PFRMAT AL 
TARGET T0084 
AUTHOR 7397-8542-2481 
METHOD A COILS2.2 search yielded significant coiled-coil scores for this peptide. 
METHOD The scores dropped to nearly zero towards the middle of the peptide,  
METHOD pointing to the occurance of an unusual residue at that position.  An  
METHOD inspection of the hydrophobic core showed an Asn residue in position D 
METHOD of the central heptad.  Asn is extremely rare at that position in two- 
METHOD stranded coiled-coils.  The following reasons lead us to conclude that this 
METHOD peptide will form a four-stranded, parallel coiled-coil: 1) Asn occurs 
METHOD fairly frequently in position A of two-stranded coiled-coils [parallel  
METHOD geometry], but not in position D [perpendicular]; 2) position A of four- 
METHOD stranded coiled-coils has a perpendicular geometry and position D a 
METHOD parallel geometry; 3) a peptide with Leu in A and Val in D forms trimers, 
METHOD and a peptide with Leu in A and Ile in D tetramers; 4) a core Asn residue 
METHOD in GCN4 specifies dimerization over trimerization, showing a preference 
METHOD for a parallel over an acute geometry.  The tetrameric GCN4 mutant was  
METHOD therefore chosen as the template.  Superposition was made according to the 
METHOD heptad pattern.    
MODEL  1 
PARENT 1gcl_A 
R   4    R   1 
E   5    M   2 
G   6    K   3 
V   7    Q   4 
L   8    I   5 
K   9    E   6 
K  10    D   7 
L  11    K   8 
R  12    L   9 
A  13    E  10 
V  14    E  11 
E  15    I  12 
N  16    L  13 
E  17    S  14 
L  18    K  15 
H  19    L  16 
Y  20    Y  17 
N  21    H  18 
K  22    I  19 
S  23    E  20 
L  24    N  21 
L  25    E  22 
E  26    L  23 
E  27    A  24 
V  28    R  25 
K  29    I  26 
D  30    K  27 
E  31    K  28 
L  32    L  29 
Q  33    L  30 
K  34    G  31 
TER 
END 
