BIOMOLECULES AND ENZYMES

Detailed explanation-1: -In the trans configuration, the two alpha carbon atoms of the connected amino acids are on the opposite sides of the peptide bond, whereas in cis configuration they are on the same side of the peptide bond. In most cases, the peptide bonds in proteins are trans.

Detailed explanation-2: -Cis peptide bonds are found primarily in bends and turns and, in the case of cis imide bonds (X-PRO), this correlation is so high that it suggests a specific role for cis imide groups in such structures.

Detailed explanation-3: -The cis/trans isomers are with the same amino acid residue content, but in different peptide bond configurations. For most peptide bonds, the trans configuration is favored about 1, 000 times more than the cis configuration.

Detailed explanation-4: -The segment shown here is joined to two others by peptide bonds. (Stick + polar H view, EnzDes coloring.) The alpha carbon is the central point in the backbone of every amino acid. The alpha carbon (-carbon or C) is what connects the amino group to the acid carboxyl group, giving amino acids their name.

Detailed explanation-5: -The vast majority of peptide bonds are trans, with a small fraction (mostly involving proline) in the cis conformation. However, programs like pdbfixer and even the topology rebuilding function of CHARMM (in my case, CHARMM35 ) will sometimes introduce cis peptide bonds into rebuilt systems.