Buried or Not.
That is the question.

Henry Jakubowski

The protein to the left is bovine heart low molecular weight protein tyrosine phosphatase. 

I. Introduction

Proteins are polymers that are constructed of 20 different amino acid monomers linked together to form a large chain.  The chain then folds on itself in 3D space to a specific, unique structure with binding pockets for other molecules.  This tutorial will show one of the 148 amino acids, Phenylalanine 10 (Phe 10), in the folded structure.  The atoms in Phe consist  mostly of C and H, so it is nonpolar and contains few slight postive and negative.  On folding does Phe 10 bury itself in the interior of the densely packed protein or is in on the surface, where the nonpolar atoms are exposed to water?  See below for the answer.

II. Structure

Wire Frame



Cartoon and Wireframe

Phe 10 Spacefill

Zoom in on Phe 10 Spacefill

The amino acids around Phe 10

The nonpolar amino acids (Val 8, Leu 9, Val 11, Cys 12, Ala 19, Ala 22, Phe 26, Ile 41, Leu 89, Leu 116, Cys 149) around Phe 10