Protein Molecular Weight Calculator

Protein & Peptide Analysis Tool

Calculate molecular weight, extinction coefficient, isoelectric point, and comprehensive protein analysis with professional accuracy for research and clinical applications.

Protein & Peptide Molecular Weight Calculator

✓ Easy to Use
Enter your amino acid sequence using single-letter codes (e.g., MVHLTPEEKS) or three-letter codes (e.g., Met-Val-His) to calculate molecular weight and other protein properties.
Use single-letter codes (A, C, D, E, etc.) or three-letter codes (Ala, Cys, Asp, Glu, etc.)
Disulfide bonds affect molecular weight
Common N-terminal modifications
Common C-terminal modifications
Molecular Weight
–
Daltons (Da)
Exact molecular mass of the protein/peptide
Amino Acid Count
–
Residues
Total number of amino acids in sequence
Extinction Coefficient
–
M⁻¹cm⁻¹
At 280 nm (reduced cysteines)
Isoelectric Point (pI)
–
pH
pH at which protein has zero net charge
Aromaticity
–
%
Percentage of aromatic amino acids
Instability Index
–
Score
Protein stability prediction

Amino Acid Composition Analysis

⚠️ Important Information
This calculator provides theoretical values based on amino acid composition. Actual protein properties may vary due to post-translational modifications, folding, and environmental conditions. For critical applications, verify results experimentally.

Advanced Protein Analysis

✓ Comprehensive Analysis
Perform detailed protein analysis including GRAVY index, aliphatic index, atomic composition, and more advanced protein properties.
Single-letter amino acid codes
For charge calculations (0-14)
GRAVY Index
–
Score
Grand Average of Hydropathicity
Aliphatic Index
–
Score
Relative volume of aliphatic side chains
Net Charge
–
Charge
At specified pH value
Hydrophobic Ratio
–
%
Percentage of hydrophobic residues
Helix Propensity
–
%
Likelihood to form alpha helix
Sheet Propensity
–
%
Likelihood to form beta sheet

Atomic Composition

⚠️ Advanced Analysis Note
Advanced calculations are based on empirical data and statistical models. Results should be validated with experimental methods for critical applications.

Amino Acid Reference Table

Complete reference for all 20 standard amino acids with their properties and molecular weights.

Amino Acid 3-Letter Code 1-Letter Code Molecular Weight (Da) Type Properties
Alanine Ala A 89.09 Nonpolar Small, hydrophobic
Arginine Arg R 174.20 Positive Basic, charged
Asparagine Asn N 132.12 Polar Amide side chain
Aspartic Acid Asp D 133.10 Negative Acidic, charged
Cysteine Cys C 121.15 Polar Thiol, disulfide bonds
Glutamic Acid Glu E 147.13 Negative Acidic, charged
Glutamine Gln Q 146.15 Polar Amide side chain
Glycine Gly G 75.07 Nonpolar Smallest, flexible
Histidine His H 155.16 Positive Aromatic, imidazole
Isoleucine Ile I 131.17 Nonpolar Hydrophobic, branched
Leucine Leu L 131.17 Nonpolar Hydrophobic, branched
Lysine Lys K 146.19 Positive Basic, charged
Methionine Met M 149.21 Nonpolar Sulfur-containing
Phenylalanine Phe F 165.19 Nonpolar Aromatic, hydrophobic
Proline Pro P 115.13 Nonpolar Cyclic, rigid
Serine Ser S 105.09 Polar Hydroxyl, phosphorylation
Threonine Thr T 119.12 Polar Hydroxyl, phosphorylation
Tryptophan Trp W 204.23 Nonpolar Aromatic, indole
Tyrosine Tyr Y 181.19 Polar Aromatic, phenol
Valine Val V 117.15 Nonpolar Hydrophobic, branched

Understanding Amino Acid Properties

🔬
Nonpolar (Hydrophobic)
Repel water, found in protein interior: Ala, Val, Leu, Ile, Met, Phe, Trp, Pro
💧
Polar (Hydrophilic)
Interact with water, found on surface: Ser, Thr, Asn, Gln, Tyr, Cys
➕
Positively Charged
Basic side chains at physiological pH: Lys, Arg, His
➖
Negatively Charged
Acidic side chains at physiological pH: Asp, Glu
🔗
Special Functions
Unique roles: Cys (disulfide bonds), Pro (flexibility), Gly (turns)
⭐
Aromatic
Contain aromatic rings: Phe, Tyr, Trp (important for UV absorption)

Understanding Protein Molecular Weight & Analysis

📚 Educational Resources
Learn about protein molecular weight calculations, analysis methods, and how to use this calculator effectively.

What is Molecular Weight?

Definition
Molecular weight (MW) is the sum of the atomic weights of all atoms in a molecule. For proteins and peptides, it’s calculated by summing the molecular weights of all constituent amino acids, minus water molecules lost during peptide bond formation.

Key Concepts:

Daltons (Da)

The unit of molecular weight. 1 Da = 1/12 of the mass of a carbon-12 atom. Proteins are often expressed in kilodaltons (kDa) or megadaltons (MDa).

Extinction Coefficient

Measures how strongly a protein absorbs light at 280 nm. Determined by aromatic amino acids (Trp, Tyr, Phe). Used to calculate protein concentration from absorbance measurements.

Isoelectric Point (pI)

The pH at which a protein has zero net electrical charge. At this pH, the protein is least soluble and may precipitate. Important for protein purification.

GRAVY Index

Grand Average of Hydropathicity. Measures overall hydrophobicity of a protein. Positive values indicate hydrophobic proteins; negative values indicate hydrophilic proteins.

Aliphatic Index

Relative volume of aliphatic side chains (Val, Ile, Leu). Higher values indicate greater thermal stability. Ranges from 0 to 100.

Instability Index

Predicts protein stability in vitro. Values < 40 indicate stable proteins; > 40 suggest instability. Based on amino acid composition.

How to Use This Calculator

Step 1: Enter Your Sequence

Use single-letter amino acid codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y) or three-letter codes (Ala, Cys, Asp, etc.). Remove spaces and special characters.

Step 2: Specify Modifications

Select any N-terminal or C-terminal modifications. Choose the number of disulfide bonds if applicable. These affect the final molecular weight.

Step 3: Click Calculate

The calculator will instantly compute molecular weight, extinction coefficient, isoelectric point, and amino acid composition.

Step 4: Interpret Results

Review the calculated values and amino acid composition. Use the reference table to understand protein properties.

Common Applications

🔬
Protein Purification
Verify molecular weight using SDS-PAGE or mass spectrometry
📊
Concentration Determination
Calculate protein concentration from extinction coefficient and absorbance
🧬
Peptide Synthesis
Verify molecular weight of synthesized peptides
💉
Drug Development
Analyze therapeutic proteins and biologics
📈
Research & Analysis
Characterize novel proteins and protein variants
⚙️
Quality Control
Ensure product consistency and purity
⚠️ Important Disclaimer
This calculator provides theoretical values based on standard amino acid molecular weights. Actual protein properties may vary due to post-translational modifications, folding, glycosylation, phosphorylation, and other chemical modifications. For critical applications, always verify results with experimental methods such as mass spectrometry, gel electrophoresis, or chromatography. This tool is for educational and research purposes only.
Medical & Scientific Disclaimer: This calculator provides theoretical values for educational and research purposes only. It is not intended for clinical diagnosis or treatment. Always consult with qualified professionals and verify results experimentally. The authors are not responsible for any errors or omissions in calculations or their consequences.