Table 1 of Sergeev, Mol Vis 4:9, 1998.


Table 1. Secondary structure occurrence frequencies of overlapping sequence tripeptides for the mouse ßA3-crystallin N-terminal extension

Residue   Observed frequencies   Preferred   Number    Entropy
             Helix    Coil         state     of hits
-------   --------------------   ---------   -------   -------
 E-29         0.50    0.25                      -       1.50
 T-28         0.31    0.62           L          4       1.85
 Q-27         0.22    0.65           L          9       1.90
 T-26         0.25    0.54           L         10       1.95
 V-25         0.48    0.24                      9       1.93
 Q-24         0.60    0.23           H         10       1.72
 R-23         0.64    0.30           H          9       1.47
 E-22         0.64    0.21           H         32       1.51
 L-21         0.65    0.21           H         15       1.58
 E-20         0.59    0.34           H         10       1.80
 T-19         0.47    0.40                     26       2.07
 L-18         0.31    0.57           L          9       2.00
 P-17         0.15    0.74           L         17       1.77
 T-16         0.17    0.66           L          8       2.09
 T-15         0.22    0.55           L         16       2.19
 K-14         0.38    0.42                      7       2.18
 M-13         0.62    0.34           H          9       1.70
 A-12         0.54    0.39           H          7       1.84
 Q-11         0.42    0.42                     12       2.05
 T-10         0.20    0.67(0.50)     L(T)       6       1.78
 N-9          0.14    0.86           L         12       1.48
 P-8          0.40    0.60           L          4       1.96
 M-7          0.33    0.67           L          4       1.73
 P-6          0.08    0.82           L          4       1.72
 G-5          0.15    0.74           L         19       1.90
 S-4          0.28    0.44                     38       2.19
 L-3          0.33    0.48                     28       2.21
 G-2          0.23    0.69           L          9       1.92
 P-1          0.42    0.43                      5       2.27

From left to right: Residue: residue and its relative position in the terminal extension (negative numbers) with residue 1 corresponding to the first residue of the proposed structural domain located after multiple sequence alignment [6]. Observed frequencies: frequencies of overlapped sequence tripeptides, calculated for the helical and coil secondary structure. Preferred states: the preferred conformation state Sj for the j-th residue with the observed frequency greater than or equal to 0.5. X-ray data: the secondary structure content, estimated from the X-ray model by the method [6], "-" correspond to residues which were not located from the electron density map [4]. Number of hits: number of tripeptide matches in the SCAN3D database [22]. Information entropy: calculated by formula [3]. "H", "L", and "T" are helical, coil, and turn residue conformations, respectively.


Sergeev, Mol Vis 1998; 4:9 <http://www.molvis.org/molvis/v4/p9>
©1998 Molecular Vision <http://www.molvis.org/molvis/>
ISSN 1090-0535