REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL201_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : TATSUYA-AKUTSU 
REMARK  ---------------------------------------------------------- 
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  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1rpo 
ATOM      1  N   SER     1      18.652   5.907  20.282  1.00  0.00              
ATOM      2  CA  SER     1      19.243   7.138  20.795  1.00  0.00              
ATOM      3  C   SER     1      18.738   7.357  22.234  1.00  0.00              
ATOM      4  O   SER     1      19.418   7.969  23.018  1.00  0.00              
ATOM      5  N   LEU     2      17.518   6.907  22.580  1.00  0.00              
ATOM      6  CA  LEU     2      17.034   7.025  23.948  1.00  0.00              
ATOM      7  C   LEU     2      17.873   6.092  24.840  1.00  0.00              
ATOM      8  O   LEU     2      18.285   6.499  25.941  1.00  0.00              
ATOM      9  N   ALA     3      18.167   4.872  24.387  1.00  0.00              
ATOM     10  CA  ALA     3      18.952   3.921  25.160  1.00  0.00              
ATOM     11  C   ALA     3      20.353   4.499  25.415  1.00  0.00              
ATOM     12  O   ALA     3      20.858   4.430  26.563  1.00  0.00              
ATOM     13  N   ALA     4      20.961   5.114  24.391  1.00  0.00              
ATOM     14  CA  ALA     4      22.292   5.694  24.523  1.00  0.00              
ATOM     15  C   ALA     4      22.231   6.897  25.449  1.00  0.00              
ATOM     16  O   ALA     4      23.128   7.060  26.302  1.00  0.00              
ATOM     17  N   LEU     5      21.208   7.741  25.361  1.00  0.00              
ATOM     18  CA  LEU     5      21.060   8.877  26.269  1.00  0.00              
ATOM     19  C   LEU     5      21.010   8.381  27.705  1.00  0.00              
ATOM     20  O   LEU     5      21.663   8.965  28.589  1.00  0.00              
ATOM     21  N   LYS     6      20.293   7.295  27.970  1.00  0.00              
ATOM     22  CA  LYS     6      20.203   6.773  29.340  1.00  0.00              
ATOM     23  C   LYS     6      21.579   6.321  29.843  1.00  0.00              
ATOM     24  O   LYS     6      21.968   6.648  30.988  1.00  0.00              
ATOM     25  N   GLU     8      22.340   5.659  28.981  1.00  0.00              
ATOM     26  CA  GLU     8      23.694   5.186  29.300  1.00  0.00              
ATOM     27  C   GLU     8      24.626   6.361  29.577  1.00  0.00              
ATOM     28  O   GLU     8      25.363   6.359  30.573  1.00  0.00              
ATOM     29  N   LEU     9      24.586   7.416  28.769  1.00  0.00              
ATOM     30  CA  LEU     9      25.450   8.562  28.976  1.00  0.00              
ATOM     31  C   LEU     9      25.047   9.318  30.231  1.00  0.00              
ATOM     32  O   LEU     9      25.915   9.782  30.983  1.00  0.00              
ATOM     33  N   GLN    10      23.750   9.328  30.547  1.00  0.00              
ATOM     34  CA  GLN    10      23.275  10.036  31.740  1.00  0.00              
ATOM     35  C   GLN    10      23.737   9.240  32.932  1.00  0.00              
ATOM     36  O   GLN    10      24.136   9.870  33.936  1.00  0.00              
ATOM     37  N   ALA    11      23.755   7.913  32.890  1.00  0.00              
ATOM     38  CA  ALA    11      24.239   7.090  33.994  1.00  0.00              
ATOM     39  C   ALA    11      25.721   7.327  34.269  1.00  0.00              
ATOM     40  O   ALA    11      26.144   7.156  35.408  1.00  0.00              
ATOM     41  N   LEU    12      26.547   7.760  33.323  1.00  0.00              
ATOM     42  CA  LEU    12      27.966   8.001  33.597  1.00  0.00              
ATOM     43  C   LEU    12      28.206   9.358  34.244  1.00  0.00              
