ID code: '4QIK' 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' --------------------------------------------------------------------------------- 4794 C1' A C 3 beta 4789 4795 4792 4816 C1' U C 4 beta 4811 4817 4814 4836 C1' G C 5 beta 4831 4837 4834 4859 C1' U C 6 beta 4854 4860 4857 4879 C1' U C 7 beta 4874 4880 4877 4899 C1' U C 8 beta 4894 4900 4897 4919 C1' U C 9 beta 4914 4920 4917 4939 C1' C C 10 beta 4934 4940 4937 4959 C1' U C 11 beta 4954 4960 4957 4979 C1' G C 12 beta 4974 4980 4977 5002 C1' G C 14 beta 4997 5003 5000 5025 C1' A C 15 beta 5020 5026 5023 5047 C1' A C 16 beta 5042 5048 5045 5069 C1' A C 17 beta 5064 5070 5067 5091 C1' A C 18 beta 5086 5092 5089 5113 C1' C C 19 beta 5108 5114 5111 5133 C1' G C 20 beta 5128 5134 5131 5156 C1' G C 21 beta 5151 5157 5154 5180 C1' G D 5 beta 5175 5181 5178 5203 C1' U D 6 beta 5198 5204 5201 5223 C1' U D 7 beta 5218 5224 5221 5243 C1' U D 8 beta 5238 5244 5241 5263 C1' U D 9 beta 5258 5264 5261 5283 C1' C D 10 beta 5278 5284 5281 5303 C1' U D 11 beta 5298 5304 5301 5323 C1' G D 12 beta 5318 5324 5321 5346 C1' U D 13 beta 5341 5347 5344 5366 C1' G D 14 beta 5361 5367 5364 5389 C1' A D 15 beta 5384 5390 5387 5411 C1' A D 16 beta 5406 5412 5409 5433 C1' A D 17 beta 5428 5434 5431 5455 C1' A D 18 beta 5450 5456 5453 5477 C1' C D 19 beta 5472 5478 5475 5497 C1' G D 20 beta 5492 5498 5495 5520 C1' G D 21 beta 5515 5521 5518 5543 C1' A D 22 beta 5538 5544 5541 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4792 C2' A C 3 OK 4794 4790 4793 4814 C2' U C 4 OK 4816 4812 4815 4834 C2' G C 5 OK 4836 4832 4835 4857 C2' U C 6 OK 4859 4855 4858 4877 C2' U C 7 OK 4879 4875 4878 4897 C2' U C 8 OK 4899 4895 4898 4917 C2' U C 9 OK 4919 4915 4918 4937 C2' C C 10 OK 4939 4935 4938 4957 C2' U C 11 OK 4959 4955 4958 4977 C2' G C 12 OK 4979 4975 4978 5000 C2' G C 14 OK 5002 4998 5001 5023 C2' A C 15 OK 5025 5021 5024 5045 C2' A C 16 OK 5047 5043 5046 5067 C2' A C 17 OK 5069 5065 5068 5089 C2' A C 18 OK 5091 5087 5090 5111 C2' C C 19 OK 5113 5109 5112 5131 C2' G C 20 OK 5133 5129 5132 5154 C2' G C 21 OK 5156 5152 5155 5178 C2' G D 5 OK 5180 5176 5179 5201 C2' U D 6 OK 5203 5199 5202 5221 C2' U D 7 OK 5223 5219 5222 5241 C2' U D 8 OK 5243 5239 5242 5261 C2' U D 9 OK 5263 5259 5262 5281 C2' C D 10 OK 5283 5279 5282 5301 C2' U D 11 OK 5303 5299 5302 5321 C2' G D 12 OK 5323 5319 5322 5344 C2' U D 13 OK 5346 5342 5345 5364 C2' G D 14 OK 5366 5362 5365 5387 C2' A D 15 OK 5389 5385 5388 5409 C2' A D 16 OK 5411 5407 5410 5431 C2' A D 17 OK 5433 5429 5432 5453 C2' A D 18 OK 5455 5451 5454 5475 C2' C D 19 OK 5477 5473 5476 5495 C2' G D 20 OK 5497 5493 5496 5518 C2' G D 21 OK 5520 5516 5519 5541 C2' A D 22 OK 5543 5539 5542 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4790 