Structural PDB Analyzer (Learning Project)

This project is a Python tool to analyze basic structural information from PDB files.

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Overview

This project performs structural analysis of proteins from PDB files, including:

• Parsing ATOM and HETATM records
• Residue extraction and classification
• Residue contact map generation
• Solvent Accessible Surface Area (SASA) calculation
• Relative SASA and residue exposure classification
• Comparative analysis of multiple proteins

The main objective was to implement core structural bioinformatics concepts manually to strengthen Python programming skills.

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What This Project Does (So Far)

1. Residue Analysis

• Counts atoms and residues
• Classifies residues into:
  • Hydrophobic
  • Polar
  • Charged
• Computes residue composition per chain

2. Contact Map

• Atom–atom distance calculation
• Residue–residue contact detection (cutoff-based)
• Binary contact matrix visualization

3. SASA and Structural Context

• Implemented using the Shrake–Rupley algorithm via Bio.PDB

• Per-residue SASA values (Ų)

• Relative SASA normalization using residue-specific reference values

• Residue exposure classification:

  • Buried (< 0.2)
  • Intermediate (0.2–0.5)
  • Exposed (> 0.5)

• Integration with residue contact analysis:

  • Number of contacts computed per residue
  • Allows comparison between solvent exposure and structural packing

• Observed trend:

  • Buried residues tend to have more contacts
  • Exposed residues tend to have fewer contacts

• Note:

  • Some residues may have relative SASA = None due to missing reference values (e.g., non-standard residues)

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Project Structure

utils.py
contact-map.py
single-protein-analyzer.py
multiple-protein-analyzer.py
sasa.py
data/

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Example Output

• Residue class bar plot
• Binary contact map
  
• CSV summary file
• Total and per-residue SASA values
• Relative SASA and exposure classification

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Notes

• The focus is educational.
• Simplified biochemical grouping for didactic purposes; therefore, it has some limitations.
• I am currently studying and exploring ways to improve the project.

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References

Berman, H. M., et al. (2000).
The Protein Data Bank.
Nucleic Acids Research, 28(1), 235–242.

Vendruscolo, M., & Domany, E. (1997).
Recovery of protein structure from contact maps.
Folding and Design.

Shrake, A., & Rupley, J. A. (1973). Environment and exposure to solvent of protein atoms. Journal of Molecular Biology.