Free energy (kcal/mol) 1 - FastContact

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The following energetic, structural and evolutionary properties are computed for each interface residue of a PPI:

• ΔG^FC: an estimate of the change of free energy (kcal/mol) for a residue upon complexation. Computed using FastContact (12). More negative values indicate a stronger interaction. 
  
  
• ΔΔG^R: an estimate of the change in free energy of an alanine mutation. Computed using Rosetta (13). More positive values indicate the mutation destabilizes the complex and thus the original residue has a stronger interaction. 
  
  
• ΔSASA: the change in solvent accessible surface area (SASA) of a residue. This is the difference between the SASA of the bound conformation of a chain in the complexed state and the bound conformation as an independent chain. Computed using naccess (http://www.bioinf.manchester.ac.uk/naccess/). 
  
  
• ΔSASA%: the relative ΔSASA as computed by naccess. Expressed as a percentage.
  
  
• Cons: a conservation score computed using Scorecons (32). A higher score indicates a higher degree of conservation. 
  
  
• Rate: an evolutionary rate computed using Rate4Site (33). A higher score indicates a higher rate and lower degree of conservation.

The full protocol for computing these properties is reported elsewhere (25). Any residue with ΔSASA > 0.05 Ų is treated as an interface residue. All possible clusters of interface residues with a maximal span of 12Å are computed. The cluster properties include the aggregated residue properties (minimum, maximum, average and total values) as well as the types of residues in the cluster, the size of the cluster (number of residues) and the maximal distance between cluster residues.