Generate graphs of average B-factor versus residue for each chain in the PDB file.In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered. Required if looking for metal-ligand or intermolecular contacts.ĭefine type of metal and expected metal-ligand distance Choice of spacegroup or list of operators Spacegroup required if looking for all contacts. Use spacegroup or list of operators to define symmetry operations Contact - Task Window Layoutįeatures to look out for in the Contact Task are: Folder title You may use up to 69 symmetry operations when looking for metal-ligand or intermolecular contacts.
CONTACT reads a standard Protein Data Bank file which mustĬontain SCALE cards if looking for metal-ligand or intermolecular contacts. Segregated into 6圆圆 Å boxes and contact searching is limited to neighbouring boxes The program uses a bricking algorithm in which atoms are Task for computing various types of contacts in protein structures. Waters which have non-zero area in both calculations are not completelyĮnclosed by protein and/or waters and so are on the 'outside' of this shell.The second are enclosed between protein and/or other waters. Waters which have non-zero area in the first calculation but zero area in.Waters with zero area in the first calculation are completely enclosed by.Theĭifferences will be the change in ASA on the protein when the ligand is bound.Īrea Differences For Waters: useful for looking for Protein-ligand complex, the second will be for the the protein only. The first area calculation will be for the Should contain the bound protein-ligand complex. Ligand/subunit binding: the supplied coordinate file The differences will be the change in ASA on the protein when it The firstĪrea calculation will be for the protein in the crystal, the second will be for the Should contain coordinates which compromise a single copy of the protein.ĭefine the spacegroup which specifies the crystallographic symmetry. Theĭifferences will be the change in ASA on the monomer when it is oligomerised.Ĭrystallographic contacts: the supplied coordinate file The first areaĬalculation will be for the oligomer, the second will be for the monomer. monomer).ĭefine the symmetry operations to use to generate the oligomers. Oligomer formation: the supplied coordinate file shouldĬontain coordinates which compromise a single protein 'unit' ( i.e. To buried area due to the interaction in question: Neighbouring protein atoms if they are treated as 'protein' then individualĪSAs will also be affected by neighbouring waters.Īrea Differences For Protein: differences in ASA correspond The ASA of individual waters will only be affected by the presence of ASA can also beĬalculated specifically for waters: if waters are treated as 'solvent' then
Treatment of waters: normally ASA is calculated for proteinĪtoms only and waters (solvent) are ignored in the calculation.
Intermolecular contacts due to symmetry-related molecules can also be included. The Areaimol task has a number of protocols to calculate the solventĪccessible surface areas (ASA) and area differences for a variety ofĪccessible Surface Area: calculates the accessible surfaceĪrea for all atoms of the requested type (protein or solvent). These reasons are described in the Task Window Made in the Protocol folder of the task (seeĪlthough certain folders are closed by default, there are specific reasons why you the number of folders present,Īnd whether these folders are open or closed by default, depends on the choices CCP4 Interface: Structure Analysis ModuleĪccessible Surface Area Calculations AreaIMol Protocols Analyse Molecular Contacts Contact - Task Window Layout Temperature Factor Analysis The Structure Analysis module contains the following tasks: Accessible Surface Areas Analyse Molecular Contacts Temperature Factor Analysis
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