C3' A C 3 OK 4788 4791 4792 4812 C3' U C 4 OK 4810 4813 4814 4832 C3' G C 5 OK 4830 4833 4834 4855 C3' U C 6 OK 4853 4856 4857 4875 C3' U C 7 OK 4873 4876 4877 4895 C3' U C 8 OK 4893 4896 4897 4915 C3' U C 9 OK 4913 4916 4917 4935 C3' C C 10 OK 4933 4936 4937 4955 C3' U C 11 OK 4953 4956 4957 4975 C3' G C 12 OK 4973 4976 4977 4998 C3' G C 14 OK 4996 4999 5000 5021 C3' A C 15 OK 5019 5022 5023 5043 C3' A C 16 OK 5041 5044 5045 5065 C3' A C 17 OK 5063 5066 5067 5087 C3' A C 18 OK 5085 5088 5089 5109 C3' C C 19 OK 5107 5110 5111 5129 C3' G C 20 OK 5127 5130 5131 5152 C3' G C 21 OK 5150 5153 5154 5176 C3' G D 5 OK 5174 5177 5178 5199 C3' U D 6 OK 5197 5200 5201 5219 C3' U D 7 OK 5217 5220 5221 5239 C3' U D 8 OK 5237 5240 5241 5259 C3' U D 9 OK 5257 5260 5261 5279 C3' C D 10 OK 5277 5280 5281 5299 C3' U D 11 OK 5297 5300 5301 5319 C3' G D 12 OK 5317 5320 5321 5342 C3' U D 13 OK 5340 5343 5344 5362 C3' G D 14 OK 5360 5363 5364 5385 C3' A D 15 OK 5383 5386 5387 5407 C3' A D 16 OK 5405 5408 5409 5429 C3' A D 17 OK 5427 5430 5431 5451 C3' A D 18 OK 5449 5452 5453 5473 C3' C D 19 OK 5471 5474 5475 5493 C3' G D 20 OK 5491 5494 5495 5516 C3' G D 21 OK 5514 5517 5518 5539 C3' A D 22 OK 5537 5540 5541 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4788 C4' A C 3 OK 4790 4787 4789 4810 C4' U C 4 OK 4812 4809 4811 4830 C4' G C 5 OK 4832 4829 4831 4853 C4' U C 6 OK 4855 4852 4854 4873 C4' U C 7 OK 4875 4872 4874 4893 C4' U C 8 OK 4895 4892 4894 4913 C4' U C 9 OK 4915 4912 4914 4933 C4' C C 10 OK 4935 4932 4934 4953 C4' U C 11 OK 4955 4952 4954 4973 C4' G C 12 OK 4975 4972 4974 4996 C4' G C 14 OK 4998 4995 4997 5019 C4' A C 15 OK 5021 5018 5020 5041 C4' A C 16 OK 5043 5040 5042 5063 C4' A C 17 OK 5065 5062 5064 5085 C4' A C 18 OK 5087 5084 5086 5107 C4' C C 19 OK 5109 5106 5108 5127 C4' G C 20 OK 5129 5126 5128 5150 C4' G C 21 OK 5152 5149 5151 5174 C4' G D 5 OK 5176 5173 5175 5197 C4' U D 6 OK 5199 5196 5198 5217 C4' U D 7 OK 5219 5216 5218 5237 C4' U D 8 OK 5239 5236 5238 5257 C4' U D 9 OK 5259 5256 5258 5277 C4' C D 10 OK 5279 5276 5278 5297 C4' U D 11 OK 5299 5296 5298 5317 C4' G D 12 OK 5319 5316 5318 5340 C4' U D 13 OK 5342 5339 5341 5360 C4' G D 14 OK 5362 5359 5361 5383 C4' A D 15 OK 5385 5382 5384 5405 C4' A D 16 OK 5407 5404 5406 5427 C4' A D 17 OK 5429 5426 5428 5449 C4' A D 18 OK 5451 5448 5450 5471 C4' C D 19 OK 5473 5470 5472 5491 C4' G D 20 OK 5493 5490 5492 5514 C4' G D 21 OK 5516 5513 5515 5537 C4' A D 22 OK 5539 5536 5538 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4787 C5' A C 3 4786 4788 4809 C5' U C 4 4808 4810 4829 C5' G C 5 4828 4830 4852 C5' U C 6 4851 4853 4872 C5' U C 7 4871 4873 4892 C5' U C 8 4891 4893 4912 C5' U C 9 4911 4913 4932 