ID code: '1T7P' 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' --------------------------------------------------------------------------------- 6081 C1' G P 12 beta 6077 6082 6080 6103 C1' C P 13 beta 6099 6104 6102 6122 C1' C P 14 beta 6118 6123 6121 6141 C1' A P 15 beta 6137 6142 6140 6162 C1' G P 16 beta 6158 6163 6161 6184 C1' T P 17 beta 6180 6185 6183 6204 C1' G P 18 beta 6200 6205 6203 6226 C1' C P 19 beta 6222 6227 6225 6245 C1' C P 20 beta 6241 6246 6244 6264 C1' A P 21 beta 6260 6265 6263 6284 C1' 2DA P 22 beta 6281 6285 6283 6374 C1' T T 5 beta 6370 6375 6373 6394 C1' T T 6 beta 6390 6395 6393 6414 C1' G T 7 beta 6410 6415 6413 6436 C1' G T 8 beta 6432 6437 6435 6458 C1' C T 9 beta 6454 6459 6457 6477 C1' A T 10 beta 6473 6478 6476 6498 C1' C T 11 beta 6494 6499 6497 6517 C1' T T 12 beta 6513 6518 6516 6537 C1' G T 13 beta 6533 6538 6536 6559 C1' G T 14 beta 6555 6560 6558 6581 C1' C T 15 beta 6577 6582 6580 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6080 C2' G P 12 6081 6078 6102 C2' C P 13 6103 6100 6121 C2' C P 14 6122 6119 6140 C2' A P 15 6141 6138 6161 C2' G P 16 6162 6159 6183 C2' T P 17 6184 6181 6203 C2' G P 18 6204 6201 6225 C2' C P 19 6226 6223 6244 C2' C P 20 6245 6242 6263 C2' A P 21 6264 6261 6283 C2' 2DA P 22 6284 6282 6373 C2' T T 5 6374 6371 6393 C2' T T 6 6394 6391 6413 C2' G T 7 6414 6411 6435 C2' G T 8 6436 6433 6457 C2' C T 9 6458 6455 6476 C2' A T 10 6477 6474 6497 C2' C T 11 6498 6495 6516 C2' T T 12 6517 6514 6536 C2' G T 13 6537 6534 6558 C2' G T 14 6559 6556 6580 C2' C T 15 6581 6578 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6078 C3' G P 12 OK 6076 6079 6080 6100 C3' C P 13 OK 6098 6101 6102 6119 C3' C P 14 OK 6117 6120 6121 6138 C3' A P 15 OK 6136 6139 6140 6159 C3' G P 16 OK 6157 6160 6161 6181 C3' T P 17 OK 6179 6182 6183 6201 C3' G P 18 OK 6199 6202 6203 6223 C3' C P 19 OK 6221 6224 6225 6242 C3' C P 20 OK 6240 6243 6244 6261 C3' A P 21 OK 6259 6262 6263 6282 C3' 2DA P 22 6280 6283 6371 C3' T T 5 OK 6369 6372 6373 6391 C3' T T 6 OK 6389 6392 6393 6411 C3' G T 7 OK 6409 6412 6413 6433 C3' G T 8 OK 6431 6434 6435 6455 C3' C T 9 OK 6453 6456 6457 6474 C3' A T 10 OK 6472 6475 6476 6495 C3' C T 11 OK 6493 6496 6497 6514 C3' T T 12 OK 6512 6515 6516 6534 C3' G T 13 OK 6532 6535 6536 6556 C3' G T 14 OK 6554 6557 6558 6578 C3' C T 15 OK 6576 6579 6580 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6076 C4' G P 12 OK 6078 6075 6077 6098 C4' C P 13 OK 6100 6097 6099 6117 C4' C P 14 OK 6119 6116 6118 6136 C4' A P 15 OK 6138 6135 6137 6157 C4' G P 16 OK 6159 6156 6158 6179 C4' T P 17 OK 6181 6178 6180 6199 C4' G P 18 OK 6201 6198 6200 6221 C4' C P 19 OK 6223 6220 6222 6240 C4' C P 20 OK 6242 6239 6241 6259 C4' A P 21 OK 6261 6258 6260 6280 C4' 2DA P 22 OK 6282 6279 6281 6369 C4' T T 5 OK 6371 6368 6370 6389 C4' T T 6 OK 6391 6388 6390 6409 C4' G T 7 OK 6411 6408 6410 6431 C4' G T 8 OK 6433 6430 6432 6453 C4' C T 9 OK 6455 6452 6454 6472 C4' A T 10 OK 6474 6471 6473 6493 C4' C T 11 OK 6495 6492 6494 6512 C4' T T 12 OK 6514 6511 6513 6532 C4' G T 13 OK 6534 6531 6533 6554 C4' G T 14 OK 6556 6553 6555 6576 C4' C T 15 OK 6578 6575 6577 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6075 C5' G P 12 6074 6076 6097 C5' C P 13 6096 6098 6116 C5' C P 14 6115 6117 6135 C5' A P 15 6134 6136 6156 C5' G P 16 6155 6157 6178 C5' T P 17 6177 6179 6198 C5' G P 18 6197 6199 6220 C5' C P 19 6219 6221 6239 C5' C P 20 6238 6240 6258 C5' A P 21 6257 6259 6279 C5' 2DA P 22 6278 6280 6368 C5' T T 5 6367 6369 6388 C5' T T 6 6387 6389 6408 C5' G T 7 6407 6409 6430 C5' G T 8 6429 6431 6452 C5' C T 9 6451 6453 6471 C5' A T 10 6470 6472 6492 C5' C T 11 6491 6493 6511 C5' T T 12 6510 6512 6531 C5' G T 13 6530 6532 6553 C5' G T 14 6552 6554 6575 C5' C T 15 6574 6576 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6093 P C P 13 OK OK 6079 6094 6095 6096 6112 P C P 14 OK OK 6101 6113 6114 6115 6131 P A P 15 OK OK 6120 6132 6133 6134 6152 P G P 16 OK OK 6139 6153 6154 6155 6174 P T P 17 OK OK 6160 6175 6176 6177 6194 P G P 18 OK OK 6182 6195 6196 6197 6216 P C P 19 OK OK 6202 6217 6218 6219 6235 P C P 20 OK OK 6224 6236 6237 6238 6254 P A P 21 OK OK 6243 6255 6256 6257 6275 P 2DA P 22 OK OK 6262 6276 6277 6278 6384 P T T 6 OK OK 6372 6385 6386 6387 6404 P G T 7 OK OK 6392 6405 6406 6407 6426 P G T 8 OK OK 6412 6427 6428 6429 6448 P C T 9 OK OK 6434 6449 6450 6451 6467 P A T 10 OK OK 6456 6468 6469 6470 6488 P C T 11 OK OK 6475 6489 6490 6491 6507 P T T 12 OK OK 6496 6508 6509 6510 6527 P G T 13 OK OK 6515 6528 6529 6530 6549 P G T 14 OK OK 6535 6550 6551 6552 6571 P C T 15 OK OK 6557 6572 6573 6574 ---------------------------------------------------------------------------------