Model building exercise
Group:
Studienr:
Q1:
In groups of 4 build two di-peptides - make sure that you build L-amino
acids.
All members in a group answer the questions in this dox
Fill in the 3-letter code for all di-peptides
Group
Di-peptide 1
1-letter
3-letter
1-letter
1
AL
SH
2
KE
FI
3
TM
IL
4
LA
GD
5
FV
SY
6
WA
DE
7
HR
IF
8
QD
VA
Di-peptide 2
3-letter
Q2:
Connect the two di-peptides such that they are in a beta-strand conformation.
Swap the side-chains such that one side of the beta-strand is hydrophobic.
Write done with 1-letter code the sequence of your peptide (peptide is a
short stretch of amino acids):
Q3:
What is the difference between a beta-strand and a beta-sheet.
What atoms form hydrogen bonds in a beta-sheet
Q4:
Draw a schematic representation of the two types of beta-sheets. Use an
arrow to indicate a beta-strand.
Q5:
Draw a di-peptide on paper with sidechain indicated with R
What are the names for the 4 backbone atoms
Write 1-letter codes for amino acids in these groups:
 Hydrophobic
 Acidic
 Basic
 Aromatic
 Special amino acids
NB ! There may be an overlap of aa between the groups
Q6:
Build an alpha-helix composed of 10 Alanines (1 model/group)
What is the hydrogen bonding pattern
What is the distance between CA(1) and CA(10) – use a ruler. Rise/aa ?