P I S A
Protein Interfaces, Surfaces and Assemblies
Contents • Glossary

Accessible Surface Area (ASA)
Area of a monomeric unit, residue or atom, which is accessible to solvent. ASA is measured in square angstroms.

Assembly
Same as complex

Atom ID
Character string that identifies an atom in coordinate file. It has the following format:

chn:res seq ic [atm]

where

chn  is  chain ID
res  is  residue name
seq  is  sequence number
ic  is  residue insertion code
atm  is   PDB (space-aligned) atom name

Buried Surface Area
Surface area, which becomes inaccessible to to solvent, e.g. at protein folding or in course of interface formation, measured in square angstroms.

Complex
Thermodynamically stable assembly of monomeric units

Configuration File
A plain-text, formatted file with specification of external resources and designated directories, needed for PISA to work. See details here.

Control Panel
Left part of QtPISA window, containing toolbar, progress indicator and result tree, see details here.

Hydrophobic Interaction
See Solvation Energy.

Hydrophobic P-value
For the given surface patch, this is the probability of finding an equal-area patch, which would be more hydrophobic. If this probability is low, then given patch is statistically surprising, or specific. A specific interface is supposed to have higher chances to be relevant to protein function.

Interface
Contact between two monomeric units, in crystals, at which some of their surface area becomes inaccessible to solvent.

Interface Area
Half of buried surface area formed on interfacing monomeric units.

mmCIF format file
A file containing macromolecular structure in mmCIF format, now superseding the more traditional PDB format, used by the Protein Data Bank. The file should contain atomic coordinates of Asymmetric Unit (AU) and crystal information: parameters of unit cell and space symmetry group. See more details on PDB-formatted files here.

Monomer ID
Character string that identifies a monomeric unit in coordinate file:
Monomeric Unit
A chemical entity in crystal, not linked covalently to anything else, such as protein or nucleic acid chain or a ligand.

NCS
Non-crystallographic symmetry.

Oligomeric State
Aggregated state of macromolecules, represented by their quaternary structures (assemblies). Oligomeric state is characterised by the multiplicity (the number of monomeric units, assembled in a complex), and structural (3-dimensional) features (as given by relative orientation of monomeric units in the assembly).

PDB code
A 4-character code identifying a structure in the Protein Data Bank. First character is always a digit, others may be either digits or latin letters.

PDB format file
A file containing macromolecular structure in PDB format, commonly used by the Protein Data Bank. The file should contain atomic coordinates of Asymmetric Unit (AU) and crystal information: parameters of unit cell and space symmetry group. See more details on PDB-formatted files here.

PISA result file
A binary file containing results of QtPISA calculations, saved for faster loading in future. These files are portable across different computational platforms and operating systems.

Residue ID
Character string that identifies a residue in coordinate file. It has the following format:

chn:res seq ic

where

chn  is  chain ID
res  is  residue name
seq  is  sequence number
ic  is  residue insertion code

Result Tree
Central part of Control Panel, which contains a tree-like representation of QtPISA output. Each node of the tree corresponds to a result page, which is displayed in Working Area, when the node is selected. See details here and here.

Solvation Effect (SEF)
Energy of interaction between monomeric unit, residue or atom, with solvent. In PISA, SEF is measured in kcal/mol. Negative values of SEFs mean that interaction results in the release of energy into thermal bath. This corresponds to the attraction between structure and solvent, or the hydrophilic effect. Positive SEFs indicate hydrophobic surfaces.

Solvation Energy (SE)
Energy difference between bound and unbound states of monomeric units, residues or atoms, which is due to the solvation effect. In bound (interfacing) state, part of structure's surface becomes inaccessible to solvent. If bound surfaces have a positive solvation effect, the total energy decreases upon binding, which is known as the hydrophobic interaction.

Solvation Energy of Folding (SEFD)
Energy difference between unfolded (linear) and folded states of macromolecular chains, which is due to the solvation effect. Note that this figure does not include other interactions tat may contribute to folding, such as disulphide bonds and electrostatic interactions. in kcal/mol. Free energy of folding is negative for stable folded states, therefore, more negative values of SEFD indicate more thermally stable structures.

Surface Area
ASA of a monomeric unit, residue or atom, measured in the absence of contact with any other structure.

Working Area
Right-hand part of QtPISA window, where all result pages are displayed.