,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 3 0 6 0 1 1 1 0 1 3 0 0 0 5 3 0 0 3 NE NH1 0 12 1 13 0 5 0 7 0 2 6 0 17 0 6 16 0 3 4 NH1 NH2 0 15 1 17 0 9 1 4 0 8 9 0 7 0 7 13 0 5 3 NH2 , LYS K ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- LYS K NZ 0 4 2 16 0 8 2 4 0 10 14 0 10 0 14 24 0 2 8 NZ , SER S ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SER S OG 0 6 1 9 0 5 0 7 0 8 7 0 1 0 10 10 0 2 6 OG , THR T ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- THR T OG1 0 8 4 6 0 3 1 5 0 3 9 0 5 0 9 5 0 2 2 OG1 , ASN N ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ASN N OD1 0 5 4 13 0 4 0 8 0 4 7 0 0 0 2 6 0 4 9 OD1 ND2 0 5 4 11 0 3 0 3 0 3 7 0 3 0 6 9 0 1 7 ND2 , GLN Q ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GLN Q OE1 0 5 0 10 0 0 0 12 0 2 5 0 2 0 4 5 0 1 1 OE1 NE2 0 1 1 3 0 7 0 0 0 2 6 0 2 0 3 4 0 1 1 NE2 , HIS H ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- HIS H ND1 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 3 0 0 0 ND1 NE2 0 5 0 1 0 2 0 2 0 0 1 0 2 0 2 0 0 1 0 NE2 , TYR Y ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TYR Y OH 0 6 2 6 0 2 0 1 0 6 3 0 1 0 6 6 0 3 5 OH , GLU E ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GLU E OE1 0 6 4 7 0 5 1 15 0 1 7 0 1 0 1 3 0 0 4 OE1 OE2 0 5 0 7 0 2 0 13 0 1 6 0 0 0 2 4 0 2 0 OE2 , ASP D ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ASP D OD1 0 3 3 3 0 1 2 3 0 2 6 0 0 0 0 5 0 2 3 OD1 OD2 0 1 4 6 0 2 0 13 0 2 5 0 1 0 3 4 0 1 2 OD2 , CYS C ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CYS C SG 0 0 0 1 0 0 0 1 0 1 1 0 0 0 1 0 0 0 0 SG , MET M ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- MET M SD 0 1 0 0 - - - - 0 0 1 0 1 - - - - - - SD , TRP W ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TRP W NE1 0 3 0 0 - - - - 0 0 1 0 0 0 1 1 0 0 2 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