Coilcheck+ Help

COILCHECK+ is an updated version of COILCHECK program, where the methodology of the algorithm remains similar but changes are made in the calculation of the energy components. The method requires a PDB file and two chain identifiers as input. The algorithm calculates the strength of interaction between the two helices forming coiled-coil and reports it as pseudoenergies. The interactions between the helices are grouped into three major energy components: Hydrogen bond energy, van der Waals energy and Electrostatic energy. The sum of these energies are normalized based on the number of residues in the system and the output is given as energy/residue value. Detailed explanation about the calculation of the energy components and energy/residue values are given in the methods section.

Form Details

Coilcheck+ form snapshot

1. The server requires PDB file as input. The PDB file could be uploaded to the form.
2. The two chain ids for which the interactions should be calculated has to be filled in the form.
3. The user has an choice to choose the mode of electrostatic energy calculation. The two options available are normal electrostatics and Distant dependent dielectric (DDD) electrostatic calculations. Electrostatic energy is calculated based on Coulombs law, where constant dielectric constant (D=20) or DDD constant (D=2r) is been used.
4. The charged patch algorithim provides an option to choose which type of residues to be included in the charged patch identification. It could be all charged residues on both the chains or only the buried charged residues present at the interface region.
5. The hydro ladder algorithm has an option to have either a normal scoring or a propensity based scoring scheme. The normal scoring scheme uses binary approach for the identified hydrophobic residues at the interface and the propensity scoring scheme used the values for hydophobic residues from MTIDK matix into calculations.
6. The user could opt for van der Waals energy calcculation for the given structure, additionally hydrogen fixed PDB files could also be used for energy calculations.

Output Details

Coilcheck+ result snapshot

The outputs are displayed in a user friendly way, where the user can view the contribution of each energy components and the type of interactions. The web server is designed in such a way that each type of interactions can be visualized indepentently with details about the residues participating and the distance between those interactions. The summary page gives details on the three energy components, total and energy/residue values for the given PDB. It also lists the number of potential interactions seen between the two chains of interest. Details on the calculation of energy could be seen in the methodology section. Independently the residues participating in different interactions and the energy contributed by them could be seen in the other tabs of the output page. This includes hydrophobic interactions, hydrogen bonds, salt bridges, short contacts, van der Waals interactions and electrostatic interactions (favorable and unfavorable electrostatic interactions).

CHAHO Outputs

CHAHO is a suite of structural analysis algorithms which are useful in identifying the spatialy charged residue patches and the continuity of hydrophobic core.

The charged-patch program identifies patches of charged residues in a coiled-coil dimer which are important for the stability of the structure. It considers all charged residues or buried charged residues, and identifies the favourable and unfavorable interactions between the inter- and intra- chain residue pair of the coiled-coil dimer. The method incorporates a variable distant shell calculations to add weight to the crucial interactions. The charged-patch score for each heptad is calculated and based on the scores the hepatds are classified as stabilizing and destabilizing heptads. The scores are plotted as a graph so that specific regions in the coiled-coil dimer which are important for the structures stability could be easily identified. Charged residue clusters which are involved in stabilizing the interactions between the two dimers are also identified.

The charged-patch program identifies patches of charged residues in a coiled-coil dimer which are important for the stability of the structure. It considers all charged residues or buried charged residues, and identifies the favourable and unfavorable interactions between the inter- and intra- chain residue pair of the coiled-coil dimer. The method incorporates a variable distant shell calculations to add weight to the crucial interactions. The charged-patch score for each heptad is calculated and based on the scores the hepatds are classified as stabilizing and destabilizing heptads. The scores are plotted as a graph so that specific regions in the coiled-coil dimer which are important for the structures stability could be easily identified. Charged residue clusters which are involved in stabilizing the interactions between the two dimers are also identified.

The hydro-ladder program finds the continuity of the core hydrophobic regions. The core 'a' and 'd' positions of coiled-coil dimers are ideally occupied by hydrophobic residues. But in most of the long coiled-coils the continuity is broken by the presence of polar residues in the core positions. The hydro-ladder program uses a normal or propensity based scoring scheme to identify the continuous hydro-ladder in coiled-coil dimers, the scores are smoothened over five heptad sliding window and plotted as a graph.

Coilcheck+ CHAHO snapshot

1. Given a coiled-coil structure with complete heptad pattern the hydro ladder algorithm assigns scores to each heptad based on the presence of hydrophobic residues at the interface core region. The ladder score is smoothened for five heptad sliding window and the scores are plotted as a graph. For long coiled-coil structures the plotted graph would give the user an idea of regions in the dimer interface where the ideal knob-into-hole interactions are maintained and where there is deviation due to the presence of polar residues which introduces breaks in the continuous ladder of hydrophobicity.
2. The charged patch algorithm as a first step scans the sequence of the dimer to identify the distribution of charged residues and find the net charge at three residue sliding window. With the defined window size the presence of charged residues (positively charged: K,R,H & negatively charged: E,D) are checked and mapped as shaded graph. At the same point both positive and negatively charged residues are considered independently to find the net charge. This is also shown as line graph, for both the chains considered. The charge distribution graph will allow the user to understand the importance of dispersed charged residues throughout the dimer.
3. For a given coiled-coil dimer with complete heptad pattern, the charged patch algorithm ascribes scores which makes each heptad either a stabilizing or a destabilizing heptad. Those scores are plotted as a graph, which would make the user to identify hot-spots and weak regions on the coiled-coil dimer with respect to their interactions with other surrounding charged residues.
4. The result files of CHAHO suite of programs are provided in downloadable form for the users convenience.

Heptad View Results

Coilcheck+ Heptad selector snapshot

The 'Heptad View' tab would provide the user the details of various interactions seen between the dimer. A particular range could be selected (eg: heptad4-heptad8), and the list of various charged interactions present between charged residues of the same and other chain and the type of interaction (attraction or repulsion) could be visualized. It also gives the hydro-ladder and charged-patch scores for the selected heptads.