Nest

Motif Glossary

Nest

Definition

A motif of three consecutive amino acid residues with dihedral angles 1,2-αRαL (RL-nests) or 1,2-αLαR (LR-nests). (The name derives from the observation that many nests have a depression or concavity in which an anion or δ-negative acceptor atom is bound by bridging from backbone nitrogen atoms.)

Sub-categories

• 1,2-αRαL (aka: RL)
• 1,2-αLαR (aka: LR)

Reference

Watson and Milner-White, J. Mol. Biol. 315:171-182 (2002)

Comments

1. Both N2N3- and N1N3-bridging (shown in the 3D view) occurs. However only N1N3 bridging results in a concave nest.

2. N1N3-bridging predominates in RL-nests, whereas N2N3-bridging predominates in LR-nests.

Occurrence

1. LR-nests are less common than RL-nests, and a smaller proportion of them exhibit bridging to anions or δ-negative acceptor atoms.

2. Nests frequently occur as parts of other motifs such as Schellman loops.

3. The anionic participant (the 'egg') is frequently a δ-ve O, although it can be the sulphur of an FeS cluster.

Introduction AlphaBeta Loop Asx Motif Asx Turn Beta Bulge Beta Bulge Loop Beta Link Beta Turn BulgeLoop Motif Crown Bridge Crown Bridge Loop Nest Niche Schellman Loop ST Loop ST Motif ST Staple ST Turn