C5' C C 10 4931 4933 4952 C5' U C 11 4951 4953 4972 C5' G C 12 4971 4973 4995 C5' G C 14 4994 4996 5018 C5' A C 15 5017 5019 5040 C5' A C 16 5039 5041 5062 C5' A C 17 5061 5063 5084 C5' A C 18 5083 5085 5106 C5' C C 19 5105 5107 5126 C5' G C 20 5125 5127 5149 C5' G C 21 5148 5150 5173 C5' G D 5 5172 5174 5196 C5' U D 6 5195 5197 5216 C5' U D 7 5215 5217 5236 C5' U D 8 5235 5237 5256 C5' U D 9 5255 5257 5276 C5' C D 10 5275 5277 5296 C5' U D 11 5295 5297 5316 C5' G D 12 5315 5317 5339 C5' U D 13 5338 5340 5359 C5' G D 14 5358 5360 5382 C5' A D 15 5381 5383 5404 C5' A D 16 5403 5405 5426 C5' A D 17 5425 5427 5448 C5' A D 18 5447 5449 5470 C5' C D 19 5469 5471 5490 C5' G D 20 5489 5491 5513 C5' G D 21 5512 5514 5536 C5' A D 22 5535 5537 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4805 P U C 4 distorted distorted 4791 4806 4807 4808 4825 P G C 5 distorted distorted 4813 4826 4827 4828 4848 P U C 6 distorted distorted 4833 4849 4850 4851 4868 P U C 7 distorted distorted 4856 4869 4870 4871 4888 P U C 8 distorted distorted 4876 4889 4890 4891 4908 P U C 9 distorted distorted 4896 4909 4910 4911 4928 P C C 10 distorted distorted 4916 4929 4930 4931 4948 P U C 11 distorted distorted 4936 4949 4950 4951 4968 P G C 12 distorted distorted 4956 4969 4970 4971 4991 P G C 14 distorted distorted 4992 4993 4994 5014 P A C 15 distorted distorted 4999 5015 5016 5017 5036 P A C 16 distorted distorted 5022 5037 5038 5039 5058 P A C 17 distorted distorted 5044 5059 5060 5061 5080 P A C 18 distorted distorted 5066 5081 5082 5083 5102 P C C 19 distorted distorted 5088 5103 5104 5105 5122 P G C 20 distorted distorted 5110 5123 5124 5125 5145 P G C 21 distorted distorted 5130 5146 5147 5148 5169 P G D 5 OK OK 5170 5171 5172 5192 P U D 6 distorted distorted 5177 5193 5194 5195 5212 P U D 7 distorted distorted 5200 5213 5214 5215 5232 P U D 8 distorted distorted 5220 5233 5234 5235 5252 P U D 9 distorted distorted 5240 5253 5254 5255 5272 P C D 10 distorted distorted 5260 5273 5274 5275 5292 P U D 11 distorted distorted 5280 5293 5294 5295 5312 P G D 12 distorted distorted 5300 5313 5314 5315 5335 P U D 13 distorted distorted 5320 5336 5337 5338 5355 P G D 14 distorted distorted 5343 5356 5357 5358 5378 P A D 15 distorted distorted 5363 5379 5380 5381 5400 P A D 16 distorted distorted 5386 5401 5402 5403 5422 P A D 17 distorted distorted 5408 5423 5424 5425 5444 P A D 18 distorted distorted 5430 5445 5446 5447 5466 P C D 19 distorted distorted 5452 5467 5468 5469 5486 P G D 20 distorted distorted 5474 5487 5488 5489 5509 P G D 21 distorted distorted 5494 5510 5511 5512 5532 P A D 22 distorted distorted 5517 5533 5534 5535 ---------------------------------------------------------------------------------