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Here is a list of useful terms and definitions in CATH and general structural biology.

Please click on the item of interest to get further information. This glossary will continue to grow as more terms and definitions are added.

Alpha Helix

2009/07/02 12:29   This motif comprises two sequential alpha helices linked by a coil, which lie adjacent in space and run approximately antiparallel. See also hairpin. The example shown is the central domain in a rRNA methyltransferase (CATH domain ID 1o9gA02). alpha
2009/07/02 12:29   alpha The alpha helix is the most abundant type of secondary structure in proteins and has been extensively documented. In brief, alpha helices are formed from stretches of consecutive amino acid residues with phi and psi angle pairs which correspond to the bottom left quadrant of the Ramachandran Plot. The mean phi and psi angles for alpha helices found in proteins are -62 degrees and -41 degrees, respectively. The alpha helix has 3.6 residues per turn, with a hydrogen bond between the CO o…
2009/07/02 12:29   alpha This is a helix-loop-helix, calcium-binding motif, in which two helices pack together at an angle of approximately 90 degrees, separated by a loop region, where calcium binds. The 'EF' notation for the motif resulted from the structure of parvalbumin, in which the 'E' and 'F' helices were originally identified to form this calcium-binding motif. The example shown is a human psoriasin (PDB code 1psr).
2009/07/02 12:29   alpha Four helix bundles are a common structural motif or architecture that has been extensively documented. They can be observed both independently and as components of larger folding units. The motif comprises four helices packed together in a variety of different ways, forming a hydrophobic core. In the most common bundles, the helices that are adjacent in the amino acid sequence are also adjacent in the three dimensional structure, forming the so-called up-down-up-down four helix bundle. …

