A protocol for protein structure analysis

Created by Possu Huang. Last updated 181229 AEC

1. Begin by analyzing the topology. 
    - Check where the termini are.
    - Check how secondary structures are connected.
2. Identify folds.
    - Some of the common folds include Rossmann, ferredoxin, TIM barrel, and helix bundle.
3. Check how reliable the given crystal structure is.
    - resolution: 2 Angstrom or lower?
    - R-factor: 0.3 or lower?
    - R-free cross validation: within 5% difference?
    - loop bending: is it an artifact due to crystallization?
4. Check packing quality.
5. Check how secondary structure ends.
6. Examine alpha helices.
    - N-terminal capping: D/N/S/T or P 
    - straight helices: salt bridges to stabilize
    - bending: pi helices or P
7. Examine specific residues.
    - tryptophan: stabilization of indole N by H-bonding
    - tyrosine: is OH on the same plane as the aromatic ring?
    - cysteine: when a disulfide is formed, is the dihedral angle around 90 degC?
8. check phi psi angles, beta turn chirality
9. buried polar groups and unsatisfied hydrogen bonds including from the backbone