorted 5083 5096 5097 5098 5117 P G X 5 distorted distorted 5103 5118 5119 5120 5140 P C X 6 distorted distorted 5125 5141 5142 5143 5160 P G X 7 distorted distorted 5148 5161 5162 5163 5183 P C X 8 distorted distorted 5168 5184 5185 5186 5203 P U X 9 distorted distorted 5191 5204 5205 5206 5223 P A X 10 distorted distorted 5211 5224 5225 5226 5245 P C X 11 distorted distorted 5231 5246 5247 5248 5265 P C X 12 distorted distorted 5253 5266 5267 5268 5286 P G Y 13 distorted distorted 5287 5288 5289 5309 P G Y 14 distorted distorted 5294 5310 5311 5312 5332 P U Y 15 distorted distorted 5317 5333 5334 5335 5352 P A Y 16 distorted distorted 5340 5353 5354 5355 5374 P G Y 17 distorted distorted 5360 5375 5376 5377 5397 P C Y 18 distorted distorted 5382 5398 5399 5400 5417 P G Y 19 distorted distorted 5405 5418 5419 5420 5440 P C Y 20 distorted distorted 5425 5441 5442 5443 5460 P U Y 21 distorted distorted 5448 5461 5462 5463 5480 P A Y 22 distorted distorted 5468 5481 5482 5483 5502 P C Y 23 distorted distorted 5488 5503 5504 5505 5522 P C Y 24 distorted distorted 5510 5523 5524 5525 ---------------------------------------------------------------------------------