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.

Amino Acid SequenceUse single-letter codes (A, C, D, E, etc.) or three-letter codes (Ala, Cys, Asp, Glu, etc.)

Disulfide Bonds Disulfide bonds affect molecular weight

N-Terminal Modification Common N-terminal modifications

C-Terminal Modification 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 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.

Amino Acid SequenceSingle-letter amino acid codes

Analysis Type

pH Value 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.