More information about Polyproline type II helix
Chebrek R, Leonard S, de Brevern AG, Gelly J-C Database Nov 7 (2014)
About PolyprOnline database statistics
The database contains 24761 protein structures.
Database is updated every 6 months.
Complete database update is performed from a PDB list generated by PISCES web service using criterions of maximal mutual sequence identity of 90% between sequence proteins,
resolution <3.0 and R <1.0.
(Wang, G., Dunbrack, R.L., Jr. (2005) PISCES: recent improvements to a PDB sequence culling server. Nucleic acids research, 33, W94-98.).
Last update: 2023-02-20 19:19:21
Statistics on secondary structures on whole protein
| Alpha Helix | Beta Sheet | PPII | Other | Coil | ||||
|---|---|---|---|---|---|---|---|---|
| Canonical alpha helix | Parallel or anti-parallel Beta Sheet | Polyproline type II helix | Other attributed secondary structures: Turn, Bend, 3-10 Helix, Pi Helix,Isolated bridge... (See Details in About section) |
Random Coil |
DSSP-PPII PROSS SEGNO XTLSTRR
Download all PDBs id in PolyprOnline database: txt
About secondary structures assignments
About half of the globular proteins are composed of repetitive regular secondary structures, α-helices and β-sheets, while the rest are constituted of irregular secondary structures such as turns or coil conformation. Other regular secondary structures are often ignored, despite their importance in biological processes. Among the other regular secondary structures the polyproline II helix (PPII) is especially interesting.
There is four main methods to assign polyproline type II helix (both with classical secondary structure):
- PROSS
- SEGNO
- XTLSSTR
- DSSP-PPII
PROSS
Secondary structure assignments are based solely on the backbone dihedral angles. PROSS coding scheme are as follow:H - α helix
T - β turn
E - β strand
P - polyproline II
C - coil
Reference:
Srinivasan R, Rose GD Proc Natl Acad Sci USA 96, 14258–14263 (1999)
XTLSSTR
Program XTLSSTR uses two angles and three distances to assign secondary structure to Xray and NMR coordinates from the Brookhaven Protein Data Bank.H and h - Alpha helix
G and g - 3^10 helix
E and e - Extended beta strand
T - Hydrogen-bonded
N - Nonhydrogen-bonded (N)
P and p - Beta-turns, and polyproline II type (3-1) helix
Reference:
King SM, Johnson WC Proteins 35, 313–320 (1999)
SEGNO
SEGNO uses also the Phi and Psi dihedral angles coupled with other angles to assign the secondary structures. This method has been used to analyze the Polypoline II helix.e and E - Strand
p and P - Polyproline II
H - alpha Helix
g and G - 3-10 Helix
I - Pi helix
O - Coil (coded as "-" in this webserver)
b and B - Isolated Strand
Reference:
Cubellis MV, Cailliez F, Lovell SC BMC Bioinformatics 6, Suppl 4S8 (2005)
DSSP and DSSP-PPII
Dictionary of Protein Secondary Structure, DSSP, is the reference method used to describe the protein secondary structure with single letter codes.Assignment of secondary structure is based on hydrogen bonding patterns. DSSP defines eight types of secondary structure coded as follows:
H - 4-turn helix (α helix). Min length 4 residues
G - 3-turn helix (310 helix). Min length 3 residues
I - 5-turn helix (π helix). Min length 5 residues
T - hydrogen bonded turn (3, 4 or 5 turn)
E - extended strand in parallel and/or anti-parallel β-sheet conformation. Min length 2 residues
B - residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)
S - bend (it is a non-hydrogen-bond based assignment)
C - coil (residues which are not in any of the above conformations). Represented as "-" on this webserver
Reference:
Kabsch W, Sander C Biopolymers 22: 2577–2637 (1983)
These eight types are usually grouped into three larger classes: helix (G, H and I), strand (E and B) and loop (all others).
To this classical assignment, we add the Polyproline II helix, as P, in the coil regions based on phi and psi angles.
Reference:
Mansiaux Y, Joseph AP, Gelly J-C, de Brevern AG PLoS One 6 (3):e18401 (2011)