ATOM     44  O   LEU    12      29.340   9.693  34.621  1.00  0.00              
ATOM     45  N   ALA    24      29.082  16.386  28.763  1.00  0.00              
ATOM     46  CA  ALA    24      28.956  17.065  27.468  1.00  0.00              
ATOM     47  C   ALA    24      28.323  16.106  26.447  1.00  0.00              
ATOM     48  O   ALA    24      27.444  16.489  25.672  1.00  0.00              
ATOM     49  N   LEU    25      28.734  14.840  26.479  1.00  0.00              
ATOM     50  CA  LEU    25      28.230  13.833  25.545  1.00  0.00              
ATOM     51  C   LEU    25      26.750  13.570  25.796  1.00  0.00              
ATOM     52  O   LEU    25      25.957  13.408  24.837  1.00  0.00              
ATOM     53  N   GLU    26      26.292  13.528  27.060  1.00  0.00              
ATOM     54  CA  GLU    26      24.885  13.338  27.394  1.00  0.00              
ATOM     55  C   GLU    26      24.052  14.532  26.887  1.00  0.00              
ATOM     56  O   GLU    26      22.973  14.346  26.328  1.00  0.00              
ATOM     57  N   SER    27      24.605  15.752  26.930  1.00  0.00              
ATOM     58  CA  SER    27      23.955  16.956  26.423  1.00  0.00              
ATOM     59  C   SER    27      23.820  16.916  24.909  1.00  0.00              
ATOM     60  O   SER    27      22.768  17.243  24.374  1.00  0.00              
ATOM     61  N   GLU    28      24.848  16.466  24.200  1.00  0.00              
ATOM     62  CA  GLU    28      24.754  16.320  22.739  1.00  0.00              
ATOM     63  C   GLU    28      23.712  15.238  22.424  1.00  0.00              
ATOM     64  O   GLU    28      22.869  15.396  21.489  1.00  0.00              
ATOM     65  N   LEU    29      23.738  14.122  23.135  1.00  0.00              
ATOM     66  CA  LEU    29      22.848  13.001  22.842  1.00  0.00              
ATOM     67  C   LEU    29      21.404  13.369  23.115  1.00  0.00              
ATOM     68  O   LEU    29      20.479  12.888  22.409  1.00  0.00              
ATOM     69  N   GLN    30      19.998  16.270  22.515  1.00  0.00              
ATOM     70  CA  GLN    30      19.593  16.955  21.305  1.00  0.00              
ATOM     71  C   GLN    30      19.481  15.922  20.182  1.00  0.00              
ATOM     72  O   GLN    30      18.579  16.036  19.317  1.00  0.00              
ATOM     73  N   ALA    31      20.348  14.920  20.106  1.00  0.00              
ATOM     74  CA  ALA    31      20.276  13.888  19.093  1.00  0.00              
ATOM     75  C   ALA    31      18.962  13.118  19.188  1.00  0.00              
ATOM     76  O   ALA    31      18.261  12.907  18.165  1.00  0.00              
ATOM     77  N   LEU    32      18.548  12.739  20.396  1.00  0.00              
ATOM     78  CA  LEU    32      17.321  12.026  20.582  1.00  0.00              
ATOM     79  C   LEU    32      16.136  12.893  20.173  1.00  0.00              
ATOM     80  O   LEU    32      15.190  12.385  19.530  1.00  0.00              
ATOM     81  N   GLU    33      16.126  14.183  20.512  1.00  0.00              
ATOM     82  CA  GLU    33      15.001  15.029  20.115  1.00  0.00              
ATOM     83  C   GLU    33      14.934  15.117  18.589  1.00  0.00              
ATOM     84  O   GLU    33      13.834  15.038  18.045  1.00  0.00              
ATOM     85  N   LYS    34      16.112  15.116  17.940  1.00  0.00              
ATOM     86  CA  LYS    34      16.218  15.228  16.493  1.00  0.00              
ATOM     87  C   LYS    34      15.719  13.923  15.859  1.00  0.00              
ATOM     88  O   LYS    34      15.037  13.925  14.814  1.00  0.00              
ATOM     89  N   LYS    35      16.000  12.788  16.498  1.00  0.00              