Beta Sheet

2009/07/02 12:29   This is a beta-pleated sheet in which adjacent beta strands in the structure point in opposite directions, for example amino-terminal to carboxy-terminal, carboxy-terminal to amino-terminal, amino-terminal to carboxy-terminal, etc. Such sheets have narrowly spaced hydrogen bond pairs that alternate with widely spaced pairs. In each residue the main chain -NH and -CO groups point in the same direction, but which alternates with successive residues.
2009/07/02 12:29   beta This describes the motif formed by two sequentially adjacent beta strands connected by a coil, which are antiparallel, but lie in different sheets, usually in a beta-sandwich architecture.
2009/07/02 12:29   beta In some instances large anti-parallel (or parallel) sheets can roll up completely to join edges and form a cylinder or closed 'barrel', in which the first strand is hydrogen bonded to the last. The strands form the 'staves' of the barrel.The example shown is porin (pdb code 2por)).
2009/07/02 12:29   beta Beta bulges are regions of irregularity in a beta sheet, where the normal pattern of hydrogen bonding is disrupted, e.g. by the insertion of an extra residue. A bulge usually involves two or more residues in the bulged strand, opposite a single residue in the adjacent strand. These irregularities have been identified and classified automatically. In all, five types of beta-bulge were identified: classic, G1, wide, bent and special. Bulges were found to occur frequently in proteins, on a…
2009/07/02 12:29   beta The simplest type of up-down antiparallel beta-sheet topology whereby two adjacent antiparallel strands are joined by a loop. This motif occurs very frequently in nature and can be observed in many different beta-sheet structures. The example given below is the epidermal growth factor-like domain of heregulin-alpha (CATH domain ID 1hreA00).
2009/07/02 12:29   beta In this mainly beta fold, the polypeptide chain is wound into a large right-handed coil (or super helix). There are two different types of beta helix, one with two beta sheets, and one with three beta sheets. In our classification scheme we describe these as 2-solenoid and 3-solenoid beta architectures, respectively.
2009/07/02 12:29   beta This is a simple 'up-and-down' beta sheet motif with three strands, which is characterised by (+1, +1) connectivities. A large sheet may comprise sequential meanders to form the up-down beta barrel. References
2009/07/02 12:29   beta The beta prism is a fold with three internal repeats, each being an antiparallel beta sheet with (+1, +1, -3) connectivity. The three sheets are arranged like the faces of a triangular prism, with internal pseudo-threefold symmetry (Shimizu and Morikawa, 1996). There are two types of prism: the orthogonal prism, in which the strands are perpendicular to the prism axis; and the aligned prism, in which the strands are parallel to the prism axis.
2009/07/02 12:29   beta This fold comprises 4, 6, 7 or 8 antiparallel beta sheets with a radial arrangement in space, giving the overall structure the appearance of a propellor. The beta sheets pack face to face, and form a closed structure, in which each beta sheet packs against two neighbours. The sheets have a mean twist and orientation that depends on the number of beta sheets that form the propellor. The beta sheets have the same topology, i.e. the propellor blades are structurally similar units (four antipa…
2009/07/02 12:29   beta This protein architecture comprises two beta sheets that pack together, face-to-face, in a layered arrangement. The connections between the strands in the sheet differ between beta sandwiches with different topologies. The example given here is beta-2-microglobulin (CATH domain ID 2hlaB00).
2009/07/02 12:29   beta The beta sheet is a major secondary structural element in globular proteins. These structures are formed from beta strands and are in an almost fully extended conformation with psi,phi bond angle pairs in the wide allowed region in the upper left-hand corner of the Ramachandran Plot. These strands are aligned adjacent to each other allowing hydrogen bonds to form between C'=O groups of one beta strand and NH groups on the adjacent one and so forth. Successive Calpha atoms are located a…
2009/07/02 12:29   beta A beta strand describes a single length of polypeptide chain that forms part of a beta sheet.
2009/07/02 12:29   beta This architecture is formed from a capped beta barrel with an internal pseudo threefold symmetry. The examples shown below are the agglutinin domain (CATH domain ID 1jlxA01), and acidic fibroblast growth factor (FGF-1) (CATH domain ID 1afcA00).
2009/07/02 12:29   beta A beta turn occurs where the polypeptide chain makes a sharp reversal by 180 degrees within 4 residues. A turn is defined by 4 consecutive residues (i to i+3) if the C-alpha(i) to C-alpha(i+3) distance is less than 7 angstroms, and if the central two residues are not helical. There is often a hydrogen bond between the CO(i) and NH(i+3). There are several different types of beta turns (see references below).
2009/07/02 12:29   beta This is a four-stranded beta sheet motif which is characterised by +3, -1, -1 connectivities in a two-dimensional schematic diagram of a protein structure, as shown here. The diagram on the left shows an N-type Greek key motif, whilst on the right is a C-type Greek key.
2008/09/19 12:46 Kathryn Garner beta The immunoglobulin (Ig) domain is found in a wide variety of proteins, in particular those involved in the immune response. This includes immunoglobulin molecules themselves (antibodies), T cell and B cell receptors, major histocompatibility (MHC) proteins (including beta-2-microglobulin), Fc receptors, as well as the CD4 and CD8 co-receptors.
2009/07/02 12:29   beta This is a fold topology that classically consists of four Greek key motifs that adopt an eight-stranded beta sandwich structure. In this fold the hydrogen bonding pattern between adjacent strands is broken in two places, and as a consequence the structure comprises two four-stranded beta sheets. Both sheets are purely antiparallel, with strands adjacent in sequence appearing in different sheets with the exception of the fourth and fifth strands, which are in the same sheet. This leads…
2009/07/02 12:29   beta A beta sheet which has both parallel and antiparallel strands. References
2009/07/02 12:29   beta This is a beta-pleated sheet in which successive beta strands all lie parallel in three dimensions. Such sheets have evenly spaced hydrogen bond pairs that lie at an angle to the beta strands. References

Mixed Structure

2008/09/19 13:11 Kathryn Garner mixed
2009/07/02 12:29   mixed This motif comprises a beta strand-loop-helix-loop-strand arrangment, with the strands lying parallel and hydrogen-bonded to the helix. The alpha helix packs against the beta strands and thus buries the hydrophobic side chains in these strands. The joining loops regions in the motif can vary in length from one residue to more than 100 residues. 99% of these motifs are right handed.
2009/07/02 12:29   mixed This fold is made up of three or more parallel beta strands linked by two alpha helices in the topological order beta-alpha-beta-alpha-beta. Two Rossmann folds, wound in opposite directions create a dinucleotide binding unit found in many enzymes, specifically in nucleotide binding proteins (hence its alternative name mononucleotide-binding motif).
2009/07/02 12:29   mixed This motif is a beta-alpha-beta motif in which the strands lie parallel in the same sheet, but are non-adjacent and not hydrogen bonded together. The number of intervening strands is usually small. These motifs are common in alpha-beta proteins with an antiparallel sheet.

