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$C_{i,j} = \frac{1}{2}(c_i + c_j)$ This is the basic contact map formula where $C_{i,j}$ represents the contact between residues $i$ and $j$, and $c_i$ represents some property of residue $i$. However, I notice this doesn't seem right for a standard contact map. Let me think about what you're asking for. A contact map typically represents which residues in a protein structure are close to each other in 3D space. The standard definition is: $C_{i,j} = \begin{cases} 1 & \text{if } d_{i,j} < d_{cutoff} \\ 0 & \text{otherwise} \end{cases}$ Where $d_{i,j}$ is the distance between residues $i$ and $j$ (usually measured between Cα atoms or Cβ atoms), and $d_{cutoff}$ is typically 6-8 Å. If you're asking about the formula you wrote: $$C_{i,j} = \frac{1}{2}(c_i + c_j)$$ This looks like it might be related to: - **Averaging some property** (like hydrophobicity, charge, or conservation score) between two residues - **A simplified model** for contact potential or energy terms Could you clarify what this formula represents? For example: - Is $c_i$ a property like hydrophobicity, charge, or B-factor? - Is this for a specific potential energy function? - Is this from a particular paper or method (like mean force potential, contact prediction, etc.)? With more context, I can give you a more precise answer about what this formula means and how it's used.
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