PolyPhen Help Appendix:
data used for calculation of structural parameters

 

Maximal accessible surface area, Ų:

(Defined as a 99%-quantile of surface area distribution for this particular amino acid type in PDB).

Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
103 234 160 164 105 181 187 87 170 133 137 197 157 169 133 125 139 195 181 120

 

 

Side chain volumes, ų:

Reference: A.A. Zamyatin, Protein Volume in Solution (1972) Prog Biophys Mol Biol 24:107-123

Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
88 173 114 111 108 144 138 60 153 167 167 168 163 190 112 89 116 227 193 140

 

 

Accessible surface propensities:

Reference: Sunyaev et al., Are knowledge-based potentials derived from protein structure
sets discriminative with respect to amino acid types? (1998) Proteins 31:225-246
[
Abstract]  [PDF format]

AA Normed accessible surface area
0 (0..5) [5..15) [15..30) [30..50) [50..75) >=75
Ala 0.59 0.06 -0.03 -0.2 -0.23 -0.18 0.18
Arg -2.99 -1.14 0.02 0.33 0.47 0.25 -0.31
Asn -1.48 -0.55 -0.27 0.06 0.26 0.45 0.39
Asp -1.35 -0.69 -0.33 0.1 0.28 0.42 0.5
Cys 0.61 0.52 0.51 -0.02 -0.75 -1.8 -2
Gln -1.55 -0.58 -0.25 0.06 0.4 0.44 -0.17
Glu -2.13 -0.98 -0.35 -0.01 0.4 0.58 0.28
Gly 0.31 -0.23 -0.07 -0.21 -0.12 0.05 0.68
His -1.09 -0.11 0.25 0.38 0.1 -0.18 -0.54
Ile 0.87 0.54 0.09 -0.04 -0.79 -1.29 -2
Leu 0.59 0.61 0.28 -0.11 -0.76 -1.21 -1.42
Lys -4.06 -2.28 -1.22 -0.08 0.6 0.75 0.39
Met 0.53 0.61 -0.01 -0.11 -0.4 -1.17 -0.62
Phe 0.47 0.64 0.36 -0.01 -0.86 -1.31 -1.75
Pro -0.98 -0.46 -0.28 -0.03 0.11 0.41 0.74
Ser -0.29 -0.21 0.04 -0.11 -0.01 0.21 0.49
Thr -0.49 -0.16 -0.11 0.1 0.23 0.09 -0.15
Trp -0.29 0.53 0.63 0.19 -0.52 -1.42 -2.54
Tyr -0.76 0.27 0.53 0.43 -0.22 -0.95 -1.87
Val 0.69 0.5 0.19 -0.13 -0.46 -1.13 -1.76

 

 

Phi-Psi map (Ramachandran map) regions:

(The map is adapted from ProCheck software definitions.)


   bBBBBBBBBBBbbbbb.....pppppgggggbbbbb
   bBBBBBBBBBBBbbbbb......ggggggggbbbbb
   bBBBBBBBBBBBbbbbbbb....ggggggggbbbbb
   bbBBBBBBBBBBBbbbbbb....ggggggggbbbbb
   bbBBBBBBBBBBBBbbbbb....ggggggggbbbbb
   bbBBBBBBBBBBBbbbbbb....gggggggggbbbb
   bbbBBBBBBBBBbbbbbbb...llllllgggggbbb
   bbbbBBBBBBBbbbbbbbblllllllllgggggbbb
   bbbbbBbbBbbbbbbbbbblllllllllgggggbbb
   bbbbbbbbbbbbbbbbbbblllllllllgggggbbb
   bbbbbbbbbbbbbbbbbbblllllllllgggggbbb
   bbbbbbbbbbbbbbb....llllllllllggggbbb
   bbbbbbbbbbbbbbb....llllllllllggggbbb
   aaaaaaaaaaaaaaa....llllLlllllggggbbb
   aaaaaaaaaaaaaaa....llllLLllllggggbbb
   aaaaaaaAaaaaaaaa...llllllllllggggbbb
   aaaaaaAAAAaaaaaaa...lllllllllggggbbb
   aaaaaaAAAAAaaaaaa...lllllllllggggbbb
   aaaaaAAAAAAAaaaaaa..lllllllllggggbbb
   aaaaaaAAAAAAAaaaaaa.lllllllllggggbbb
   aaaaaaAAAAAAAAaaaaa.lllllllllggggbbb
   aaaaaaaAAAAAAAaaaaaa....gggggggggbbb
   aaaaaaaaAAAAAAAaaaaa...ggggggggggbbb
   aaaaaaaaaAAAAAAaaaaaa..ggggggggggbbb
   aaaaaaaaaaaAAAAaaaaaa..ggggggggggbbb
   aaaaaaaaaaaaaaaaaaaaa..ggggggggggbbb
   aaaaaaaaaaaaaaaaaaaaa.gggggggggggbbb
   .aaaaaaaaaaaaaaaaaaaa.gggggggggggggg
   gggaaaaaaaaaaaaaaaaa..gggggggggggggg
   gggbbbbbbbbbbbbbb.....gggggggggggggg
   bbbbbbbbbbbbbb.......pppppgggggggggg
   bbbbbbbbbbbbbb.......pppppgggggggggg
   bbbbbbbbbbbbbbb......ppPpppggggggggg
   bbbbbbbbbbbbbbb......ppPpppggggggbbb
   bbbbbbbbbbbbbbb......ppPPppggggggbbb
   bbbbbbbbbbbbbbb......ppppppggggggbbb                                  

 

 

Ligands excluded from contact calculation:

(See also [Current Het Group Dictionary] at [PDB])

PO4 PI SO4 SUL CL BR NO3 SCN NH4 K NA LI MG DOD NAG MAN GOL SO4 CL CO3 FS4

 

 

Importance of contact evaluation in all related protein structures:

The figure below is from
Shamil Sunyaev, Vasily Ramensky, Ina Koch, Warren Lathe III, Alexey S. Kondrashov and Peer Bork
Prediction of deleterious human alleles [Hum Mol Genet] (2001) 10:591-597 [PDF format]

Figure 2. In some cases our straightforward rules fail to predict the deleterious effect of an amino acid substitution; however, more detailed analysis is capable of revealing the damaging character of the mutation. This suggests that further improvement of the method can significantly reduce the fraction of false-negative predictions. As an example, structural analysis (PDB entry 2pab) predicts the Ile->Ser replacement in transthyretin that causes amyloidosis type II to be a neutral substitution, because this is a substitution of a hydrophobic residue for a hydrophilic one on the surface, distant from the thyroid hormone binding site. (A). Comparative analysis also fails to detect the deleterious effect of the mutation because transthyretin from Sparus aurata (Gilthead sea bream) has a Ser residue in the corresponding site, probably as a result of a correlated mutation (B). However, analysis of the structure of the complex of transthyretin with the retinol binding protein (PDB entry 1qab) shows a critical role of the Ile residue for the complex formation (C).