5.1 Class: MADS box factors (MADS)
Description: TRANSFAC® class description C0014: Proteins of this class comprise a region of homology. The DNA-binding domain also comprises the dimerization capability. In the DNA-bound dimer (shown for SRF), two antiparallel amphipathic alpha-helices (alpha-I), form a coiled coil and are oriented approximately parallel on the minor groove. These helices make minor and major groove contacts, the N-terminal extensions form minor groove contacts. The bound DNA is bent and wrapped around the protein. It exhibits a compressed minor groove in the center and widened minor groove in the flanks. (PMID 7637780)
Aligned domain sequences: Alignment of HMG domains
Download fasta file
Logo plot:
Blue: basic residues (KRH); red: acidic residues (DE); purple: amides (QN); black: hydrophobic residues (AVLIPWFM); green: polar (CSTYG) (http://weblogo.berkeley.edu/)