PFRMAT AL 
TARGET T0073 
AUTHOR 7648-2940-6918 
REMARK The sequence forms 2 alpha helices 
REMARK  
REMARK alpha helix A: 
REMARK ==>residues 22-48: 4 heptads  
REMARK alpha helix B: 
REMARK ==>residues 1-12: 1-2 heptads (one is an incomplete heptad) 
REMARK 
REMARK These 2 helices are separated by a short loop/turn forms by the sequence 
REMARK (N-terminal)KKEGFSPEE. The interaction of hydrophobic residues at 
REMARK positions a and d of the repeating heptad sequence designated (abcdefg)n 
REMARK stabilises the structure of T0073 [1]. 
REMARK 
REMARK 2: Leu (helix B) interacts with 32:Leu (helix A) 
REMARK 5: Leu (helix B) interacts with 29:Leu (helix A) 
REMARK 9: Leu (helix B) interacts with 25:Leu (helix A) 
REMARK 12:Leu (helix B) interacts with 22:Leu (helix A) 
REMARK 
REMARK Orientation for the 2 helices is predicted to be anti-parallel. 
REMARK 
REMARK [1] Mclachlan AD, Stewart M. 1975. Tropomycin coiled-coil interactions: 
REMARK Evidence for an unstaggered structure. J. Mol. Biol. 98: 293-304. 
REMARK 
METHOD We align a target sequence with structurally aligned sequences 
METHOD (i.e., multiple structure alignment), where a multiple structure 
METHOD alignment is computed from results of pairwise structure alignments 
METHOD for similar structures.  
METHOD Pairwise structure alignments are computed using a computer 
METHOD program STRALIGN [1] developed by the group-leader and they are 
METHOD combined into a multiple structure alignment using a method like 
METHOD center-star alignment. 
METHOD A simple dynamic programming procedure (Smith-Waterman like procedure) 
METHOD is used for computing an alignment between a target sequence and 
METHOD the aligned sequences. 
METHOD Finally, an alignment between a target and one of the aligned 
METHOD sequences (i.e., template sequence) is extracted and refined. 
METHOD Human knowledge is also used to find template structures and 
METHOD to refine alignments. 
METHOD 
METHOD [1] T. Akutsu: Protein structure alignment using dynamic programming 
METHOD and iterative alignment, IEICE Transactions on Information and Systems, 
METHOD vol. E79-D, pp. 1629--1636, 1996. 
METHOD 
METHOD Program code of STRALIGN is available via 
METHOD http://www.hgc.ims.u-tokyo.ac.jp/service/tooldoc/stralign/intro.html 
MODEL  1 
PARENT 1rpo 
S   1    T  19 
L   2    L  20 
A   3    T  21 
A   4    L  22 
L   5    L  23 
K   6    E  24 
E   8    K  25 
L   9    L  26 
Q  10    N  27 
A  11    E  28 
L  12    L  29 
A  24    E  35 
L  25    Q  36 
E  26    A  37 
S  27    D  38 
E  28    I  39 
L  29    C  40 
Q  30    S  42 
A  31    L  43 
L  32    H  44 
E  33    D  45 
K  34    H  46 
K  35    A  47 
L  36    D  48 
A  37    E  49 
A  38    L  50 
L  39    Y  51 
K  40    R  52 
S  41    S  53 
K  42    C  54 
L  43    L  55 
Q  44    A  56 
A  45    R  57 
L  46    F  58 
TER 
END 
