COLOR CODE JMOL HELIX SEET FULL
COLOR CODE JMOL HELIX SEET DOWNLOAD

Ramachandran plot lets to visually inspect u and w angle PPII value distributions and help the user to apprehend the relevance of each assignment. Indeed assignments provided by the various tools can be quite different between them. The image is mouse sensitive and gives additional information on residue number, nature and u and w angle values of assigned as PPII. Residues assigned as PPIIs are represented as white points.

Statistics about areas were derived from our previous study (10). The most frequent areas for a -helix and b -sheet are shown in the background of the plot (represented by a colour scale). Ramachandran plots give the distribution of u and w torsion angles for each assignment method. All data from protein structure analysed can be downloaded. helix residue in red, strand in green, PPII helix in blue non-regular secondary structure in grey, coil being in dark grey colour) for a fast visualization of overall local structures. Letters are coloured accordingly to more general class of secondary structure (e.g. To better visualize the secondary structure and PPII assignments given by PROSS (21), SEGNO (22), XTLSSTR (23) and our DSSP- PPII (10, 14), they are all displayed at the bottom of sequence One letter code is used to represent specific conformation. We have recently underlined the discrepancies between the three different secondary structure methods able to assign PPIIs, and proposed a novel PPII assignment using the de facto standard DSSP assignment method (10, 14). The PolyprOnline web server provides access to different assignment methods and allows visualization of both regular secondary structure and PPII helix ( Figure 3).

COLOR CODE JMOL HELIX SEET DOWNLOAD

You can also download the assignment of each protein in classical fasta format. All proteins in the table are identifiable by PDB code, title, size, resolution and PPII content. Results in the table can also be directly downloaded in text format. are displayed in a table that can be sorted accordingly to the values in different columns ( Figure 2). helix residue in red, strand in green, PII helix in blue and non-regular secondary structure in grey). Local conformations are coloured with the same colour scheme as used for the 1D alignment in (A i.e.

COLOR CODE JMOL HELIX SEET FULL

( C ) Full 3D structure visualization and animation using a JMol applet of different assignment can be dynamically displayed (C a trace only, cartoon). Statistics about areas were derived from our previous study. ( B ) Ramachandran plots give the distribution of u and w torsion angles of PPII amino acids for each method. Letters are coloured accordingly to more general class of secondary structure (i.e. One letter code is used to represent a specific conformation. ( A ) Sequence and analysis of secondary structures using four different protein secondary structure assignment methods are printed on a 1D alignment. Detailed analysis of a protein structure (3KWEA 25).

Color code jmol helix seet