,Espinosa Angarica,V. et al.(2008) Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics, 9:436. ,Fri Dec 13 01:49:46 2024 entries=634 ,----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- , AMINOACIDS THYMINE CYTOSINE ADENINE GUANINE AMINOACIDS ,----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ,----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- , N1 O2 N3 O4 N1 O2 N3 N4 N9 N7 N6 N1 N3 N9 N7 O6 N1 N2 N3 ,----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- , , ARG R ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ARG R NE 0 14 0 9 0 14 0 0 0 1 0 0 7 0 32 21 0 0 3 NE NH1 0 59 0 22 0 27 5 0 0 11 0 0 24 0 120 123 0 0 10 NH1 NH2 0 58 0 33 0 25 11 0 0 4 0 0 21 0 154 179 0 0 17 NH2 , LYS K ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- LYS K NZ 0 46 0 40 0 20 3 0 0 19 0 0 14 0 89 121 0 0 5 NZ , SER S ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SER S OG 0 19 5 16 0 6 5 17 0 24 11 0 9 0 19 12 0 9 4 OG , THR T ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- THR T OG1 0 4 4 11 0 2 1 8 0 5 2 0 2 0 4 7 0 7 1 OG1 , ASN N ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ASN N OD1 0 0 12 0 0 0 0 13 0 0 45 0 0 0 0 0 0 14 0 OD1 ND2 0 28 0 37 0 18 0 0 0 38 0 0 8 0 11 26 0 0 14 ND2 , GLN Q ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GLN Q OE1 0 0 6 0 0 0 0 11 0 0 31 0 0 0 0 0 0 16 0 OE1 NE2 0 12 0 29 0 7 1 0 0 35 0 0 7 0 6 23 0 0 12 NE2 , HIS H ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HIS H ND1 0 0 0 4 0 1 1 1 0 0 2 0 0 0 8 7 0 0 1 ND1 NE2 0 6 0 9 0 4 0 1 0 2 0 0 2 0 9 27 0 1 1 NE2 , TYR Y ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TYR Y OH 0 5 1 5 0 3 2 9 0 6 7 0 7 0 5 2 0 8 4 OH , GLU E ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GLU E OE1 0 0 3 0 0 0 0 37 0 0 4 0 0 0 0 0 0 10 0 OE1 OE2 0 0 4 0 0 0 0 30 0 0 5 0 0 0 0 0 0 7 0 OE2 , ASP D ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ASP D OD1 0 0 1 0 0 0 0 17 0 0 5 0 0 0 0 0 0 12 0 OD1 OD2 0 0 7 0 0 0 0 34 0 0 5 0 0 0 0 0 0 15 0 OD2 , CYS C ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CYS C SG 0 0 0 4 0 1 0 0 0 1 1 0 1 - - - - - - SG , MET M ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MET M SD 0 0 1 0 - - - - 0 0 2 0 0 - - - - - - SD , TRP W ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TRP W NE1 0 3 0 1 0 4 0 0 - - - - - - - - - - - NE1 ,----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ,----------------------------------------------------- , AMINOACID CODE TOTAL AA TOTAL CONTACTS ,----------------------------------------------------- , ARG R 11680 1243 , LYS K 12775 494 , SER S 10746 248 , THR T 8928 143 , ASN N 7580 404 , GLN Q 7534 284 , GLY G 10883 0 , HIS H 4483 114 , TYR Y 6161 136 , ALA A 12886 34 , GLU E 12778 205 , ILE I 10804 18 , ASP D 9634 183 , VAL V 11410 38 , CYS C 2590 15 , PHE F 7289 38 , LEU L 18142 28 , MET M 3631 15 , TRP W 2399 28 , PRO P 7699 15 , ,----------------------------- ,BASE TOTAL ,----------------------------- , DT 7577 , DC 5925 , DA 6843 , DG 5956 ,----------------------------------------------------- ,Total aminoacids = 180032 ,Total bases = 26301