ID code: '3BT7' 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' --------------------------------------------------------------------------------- 5931 C1' G C 48 beta 5926 5932 5929 5954 C1' C C 49 beta 5949 5955 5952 5974 C1' U C 50 beta 5969 5975 5972 5994 C1' G C 51 beta 5989 5995 5992 6017 C1' U C 52 beta 6012 6018 6015 6037 C1' G C 53 beta 6032 6038 6035 6058 C1' 5MU C 54 beta 6064 6049 6059 6081 C1' U C 55 beta 6076 6082 6079 6101 C1' C C 56 beta 6096 6102 6099 6121 C1' G C 57 beta 6116 6122 6119 6144 C1' A C 58 beta 6139 6145 6142 6166 C1' U C 59 beta 6161 6167 6164 6186 C1' C C 60 beta 6181 6187 6184 6206 C1' C C 61 beta 6201 6207 6204 6226 C1' A C 62 beta 6221 6227 6224 6248 C1' C C 63 beta 6243 6249 6246 6268 C1' A C 64 beta 6263 6269 6266 6290 C1' G C 65 beta 6285 6291 6288 6313 C1' C C 66 beta 6308 6314 6311 6334 C1' G D 48 beta 6329 6335 6332 6357 C1' C D 49 beta 6352 6358 6355 6377 C1' U D 50 beta 6372 6378 6375 6397 C1' G D 51 beta 6392 6398 6395 6420 C1' U D 52 beta 6415 6421 6418 6440 C1' G D 53 beta 6435 6441 6438 6461 C1' 5MU D 54 beta 6467 6452 6462 6484 C1' U D 55 beta 6479 6485 6482 6504 C1' C D 56 beta 6499 6505 6502 6524 C1' G D 57 beta 6519 6525 6522 6547 C1' A D 58 beta 6542 6548 6545 6569 C1' U D 59 beta 6564 6570 6567 6589 C1' C D 60 beta 6584 6590 6587 6609 C1' C D 61 beta 6604 6610 6607 6629 C1' A D 62 beta 6624 6630 6627 6651 C1' C D 63 beta 6646 6652 6649 6671 C1' A D 64 beta 6666 6672 6669 6693 C1' G D 65 beta 6688 6694 6691 6716 C1' C D 66 beta 6711 6717 6714 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5929 C2' G C 48 OK 5931 5927 5930 5952 C2' C C 49 OK 5954 5950 5953 5972 C2' U C 50 OK 5974 5970 5973 5992 C2' G C 51 OK 5994 5990 5993 6015 C2' U C 52 OK 6017 6013 6016 6035 C2' G C 53 OK 6037 6033 6036 6059 C2' 5MU C 54 OK 6058 6061 6060 6079 C2' U C 55 OK 6081 6077 6080 6099 C2' C C 56 OK 6101 6097 6100 6119 C2' G C 57 OK 6121 6117 6120 6142 C2' A C 58 OK 6144 6140 6143 6164 C2' U C 59 OK 6166 6162 6165 6184 C2' C C 60 OK 6186 6182 6185 6204 C2' C C 61 OK 6206 6202 6205 6224 C2' A C 62 OK 6226 6222 6225 6246 C2' C C 63 OK 6248 6244 6247 6266 C2' A C 64 OK 6268 6264 6267 6288 C2' G C 65 OK 6290 6286 6289 6311 C2' C C 66 OK 6313 6309 6312 6332 C2' G D 48 OK 6334 6330 6333 6355 C2' C D 49 OK 6357 6353 6356 6375 C2' U D 50 OK 6377 6373 6376 6395 C2' G D 51 OK 6397 6393 6396 6418 C2' U D 52 OK 6420 6416 6419 6438 C2' G D 53 OK 6440 6436 6439 6462 C2' 5MU D 54 OK 6461 6464 6463 6482 C2' U D 55 OK 6484 6480 6483 6502 C2' C D 56 OK 6504 6500 6503 6522 C2' G D 57 OK 6524 6520 6523 6545 C2' A D 58 OK 6547 6543 6546 6567 C2' U D 59 OK 6569 6565 6568 6587 C2' C D 60 OK 6589 6585 6588 6607 C2' C D 61 OK 6609 6605 6608 6627 C2' A D 62 OK 6629 6625 6628 6649 C2' C D 63 OK 6651 6647 6650 6669 C2' A D 64 OK 6671 6667 6670 6691 C2' G D 65 OK 6693 6689 6692 6714 C2' C D 66 OK 6716 6712 6715 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5927 