In this version of scop we give short descriptions of the protein folds in the all-alpha, all-beta, and alpha/beta classes. Preliminary descriptions are also given for some of the folds in other classes: in later versions these will be refined and extended to folds without descriptions at present.
We list here short definitions of the terms used in the fold descriptions. Full definitions, and discussions of the significance of these terms, can be found in the papers listed in the scop bibliography. The short descriptions apply to the whole protein/domain or, in the case of folds whose members differ in size, the common core.
The core is the region common to the most of structures grouped in a given Common Fold or Superfamily. Many members have additional secondary structures; in rare cases, one or a few members lack one of the core secondary structures.
meander is a simple topology of a beta-sheet where any two consecutive strands are adjacent and antiparallel.
up-and-down is the simplest topology for a helical bundle or folded leaf, in which consecutive helices are adjacent and antiparallel; it is approximately equivalent to the meander topology of a beta-sheet.
crossover connection links secondary structures at the opposite ends of the structural core and goes across the surface of the domain.
Greek-key is a topology for a small number of beta sheet strands in which some interstrand connections going across the end of barrel or, in a sandwich fold, between beta sheets.
jelly-roll is a variant of Greek key topology with both ends of a sandwich or a barrel fold being crossed by two interstrand connections.
all-alpha class has the number of secondary structures in the domain or common core described as 3-, 4-, 5-, 6- or multi- helical.
bundle an array of alpha-helices each oriented roughly along the same (bundle) axis. It may have twist, left-handed if each helix makes a positive angle to the bundle axis, or, right-handed if each helix makes a negative angle to the bundle axis.
folded leaf a layer of alpha-helices wrapped around a single hydrophobic core but not with the simple geometry of a bundle.
array (of hairpins) is an assemble of alpha-helices that can not be described as a bundle or a folded leaf.
closed, partly opened and opened for all-alpha structures describes the extent in which the hydrophobic core is screened by the comprising alpha-helices. Opened means that there is space for at least one more helix to be easily attached to the core.
beta-sheet can be antiparallel (i.e. the strand direction in any two adjacent strands are antiparallel), parallel (all strands are parallel each other) and mixed (there is one strand at least that is parallel to one of its two neighbours and antiparallel to the other).
all-beta class includes two major fold groups: sandwiches and barrels.. The sandwich folds are made of two beta-sheets which are usually twisted and pack so their strands are aligned. The barrel fold are made of single beta-sheet that twists and coils upon itself so, in most cases, the first strand in the beta sheet hydrogen bond to the last strand. The strand directions in the two opposite sides of a barrel fold are roughly orthogonal. Orthogonal packing of sheets is also seen in a few special cases of sandwich folds
barrel structures are usually closed by main-chain hydrogen bonds between the first and last strands of the beta sheet, in this case it is defined by the two integer numbers: the number of strand in the beta sheet, n, and a measure of the extent the extent to which the strands in the sheet are staggered the shear number, S. (see McLachlan, 1979 and Murzin et al., 1994).
partly open barrel has the edge strands not properly hydrogen bonded because one of the strands is in two parts connected with a linker of more than than one residue. These edge strands can be treated as a single but interrupted strand, allowing classification with the effective strand and shear numbers, n* and S*. In the few open barrels the beta sheets are connected by only a few side-chain hydrogen bonds between the edge strands.
Full discussions of the terms given here can be found in the papers listed in the alpha/beta section of the scop bibliography.
The descriptions are based upon the central sheet of the domain. These can be parallel or a mixture of parallel and antiparallel strands (here referred to as mixed sheets).
There are several different geometries of the central sheet:
For convenience, multi-domain proteins where all domains are alpha/beta and for which no clear homologues are known for any domain are not split into their domains, and are grouped independently of the above groups.
With two exceptions, the alpha/beta folds are grouped together in terms of these features. Within any group, we move from simpler to more complex structures. The first exception is for alpha/beta proteins which have the same function but different folds, which are placed adjacent to each other. The second is for two proteins which have a beta/beta/alpha structure; these follow the barrel group of alpha/beta folds.
Note that in this version of scop the descriptions given for the folds in the alpha+beta and other classes are in a preliminary state. Full descriptions and definitions of the terms used in these descriptions will be given in later releases of scop.