Protein analysis

• Secondary Structure, symmetry and accessibility
• The secondary structure according to DSSP will be listed. Residues that make a symmetry contact in the crystal and residues that are clearly accessible to solvent (this time not taking crystal contacts into account) will be indicated.

  This is a secondary structure determination from 3D coordinates, and NOT a secondary structure prediction.
  
  
  

• Torsion angles
• The torsion angles in all amino acids in the PDB file will be tabulated. Angles will be in degrees. A torsion angle of 999 degrees indicates that this torsion angle does not exist (e.g. phi of the N-terminal residue), or that there is something wrong with at least one of the atoms involved.
  
  
  
• Accessible Polar Fraction
• Using this service you can calculate the scores described by Bowie, Luthy and EiseNberg.
  
  
  
• Check for Short Interatomic Distances
• Find interatomic clashes (bumps).
  
  
  
• Relative Surface exposure.
• Often normal accessibility calculations exaggerate things. This server calculates for every residue what its accessibility would be if you would have mutated it into an alanine.
  
  
  
• Accessible Molecular Surface
• The accessible molecular surface is calculated using the WHAT IF method as described in chapter 9 of the WHAT IF writeup.
  
  
  
• Accessible Molecular Surface, Relative to Vaccum
• The accessible molecular surface is calculated, relative to what the accessibility would be in vacuum. See chapter 9 of the WHAT IF writeup.
  
  
  
• Analyse Protein - Cofactor Contacts
• This server calculates contacts between macromolecules (protein and nucleic acids) at the one hand and co-factors, ligands, drugs and ions at the other.
  
  
  
• Analyse Protein-DNA/RNA Contacts
• This server calculates contacts between proteins at the one hand and nucleic acids at the other.
  
  
  
• Bond angles
• The backbone bond angles in all amino acids in the PDB file will be tabulated. Angles will be in degrees. The first and last amino acid of each chain will be skipped.