| In this spacefilling-view, residues are colored according to the following scheme: | |
Lysine colored Blue To confirm ion pairs it is necessary to measure the distance between the Oxygen of a negative group and the Nitrogen of a positive group, to verify that they are within 3-4 Angstroms. This is done in Jmol by double-clicking the first atom, then release the mouse and move to the second atom. When you double-click on the next atom, the distance is shown on screen. If you open the Console, the information is shown. The relevant distance must be between an "O" and an "N" For example: [HIS]56.NE2 and [HIS]56.ND1 refer to the 2 Nitrogens in the side chain of Histidine. 9.1. Identify the partners of 4 ion pairs. Determine if the ion pairs are simple ( 2 residues), or complex (network) ion pairs (with 3 or more residues). For each ion pair, determine whether the pair is: between 2 residues in the same alpha-helix between 2 residues in different alpha-helices. , between 2 residues in the same beta-strand. between 2 residues in different beta-strands. To complete the last part use this method: If you find an ion pair between residues 10 and 15, then type in the box, or open the console and type there: select 10 or 15; color structure. The residues will be golden if beta-strand, magenta if helix. To see if they are in the same or in different elements of secondary structure, type: select all; cartoon only Next: Glycines
|
|