C3' G C 48 OK 5925 5928 5929 5950 C3' C C 49 OK 5948 5951 5952 5970 C3' U C 50 OK 5968 5971 5972 5990 C3' G C 51 OK 5988 5991 5992 6013 C3' U C 52 OK 6011 6014 6015 6033 C3' G C 53 OK 6031 6034 6035 6061 C3' 5MU C 54 OK 6062 6063 6059 6077 C3' U C 55 OK 6075 6078 6079 6097 C3' C C 56 OK 6095 6098 6099 6117 C3' G C 57 OK 6115 6118 6119 6140 C3' A C 58 OK 6138 6141 6142 6162 C3' U C 59 OK 6160 6163 6164 6182 C3' C C 60 OK 6180 6183 6184 6202 C3' C C 61 OK 6200 6203 6204 6222 C3' A C 62 OK 6220 6223 6224 6244 C3' C C 63 OK 6242 6245 6246 6264 C3' A C 64 OK 6262 6265 6266 6286 C3' G C 65 OK 6284 6287 6288 6309 C3' C C 66 OK 6307 6310 6311 6330 C3' G D 48 OK 6328 6331 6332 6353 C3' C D 49 OK 6351 6354 6355 6373 C3' U D 50 OK 6371 6374 6375 6393 C3' G D 51 OK 6391 6394 6395 6416 C3' U D 52 OK 6414 6417 6418 6436 C3' G D 53 OK 6434 6437 6438 6464 C3' 5MU D 54 OK 6465 6466 6462 6480 C3' U D 55 OK 6478 6481 6482 6500 C3' C D 56 OK 6498 6501 6502 6520 C3' G D 57 OK 6518 6521 6522 6543 C3' A D 58 OK 6541 6544 6545 6565 C3' U D 59 OK 6563 6566 6567 6585 C3' C D 60 OK 6583 6586 6587 6605 C3' C D 61 OK 6603 6606 6607 6625 C3' A D 62 OK 6623 6626 6627 6647 C3' C D 63 OK 6645 6648 6649 6667 C3' A D 64 OK 6665 6668 6669 6689 C3' G D 65 OK 6687 6690 6691 6712 C3' C D 66 OK 6710 6713 6714 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5925 C4' G C 48 OK 5927 5924 5926 5948 C4' C C 49 OK 5950 5947 5949 5968 C4' U C 50 OK 5970 5967 5969 5988 C4' G C 51 OK 5990 5987 5989 6011 C4' U C 52 OK 6013 6010 6012 6031 C4' G C 53 OK 6033 6030 6032 6062 C4' 5MU C 54 OK 6061 6065 6064 6075 C4' U C 55 OK 6077 6074 6076 6095 C4' C C 56 OK 6097 6094 6096 6115 C4' G C 57 OK 6117 6114 6116 6138 C4' A C 58 OK 6140 6137 6139 6160 C4' U C 59 OK 6162 6159 6161 6180 C4' C C 60 OK 6182 6179 6181 6200 C4' C C 61 OK 6202 6199 6201 6220 C4' A C 62 OK 6222 6219 6221 6242 C4' C C 63 OK 6244 6241 6243 6262 C4' A C 64 OK 6264 6261 6263 6284 C4' G C 65 OK 6286 6283 6285 6307 C4' C C 66 OK 6309 6306 6308 6328 C4' G D 48 OK 6330 6327 6329 6351 C4' C D 49 OK 6353 6350 6352 6371 C4' U D 50 OK 6373 6370 6372 6391 C4' G D 51 OK 6393 6390 6392 6414 C4' U D 52 OK 6416 6413 6415 6434 C4' G D 53 OK 6436 6433 6435 6465 C4' 5MU D 54 OK 6464 6468 6467 6478 C4' U D 55 OK 6480 6477 6479 6498 C4' C D 56 OK 6500 6497 6499 6518 C4' G D 57 OK 6520 6517 6519 6541 C4' A D 58 OK 6543 6540 6542 6563 C4' U D 59 OK 6565 6562 6564 6583 C4' C D 60 OK 6585 6582 6584 6603 C4' C D 61 OK 6605 6602 6604 6623 C4' A D 62 OK 6625 6622 6624 6645 C4' C D 63 OK 6647 6644 6646 6665 C4' A D 64 OK 6667 6664 6666 6687 C4' G D 65 OK 6689 6686 6688 6710 C4' C D 66 OK 6712 6709 6711 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5924 C5' G C 48 5923 5925 5947 C5' C C 49 5946 5948 5967 C5' U C 50 5966 5968 5987 C5' G C 51 5986 5988 6010 C5' U C 52 6009 6011 6030 C5' G C 53 6029 6031 6065 C5' 5MU C 54 6066 6062 6074 C5' U C 55 6073 6075 6094 C5' C C 56 6093 6095 6114 