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. 2019 Jun 28;10:1485. doi: 10.3389/fimmu.2019.01485

Table 3.

Comparison of the average number of peptide-HLA-B7 binding cleft hydrogen bonds observed during the MD simulations for the bound MPO2/5 peptides.

MPO2-HLA-B*07:02 MPO5-HLA-B*07:02 <hb>MPO2- < hb>MPO5
Entire peptide <hb>a Entire peptide <hb>
SCb 1.13 SC 4.36 −3.23
BBc 7.51 BB 6.53 0.98
SC+BB 8.64 SC+BB 10.89 −2.25
Individual peptide residues Individual peptide residues
P1 P1
T1SC 0.43 N1SC 1.14 −0.71
T1BB 1.26 N1BB 1.78 −0.52
T1SC+BB 1.69 N1SC+BB 2.92 −1.23
P3 P3
A3SC 0.00 R3SC 2.01 −2.01
A3BB 0.66 R3BB 0.39 0.27
A3SC+BB 0.66 R3SC+BB 2.40 −1.74
Missing residue P4
/ 0.00 W4SC 0.46 −0.46
P4 P5
Q4SC 0.17 D5SC 0.23 −0.06
Q4BB 0.25 D5BB 0.04 0.21
Q4SC+BB 0.42 D5SC+BB 0.27 0.15
P5 P6
L5BB 0.27 G6BB 0.11 0.16
P6 P7
N6SC 0.53 E7SC 0.00 0.53
N6BB 0.22 E7BB 0.15 0.07
N6SC+BB 0.75 E7SC+BB 0.15 0.60
P7 P8
V7SC 0.00 R8SC 0.52 −0.52
V7BB 0.61 R8BB 0.67 −0.06
V7SC+BB 0.61 R8SC+BB 1.19 −0.58
P8 P9
L8BB 4.24 L9BB 3.39 0.85

The upper part of the table compares the overall average number of hydrogen bonds for both peptides. The average number of hydrogen bonds are further subdivided in peptide side chain (SC)-mediated and peptide backbone (BB)-mediated hydrogen bonds. The lower part of the table compares the average number of hydrogen bonds for structurally equivalent residue positions in both peptides. Red: the MPO2 peptide forms less hydrogen bonds at a specific residue position compared to the MPO5 peptide, green: the MPO2 peptide forms more hydrogen bonds at a specific residue position compared to the MPO5 peptide. Only peptide residues that form SC- or BB-mediated hydrogen bonds with the HLA-B7 protein for at least one of the two peptides are listed and in these cases SC- or BB-mediated hydrogen bonds are always listed for both peptides.

a

Average number of hydrogen bonds per molecular dynamics time frame;

b

SC, only side chain hydrogen bond interactions of the corresponding peptide or residue are considered;

c

BB, only backbone hydrogen bond interactions of the corresponding peptide or residue are considered.