BS1005 Lab Report 2
SCHOOL OF BIOLOGICAL SCIENCES
BS1005 BIOCHEMISTRY 1
Name: Kingston Tan Lee Kang
Matriculation Number: U1440619E
Tutorial Group: 8
LAB REPORT
Practical 2- Macromolecule Structure Study
School of Biological Science, NTU
BS1005 Practical: Macromolecule Structure Study
Results & Discussion of Problems
Peptide I – PDB I (β – Sheet)
Figure 1. ‘Cartoon view’ of Peptide I showing its secondary structure
Figure 1 illustrates the secondary structure of PDB file 1 which shows a β – Sheet. 3 hydrogen bond interactions between an amide and oxygen group were identified. The 3 sets of residues that hydrogen bonds were formed between were identified and shown below in
Figure 2. Bond distances and bond angles were identified. (Bond distance – Coloured blue,
Bond angle – Coloured yellow)
Figure 2. Structure of Peptide I with residues with their bond angles & bond distances
Residues involved in the hydrogen bond
LEU-144 & TYR 137
LEU-146 & VAL-135
TYR-148 & ILE-133
Bond Distance (Å)
Bond Angle (o)
2.07
1.86
1.92
158.99
161.49
159.80
Table 1. Bond distance & Bond angles between hydrogen bonds
Page 1
School of Biological Science, NTU
BS1005 Practical: Macromolecule Structure Study
Figure 3. Phi & Psi angles for peptide I
Residue of Peptide I
ILE-133
TYR-148
VAL-135
LEU-146
TYR-137
LEU-144
Phi φ angle(o)
-131.35
-135.47
-137.77
-141.99
-146.03
-111.41
Psi ψ angle(o)
134.40
122.82
132.49
135.41
126.49
140.98
Table 2. Phi φ angle & Psi ψ angle for Peptide I
As observed from Figure 3, calculation of backbone torsion angle of residues (Coloured orange) was done via the measurement function of PyMOL and recorded in the table seen above. As illustrated in Figure 1, Peptide 1 is observed to have an anti-parallel β – Sheets based on the visualized secondary structure whereby strands are seen to be moving in opposite directions. Furthermore, Table 1 gives further information to shows that when residues from
1 of the β – Sheet increases in residue number, the other β – Sheet
BS1005 BIOCHEMISTRY 1
Name: Kingston Tan Lee Kang
Matriculation Number: U1440619E
Tutorial Group: 8
LAB REPORT
Practical 2- Macromolecule Structure Study
School of Biological Science, NTU
BS1005 Practical: Macromolecule Structure Study
Results & Discussion of Problems
Peptide I – PDB I (β – Sheet)
Figure 1. ‘Cartoon view’ of Peptide I showing its secondary structure
Figure 1 illustrates the secondary structure of PDB file 1 which shows a β – Sheet. 3 hydrogen bond interactions between an amide and oxygen group were identified. The 3 sets of residues that hydrogen bonds were formed between were identified and shown below in
Figure 2. Bond distances and bond angles were identified. (Bond distance – Coloured blue,
Bond angle – Coloured yellow)
Figure 2. Structure of Peptide I with residues with their bond angles & bond distances
Residues involved in the hydrogen bond
LEU-144 & TYR 137
LEU-146 & VAL-135
TYR-148 & ILE-133
Bond Distance (Å)
Bond Angle (o)
2.07
1.86
1.92
158.99
161.49
159.80
Table 1. Bond distance & Bond angles between hydrogen bonds
Page 1
School of Biological Science, NTU
BS1005 Practical: Macromolecule Structure Study
Figure 3. Phi & Psi angles for peptide I
Residue of Peptide I
ILE-133
TYR-148
VAL-135
LEU-146
TYR-137
LEU-144
Phi φ angle(o)
-131.35
-135.47
-137.77
-141.99
-146.03
-111.41
Psi ψ angle(o)
134.40
122.82
132.49
135.41
126.49
140.98
Table 2. Phi φ angle & Psi ψ angle for Peptide I
As observed from Figure 3, calculation of backbone torsion angle of residues (Coloured orange) was done via the measurement function of PyMOL and recorded in the table seen above. As illustrated in Figure 1, Peptide 1 is observed to have an anti-parallel β – Sheets based on the visualized secondary structure whereby strands are seen to be moving in opposite directions. Furthermore, Table 1 gives further information to shows that when residues from
1 of the β – Sheet increases in residue number, the other β – Sheet