C5' G C 57 6113 6115 6137 C5' A C 58 6136 6138 6159 C5' U C 59 6158 6160 6179 C5' C C 60 6178 6180 6199 C5' C C 61 6198 6200 6219 C5' A C 62 6218 6220 6241 C5' C C 63 6240 6242 6261 C5' A C 64 6260 6262 6283 C5' G C 65 6282 6284 6306 C5' C C 66 6305 6307 6327 C5' G D 48 6326 6328 6350 C5' C D 49 6349 6351 6370 C5' U D 50 6369 6371 6390 C5' G D 51 6389 6391 6413 C5' U D 52 6412 6414 6433 C5' G D 53 6432 6434 6468 C5' 5MU D 54 6469 6465 6477 C5' U D 55 6476 6478 6497 C5' C D 56 6496 6498 6517 C5' G D 57 6516 6518 6540 C5' A D 58 6539 6541 6562 C5' U D 59 6561 6563 6582 C5' C D 60 6581 6583 6602 C5' C D 61 6601 6603 6622 C5' A D 62 6621 6623 6644 C5' C D 63 6643 6645 6664 C5' A D 64 6663 6665 6686 C5' G D 65 6685 6687 6709 C5' C D 66 6708 6710 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5920 P G C 48 distorted distorted 5921 5922 5923 5943 P C C 49 distorted distorted 5928 5944 5945 5946 5963 P U C 50 distorted distorted 5951 5964 5965 5966 5983 P G C 51 distorted distorted 5971 5984 5985 5986 6006 P U C 52 distorted distorted 5991 6007 6008 6009 6026 P G C 53 distorted distorted 6014 6027 6028 6029 6067 P 5MU C 54 distorted distorted 6034 6068 6069 6066 6070 P U C 55 distorted distorted 6063 6071 6072 6073 6090 P C C 56 distorted distorted 6078 6091 6092 6093 6110 P G C 57 distorted distorted 6098 6111 6112 6113 6133 P A C 58 distorted distorted 6118 6134 6135 6136 6155 P U C 59 distorted distorted 6141 6156 6157 6158 6175 P C C 60 distorted distorted 6163 6176 6177 6178 6195 P C C 61 distorted distorted 6183 6196 6197 6198 6215 P A C 62 distorted distorted 6203 6216 6217 6218 6237 P C C 63 distorted distorted 6223 6238 6239 6240 6257 P A C 64 distorted distorted 6245 6258 6259 6260 6279 P G C 65 distorted distorted 6265 6280 6281 6282 6302 P C C 66 distorted distorted 6287 6303 6304 6305 6323 P G D 48 distorted distorted 6324 6325 6326 6346 P C D 49 distorted distorted 6331 6347 6348 6349 6366 P U D 50 distorted distorted 6354 6367 6368 6369 6386 P G D 51 distorted distorted 6374 6387 6388 6389 6409 P U D 52 distorted distorted 6394 6410 6411 6412 6429 P G D 53 distorted distorted 6417 6430 6431 6432 6470 P 5MU D 54 distorted distorted 6437 6471 6472 6469 6473 P U D 55 distorted distorted 6466 6474 6475 6476 6493 P C D 56 distorted distorted 6481 6494 6495 6496 6513 P G D 57 distorted distorted 6501 6514 6515 6516 6536 P A D 58 distorted distorted 6521 6537 6538 6539 6558 P U D 59 distorted distorted 6544 6559 6560 6561 6578 P C D 60 distorted distorted 6566 6579 6580 6581 6598 P C D 61 distorted distorted 6586 6599 6600 6601 6618 P A D 62 distorted distorted 6606 6619 6620 6621 6640 P C D 63 distorted distorted 6626 6641 6642 6643 6660 P A D 64 distorted distorted 6648 6661 6662 6663 6682 P G D 65 distorted distorted 6668 6683 6684 6685 6705 P C D 66 distorted distorted 6690 6706 6707 6708 ---------------------------------------------------------------------------------