ATOM     90  CA  LYS    35      15.536  11.499  16.039  1.00  0.00              
ATOM     91  C   LYS    35      14.007  11.382  16.162  1.00  0.00              
ATOM     92  O   LYS    35      13.305  10.865  15.267  1.00  0.00              
ATOM     93  N   LEU    36      13.464  11.919  17.261  1.00  0.00              
ATOM     94  CA  LEU    36      12.037  11.922  17.467  1.00  0.00              
ATOM     95  C   LEU    36      11.360  12.792  16.422  1.00  0.00              
ATOM     96  O   LEU    36      10.339  12.362  15.883  1.00  0.00              
ATOM     97  N   ALA    37      11.923  13.958  16.116  1.00  0.00              
ATOM     98  CA  ALA    37      11.363  14.852  15.092  1.00  0.00              
ATOM     99  C   ALA    37      11.338  14.137  13.728  1.00  0.00              
ATOM    100  O   ALA    37      10.329  14.188  13.014  1.00  0.00              
ATOM    101  N   ALA    38      12.398  13.433  13.342  1.00  0.00              
ATOM    102  CA  ALA    38      12.466  12.696  12.093  1.00  0.00              
ATOM    103  C   ALA    38      11.396  11.613  12.054  1.00  0.00              
ATOM    104  O   ALA    38      10.679  11.471  11.034  1.00  0.00              
ATOM    105  N   LEU    39      11.256  10.827  13.118  1.00  0.00              
ATOM    106  CA  LEU    39      10.272   9.766  13.140  1.00  0.00              
ATOM    107  C   LEU    39       8.867  10.343  12.979  1.00  0.00              
ATOM    108  O   LEU    39       8.077   9.863  12.142  1.00  0.00              
ATOM    109  N   LYS    40       8.509  11.393  13.711  1.00  0.00              
ATOM    110  CA  LYS    40       7.167  11.967  13.614  1.00  0.00              
ATOM    111  C   LYS    40       6.934  12.566  12.213  1.00  0.00              
ATOM    112  O   LYS    40       5.842  12.445  11.644  1.00  0.00              
ATOM    113  N   SER    41       7.943  13.166  11.578  1.00  0.00              
ATOM    114  CA  SER    41       7.853  13.702  10.220  1.00  0.00              
ATOM    115  C   SER    41       7.630  12.544   9.227  1.00  0.00              
ATOM    116  O   SER    41       6.801  12.650   8.308  1.00  0.00              
ATOM    117  N   LYS    42       8.329  11.418   9.340  1.00  0.00              
ATOM    118  CA  LYS    42       8.118  10.257   8.488  1.00  0.00              
ATOM    119  C   LYS    42       6.729   9.687   8.704  1.00  0.00              
ATOM    120  O   LYS    42       6.047   9.368   7.723  1.00  0.00              
ATOM    121  N   LEU    43       6.228   9.600   9.934  1.00  0.00              
ATOM    122  CA  LEU    43       4.921   9.019  10.214  1.00  0.00              
ATOM    123  C   LEU    43       3.845   9.886   9.583  1.00  0.00              
ATOM    124  O   LEU    43       2.948   9.389   8.882  1.00  0.00              
ATOM    125  N   GLN    44       4.004  11.196   9.694  1.00  0.00              
ATOM    126  CA  GLN    44       3.019  12.114   9.157  1.00  0.00              
ATOM    127  C   GLN    44       2.993  12.091   7.639  1.00  0.00              
ATOM    128  O   GLN    44       1.943  12.150   7.025  1.00  0.00              
ATOM    129  N   ALA    45       4.149  12.020   6.994  1.00  0.00              
ATOM    130  CA  ALA    45       4.218  12.058   5.541  1.00  0.00              
ATOM    131  C   ALA    45       3.759  10.764   4.901  1.00  0.00              
ATOM    132  O   ALA    45       3.115  10.778   3.844  1.00  0.00              
ATOM    133  N   LEU    46       4.134   9.628   5.478  1.00  0.00              
ATOM    134  CA  LEU    46       3.886   8.338   4.855  1.00  0.00              
ATOM    135  C   LEU    46       2.632   7.620   5.337  1.00  0.00              
ATOM    136  O   LEU    46       2.194   6.688   4.664  1.00  0.00              
END
