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. 2009 Dec 21;19(2):327–348. doi: 10.1002/pro.314

Table IV.

Hydrogen-Bond Frequency and Accessible Surface Area in Amyloidogenic and Non-amyloidogenic Residues

Amyloidogenic
 Non-amyloidogenic
Hydrogen-bonds/residuea
 Relative ASA/residueb %
Protein PDB ID of protein model Amyloidogenic sequence(s) Average for sequence Average for protein Average for sequence Average for protein Hydrogen-bonds/ residuea Relative ASA/residueb %
α-Synuclein 1XQ8 51–56 1.17 1.07 53.7 62.5 0.78 71.4
66–74 1.33 58.5
77–82 1.00 70.6
86–92 0.71 68.3
β-Lactoglobulin 1BEB (dimer) A&B:11–20 1.25 1.29 30.5 18.6 1.03 33.6
A&B:101–110 1.55 15.4
A&B:116–126 1.14 12.7
A&B:146–152 1.00 15.3
β2-Microglobulin 1B0G 58–71 1.14 0.93 22.9 33.1 0.83 29.4
83–89 0.87 45.5
91–96 0.50 42.5
AcP 1APS 16–31 1.13 0.89 11.4 10.6 1.20 6.60
87–98 0.58 9.64
Amphoterin 1CKT 12–27 1.38 1.38 19.4 19.4 1.13 41.8
ApoC-II 1SOH 60–70 1.09 1.09 58.8 58.8 0.93 59.9
B. subtilis cspB 2ES2 1–22 0.91 0.91 36.9 36.9 0.71 40.5
Gelsolin 1KCQ 182–192 1.18 1.18 5.46 5.46 0.98 39.4
Human complement receptor 1, SRC3 1GKG 1038–1054 0.76 0.76 39.0 39.0 0.62 43.6
Insulin 1XDAc A: 13–18 1.33 1.08 49.2 44.4 0.92 47.0
B: 11–17 0.86 40.4
Kerato-epithelin 1X3B 515–525 1.18 1.18 30.3 30.3 0.69 41.9
Lactoferrin 1LFH 538–545 0.50 0.50 13.4 13.4 1.07 27.0
Laminin 2JD4c 2919–2930 1.08 1.08 21.6 21.6 0.91 29.4
Lysozyme 1REX 56–61 1.33 1.33 4.72 4.72 1.14 34.2
Medin 3BN6d 299–308 1.20 1.17 8.00 20.2 0.94 31.8
309–316 1.13 35.3
Myoglobin 1WLA 101–118 1.06 1.06 24.9 24.9 1.23 36.0
Prolactin 1RW5 7–34 1.25 1.05 39.8 44.1 1.01 35.6
43–57 0.67 52.1
hPrP 1QLX 113–127e 0.33 1.09 73.6 43.8 0.90 40.7
138–144 0.86 54.2
170–175 1.50 46.5
178–193 1.19 32.7
repA, pPS10 Pseudomonas 1HKQ (dimer) 26–34 0.83 0.83 18.9 18.9 1.16 36.2
Transthyretin 1TTA (tetramer) 105–115 1.18 1.18 9.64 9.64 0.96 30.0
B. subtilis ‘YjcG’ protein 2D4G (dimer) 151–156 1.17 1.17 26.6 26.6 0.95 32.5
M. jannaschii tRNA endonuclease 1A79 (tetramer) 47–53 1.46 1.46 2.86 2.86 1.06 27.2
DNA polymerase III subunit alpha, E. coli 2HNH 513–518 0.67 0.67 1.52 1.52 1.09 27.4
20S proteasome Bos taurus 1IRU 18–23 (Chains N&2) 0.83 0.83 5.83 5.83 1.05 21.3
Enterotoxin, S. aureus 2NTT (dimer) 50–54 2.50 2.50 37.6 37.6 1.03 29.8
Na+/Ca2+-exchange protein 1, C. familiaris 2DPK 455–459 1.80 1.80 17.5 17.5 0.86 38.5
Cytochrome b, R. sphaeroides 2QJPc 337–341 (Chains A&D) 1.10 1.10 25.0 25.0 1.05 27.7
Thymidine kinase, cystolic, human 1W4Rc 133–137 (Chains A,B,C&D) 1.00 1.00 23.1 23.1 0.99 25.1
Glycyl-tRNA synthetase, Thermus thermophilus 1ATI (dimer) 399–403 1.40 1.40 2.11 2.11 1.10 24.3
Leucine-binding protein, E. coli 1USG 3–7 0.80 0.80 14.3 14.3 1.10 28.9
Mean (±SD) 1.09 (±0.37) 1.13 (±0.37) 30 (±20) 24 (±16) 0.98 (±0.15) 35 (±12)
1

Number of hydrogen-bonds per residue estimated by the VADAR program.83

2

Accessible surface area, average relative surface area per residue (%) computed by the NACCESS program.91

3

Biological molecule 1 used for analysis.

4

The model 3BN6 is bovine lactadherin C2 domain, which shares 70% SID with human lactadherin of which residues 268–317 are medin. Residues Val70–Val87 in 3BN6 are equivalent to the amyloidogenic sequence in human medin between residues 299 and 316.

5

Residues 125–127 only are represented in 1QLX.