Conserved features of protein-DNA interaction in all X-ray characterized families of DNA-binding proteins N.N. (GI/MR/M) / N.N. (GI/MR/M) Introduction bbb Figure 1 Nucleic Acid – Protein Interaction DataBase Figure 2 SCOP family characteristic Figure 3 Classification of protein-DNA interactions Figure 4 Type example Summary & Outlook All 110 well-represented by structural data protein domain families were characterized and conserved features were identified. Proposed classification into types of protein-DNA interaction allows revealing specific features of interaction with DNA within protein families. The results are included into NPIDB. Thus, NPIDB provides users with comprehensive information on structural features of protein domains interacting with DNA. Review of types of protein-DNA interactions basing on the obtained information will be done in forthcoming publication. All these results are publicly available at NPIDB site ( №Protein recognizing element(s) DNA (groove /backbon e) Protein recognizing element(s) DNA (groove /backbon e) 1HelixesMajor grv. 2Helixes +LoopsMajor grv. 3Sheets + LoopsMajor grv. 4LoopsMajor grv. 5HelixesMinor grv. 6Helixes +LoopsMinor grv. 7Sheets + LoopsMinor grv. 8LoopsMinor grv. 9HelixesMajor grv.Any element(s)Minor grv. 10Helixes +LoopsMajor grv.Any element(s)Minor grv. 11Sheets + LoopsMajor grv.Any element(s)Minor grv. 12Helixes +Sheets +LoopsMajor grv.Any element(s)Minor grv. 13LoopsMajor grv.Any element(s)Minor grv. 14Any element(s)Major grv.HelixesMinor grv. 15Any element(s)Major grv.Helixes +LoopsMinor grv. 16Any element(s)Major grv.Sheets + LoopsMinor grv. 17Any element(s)Major grv.Helixes +Sheets +LoopsMinor grv. 18Any element(s)Major grv.LoopsMinor grv. 19Any element(s)Major grv.Any element(s)Minor grv. 20Non-specific interaction with backbone Major groove: 14,15,16,17,18) Any element Minor groove: 14)Helices 15)Helices +Loops 16)Sheets + Loops 17)Helices + Sheets +Loops 18)Loops AND  -sheet in minor groove Prokaryotic DNA-bending protein 1owf_A "Histone-like" proteins from Archaea 1azp_A DNA repair protein MutS, domain I 1w7a_A2-116 TATA-box binding protein (TBP), C-terminal domain 1cdw_A Introduction At the moment more than 1500 structures of protein-DNA complexes are available. Among them there are complexes with proteins that specifically or non-specifically interact with DNA. Proteins interact with DNA in different ways: using helixes, sheets, strands and turns of protein; via major/minor groove, sugar-phosphate backbone of DNA; different combinations of interactions are possible. Development of approaches in systematization of protein-DNA complexes is necessary for understanding mechanisms of protein-DNA interaction. Results In our group, Nucleic Acid – Protein Interaction DataBase (NPIDB; Spirin,S. et.al. Bioinformatics 2007, 23 (23):3247-8) was created. NPIDB contains structures of DNA-protein and RNA-protein complexes supported with search, navigation and analysis tools. For each structure from NPIDB it is possible to download the PDB-structure, find hydrophobic clusters, hydrogen bonds, potential water bridges between protein and DNA; view sequence, view the 3D structure in Jmol, explore link to Pfam and SCOP [fig.1]. Systematization of structural data is performed by classification of protein-DNA interactions. As units of classification, we used structural SCOP (release 1.73, November 2007) domains {fig2}. Basing on interacting elements of protein (helix, sheet, strand, turn) and DNA (the major/minor groove, sugar-phosphate backbone), 20 types of protein-DNA interaction were suggested [fig.3]. Specific contacts and the type of protein-DNA interaction are determined for each DNA-binding protein [fig.4]. Also 110 SCOP domain families containing more than one structure of protein in contact with DNA in PDB files were characterized. For each family, a sequence alignment and a structural alignment were constructed; conserved features including conserved protein-DNA interaction were identified [fig.2]. Types of protein-DNA interaction Examples of some types of protein-DNA interaction Distribution of SCOP families number in each type