The Molecular Biology Notebook OnlineYou are here: >
Protein Alpha-Helix
The alpha-helix (also written 
-helix) is a rod like structure stabilized by hydrogen bonds between the CO and the NH groups of the main chain.
Diagram 1 shows a ribbon representation of the alpha - helix with only the alpha carbons represented. It is a representation of a right-handed alpha - helix.
|
If we represent the backbone structure (Diagram 2) , we see that alpha carbons spaced three and four in the linear sequence are actually quite close together in an alpha - helix structure. The hydrogen bonds are shown in green, and it is then obvious that all the main chain CO and NH groups are hydrogen bonded. This structure is quite sturdy. |
|
The next 3 diagrams (3-1, 3-2, 3-3) were obtained using the RasMol software. The initial protein is bovine pancreatic hormone. We concentrate on the residues 16 to 30 which are arranged in an alpha - helix.
Legend to figure 3-1, 3-2, 3-3
|
|
Diagram 3-1: backbone of part of a protein. Bovine pancreatic hormone contains a large alpha - helix whose backbone is shown here. The hydrogen bonds that give stability to the molecule are shown in green. The carboxyl groups (CO, in red) are all facing the same direction. |
|
Diagram 3-2: a fragment of bovine pancreatic hormone. Side chains of the amino acids were added and the backbone highlighted in red. Note that the side chains are outside the helix. |
 |
Diagram 3-3: cross section of the helix |
Study an alpha - helix with RasMol: Pancreatic Hormone is a good example to look at. You might need to modify some of the settings to get the most out of RasMol.
In this case you can use the following line commands in any order:
- restrict 16-30
- backbone 20
- background white
- color backbone red,
- restrict backbone
- hbonds
- color hbonds green
To recover the full protein type :
- restrict all
- wireframe on
Tweet
Database Proteins on Wikipedia
Database Proteins at Answers. com
Related Links
-CATH: Protein Structure ClassificationCATH is a novel hierarchical classification of protein domain structures, which clusters proteins at
-ChromDB: The Plant Chromatin Database
The mission of ChromDB is to bring together information on homologs of chromatin-associated proteins
-DIP: Database of Interactive Proteins
The DIPTM database catalogs experimentally determined interactions between proteins. It combines inf
-PDBsum
Summaries and structural analyses of PDB data files.
-Pfam Homepage
Pfam is a high-quality comprehensive collection of protein domain families.
-Prodom
The ProDom protein domain database consists of an automatic compilation of homologous
-Prosite
PROSITE is a database of protein families and domains. It consists of biologically significant sites
-Protein Data Bank Docs
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures
-Protein Information Resource
The Protein Information Resource (PIR), maintains the PIR-International Protein Sequence Database --
-SWISS-PROT : Annotated Protein Database
SWISS-PROT is a curated protein sequence database which strives to provide a high level of
-TOPSAN
The TOPSAN project was developed to collect, share, and distribute information about protein three-d
-UniProt
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and
-UniProtKB
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional informatio