Heptad Hydrophobicity
Score a/d heptad hydrophobicity as a coiled-coil candidate feature.
Description
A heptad hydrophobicity screen samples a/d-like positions in a fixed register.
A heptad hydrophobicity screen samples a/d-like positions in a fixed register. It reports their composition against a caller-selected hydrophobic residue set.1
Score a/d heptad hydrophobicity as a coiled-coil candidate feature.
When to use Heptad Hydrophobicity
Use this tool to score a/d heptad hydrophobicity as a coiled-coil candidate feature.
Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
How to use Heptad Hydrophobicity and understand its results
- Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
- Enter sequence, hydrophobicResidues, minimumCoreFraction using the field table and calculation rules, then run the tool.
- Read coreFraction, coiledCoilCandidate. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| sequence | Sequence | string | Required |
| hydrophobicResidues | Hydrophobic residues | string | Required |
| minimumCoreFraction | Minimum core fraction | number | Required |
Enter at least seven canonical residues, a case-sensitive hydrophobic-set string and minimum fraction in 0–1. Include trailing partial-heptad positions, then return fraction and inclusive candidate flag.
The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.
core={i:i mod7=0 or3}; coreFraction=hydrophobicCoreResidues/coreSize Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| coreFraction | Core fraction | number |
| coiledCoilCandidate | Coiled coil candidate | boolean |
{
"input": {
"sequence": "AAAAAAAAAAAAAA",
"hydrophobicResidues": "AILMVF",
"minimumCoreFraction": 0.75
},
"output": {
"coreFraction": 1,
"coiledCoilCandidate": true
}
}Limitations and assumptions
Register is fixed at zero rather than optimized. The set is not normalized; structure, partner interactions and a validated coiled-coil classifier are not modeled.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Coiled Coil Register: Score coiled-coil heptad register by hydrophobic a/d positions. For a complementary task, use Leucine Zipper Pattern: Scan every seventh residue for leucine-zipper runs.
References
-
Heptad Hydrophobicity — tool.io
Similar or alternative tools
- Coiled Coil Register
Score coiled-coil heptad register by hydrophobic a/d positions.
- Leucine Zipper Pattern
Scan every seventh residue for leucine-zipper runs.