Example 1 - Comparison of Alpha and Beta Chains in Human Hemoglobin


Explanation

At top left (WPDB window) we see that the hemoglobin structure with the PDB code 1BAB has been chosen. A sequence alignment between the A and B chains (Align window) by the method of Needleman and Wunsch reveals a 44% similarity. These aligned structures are then superimposed according to the method of Hendrickson based on their Calpha coodinates (3D view window). The Contact map window reveals the interactions at a default cut-off of 7 Å between Calpha atoms. Red indicates intrachain contacts (i.e. contacts with itself) observed in both 1BAB_A and 1BAB_B; green indicates intrachain contacts observed in 1BAB_A only and blue - in 1BAB_B only.


Explanation

This shows further details of the interaction between the A and B chains. The Profile window has been zoomed to show the exposure according to Lee and Richards for a segment of the aligned sequences. Red represents both the A and the B chain; blue chain A only; green chain B only. The Contact map window has been zoomed to show the interaction between individual residues. A further click would reveal the specific atoms in contact. The 3D view window shows a solid representation of the molecule in a gray scale where the darker the color the farther the residue from the viewer.

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