From: Discrimination of thermophilic and mesophilic proteins
Numerical index | Thermophile (127 pairs) | Hyperthermophile (122 pairs) |
---|---|---|
Contact Network Derived Quantities | ||
coordination number (no cutoff) | 0.559 | 0.689 |
clustering coefficient (no cutoff) | 0.551 | 0.672 |
characteristic path (no cutoff) | 0.520 | 0.631 |
Combined Sequence and Structure Including Threading Potentials | ||
total count 400 over-rep quads/residue | 0.850 | 0.943 |
4-body potential/residue (20Ã… cutoff) | 0.858 | 0.844 |
4-body potential/residue (no cutoff) | 0.843 | 0.852 |
4-body potential/res (hyper only, no cutoff) | ----- | 0.820 |
4-body potential/res (meso only, no cutoff) | 0.732 | 0.803 |
4-body potential/res (thermo only,no cutoff) | 0.866 | ----- |
ProsaII combined score | 0.554 | 0.693 |
Delaunay Simplex Geometry | ||
median circumsphere radius(no cutoff) | 0.701 | 0.639 |
mean tetrahedrality (no cutoff) | 0.598 | 0.574 |
number simplices/residue (10Ã… cutoff) | 0.528 | 0.557 |
number simplices/residue (no cutoff) | 0.567 | 0.697 |
Volume/Surface Area/Compactness | ||
Naccess solvent accessible area | 0.567 | 0.598 |
Delaunay surface area (no cutoff) | 0.606 | 0.669 |
van der Waals area | 0.559 | 0.549 |
Delaunay volume (no cutoff) | 0.598 | 0.701 |
Van der Waals volume | 0.528 | 0.598 |
Delaunay area/volume (10Ã… cutoff) | 0.583 | 0.549 |
Delaunay area/volume (no cutoff) | 0.669 | 0.803 |
van der Waals area/volume | 0.512 | 0.557 |
packing density | 0.543 | 0.549 |
van der Waals volume/Delaunay volume | 0.685 | 0.779 |
Rigidity | ||
mean B-factor | 0.661 | 0.533 |
Secondary Structure | ||
secondary structure content (H+E 3 state DSSP) | 0.614 | 0.689 |
Sequence Length | ||
number of residues | 0.528 | 0.672 |
Sequence Composition | ||
total Kyte-Doolittle hydrophobicity | 0.575 | 0.549 |
sd Kyte-Doolittle hydrophobicity | 0.677 | 0.836 |
CvP bias | 0.803 | 0.918 |
(E+K)/(Q+H) | 0.591 | 0.861 |
IVYWREL | 0.827 | 0.926 |