CHC_FIND

CHC_FIND identifies conserved hydrophobic contacts (CHCs) within protein families and superfamilies using 3D structural data and homologous sequences to reveal structural and functional conservation.

Key Features:

• Conservation analysis: Identifies conserved residue-to-residue hydrophobic contacts involving apolar atoms across multiple protein 3D conformations within a family or superfamily.
• Structural and sequence alignment integration: Requires a multiple sequence alignment and a structural alignment of structurally conserved regions (SCRs) to map equivalent residues across homologues for CHC assessment.
• Structurally conserved region (SCR) identification: Detects segments that maintain similar main-chain conformations to restrict contact analysis to structurally relevant residues.
• Visualization of conserved features: Produces representations of SCRs, CHCs, and evolutionarily conserved residues (ECRs) on superposed protein structures.

Scientific Applications:

• Functional insights: Elucidates conserved hydrophobic interactions that contribute to protein stability, interaction interfaces, and active sites.
• Structural conservation studies: Assesses evolutionary constraints on protein architecture across homologous sequences and superfamilies.
• Drug design and protein engineering: Identifies conserved hydrophobic regions relevant for targeting binding sites or preserving essential structural features during engineering.

Methodology:

Analyzes homologous sequences and corresponding 3D structures, uses multiple sequence alignments and structural alignments of SCRs, and computes residue-to-residue hydrophobic contacts conserved across the analyzed protein set by identifying segments with similar main-chain conformations.