Other Related Terms

2008/08/14 13:15 Ian Sillitoe classification pdb Structures in the PDB repository are of varying quality. In order to maintain accuracy when classifying and clustering protein domains, it is important only to include high quality structures. For this reason we have defined a strict set of criteria, called SIFT, to state whether or not a PDB chain can be accepted into CATH.
2009/07/02 12:29   structure This describes the overall shape of the domain structure as determined by the orientations of the secondary structures but ignores the connectivity between the secondary structures. It is currently assigned manually using a simple description of the secondary structure arrangement e.g. barrel or 3-layer sandwich. Reference is made to the literature for well-known architectures (e.g the beta-propellor or alpha four helix bundle).
2009/07/02 12:29   structure This is the highest level of classification and is derived from the gross secondary structure content. There are 4 classes defined in the CATH classification. * Mainly Alpha * Mainly Beta * Alpha Beta * Few Secondary Structures.
2009/07/02 12:29   structure This is a term used to describe one possible type of backbone connection observed between beta strands in which the chain loops around to re-enter the sheet on the opposite end. For beta sheet connectivity, cross over connections are denoted by nx, where n denotes how many strands it moves over in the sheet and in which direction. +1x denotes a crossover connection between nearest neighbours, +2x denotes a crossover connection that misses one intervening strand in the sheet, and so o…
2009/07/02 12:29   structure Domains are regions of contiguous polypeptide chain that have been described as compact, local, and semi-independent units. Within a protein, domains can be anything from independant globular units joined only by a flexible length of polypeptide chain, to units which have a very extensive interface. There are a number of algorithms that have been developed to detect domains automatically, some of which have been incorporated into the CATH update protocol. Many domains, however, still …
2009/07/02 12:29   structure This is a term used to describe a motif of two sequential secondary structures joined by a loop which folds back on itself to form a 'hairpin' structure. e.g. beta hairpin, alpha hairpin.
2008/08/13 15:40 Alison structure Homologous Superfamily This level of the CATH hierarchy groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous. Similarities are identified either by high sequence identity or structure comparison using SSAP. Structures are clustered into the same homologous superfamily if they satisfy two or more of the following criteria:
2009/07/02 12:29   structure A hydrogen bond is a polar interaction between two electronegative atoms, a donor and an acceptor. In proteins hydrogen bonds involving the main chain oxygen and amide are critical in forming the secondary structures. The polar side chains also form hydrogen bonds. Energetically it is important to satisfy all hydrogen bond donors and acceptors. In proteins more than 90% of side chain atoms are 'satisfied' by forming hydrogen bonds to protein atoms or solvent.
2009/07/02 12:29   structure A protein loop is any stretch of non-regular polypeptide chain connecting secondary structures. Short loops commonly have little structure and are often found joining two adjacent beta strands . They are often referred to as reverse turns.
2009/07/02 12:29   structure A commonly occuring substructure, usually comprising two to three secondary structures.
2009/07/02 12:29   structure An omega loop has been defined as a continous segment of polypeptide chain that adopts a 'loop-shaped' conformation in three-dimensional space, with a small distance between its segment termini. The main chain of an idealized loop has the appearance of a Greek letter omega (hence the term 'omega loop').
2009/07/02 12:29   structure A superfold is defined as a protein fold which has been observed in three or more non-homologous proteins. There are nine superfolds which have been identified so far, including the beta trefoil and the jelly roll . References
2008/08/13 15:37 Alison structure Topology (Fold Group) This level of the CATH hierarchy describes structures that are grouped according to whether they share the same topology or fold in the core of the domain, that is, if they share the same overall shape and connectivity of the secondary structures in the domain core. Domains in the same fold group may have different structural decorations to the common core.
2009/07/02 12:29   other This is a diagram of the sterically allowed regions for a dipeptide unit in phi,psi space. The conformation of the dipepetide is defined by 2 dihedral angles: phi (the angle of rotation around the N-C-alpha bond in a peptide unit), and psi (the angle of rotation around the C-alpha-C' bond in a peptide unit). The plot indicates whether a given phi,psi conformation is sterically allowed. A conformation is not allowed if atoms approach closer than the sum of their van der Waals radii. The di…
2009/07/02 12:29   other Full name: Secondary Structure Alignment Program. This secondary structure alignment program uses dynamic programming to align proteins by matching vectors between residues. For each residue in a protein, a local structural environment is defined by a set of inter-atomic vectors. The method matches residues by comparing these structural environments. An important aspect of these environments is that because they are defined independently for each residue, they are rotationally invariant,…