
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   37 (  148),  selected   37 , name T0343AL381_2
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343AL381_2.T0343.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       2           -
LGA    -       -      W       3           -
LGA    -       -      R       4           -
LGA    -       -      E       5           -
LGA    -       -      I       6           -
LGA    -       -      L       7           -
LGA    -       -      R       8           -
LGA    -       -      K       9           -
LGA    -       -      E      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      D      14           -
LGA    -       -      L      15           -
LGA    -       -      G      16           -
LGA    K       9      E      17          3.083
LGA    E      10      F      18          1.044
LGA    G      11      I      19          1.086
LGA    F      12      V      20          1.043
LGA    L      13      E      21          1.020
LGA    D      14      L      22          4.429
LGA    L      15      V      23          4.253
LGA    G      16      -       -           -
LGA    E      17      -       -           -
LGA    F      18      Y      24          2.415
LGA    I      19      -       -           -
LGA    V      20      -       -           -
LGA    E      21      I      25          3.278
LGA    L      22      D      26          0.569
LGA    V      23      C      27          2.756
LGA    Y      24      -       -           -
LGA    I      25      -       -           -
LGA    D      26      P      28          0.720
LGA    C      27      C      29          2.460
LGA    P      28      -       -           -
LGA    E      30      E      30          1.415
LGA    P      31      P      31          3.467
LGA    I      32      I      32          3.042
LGA    P      33      P      33          4.581
LGA    P      34      P      34          3.179
LGA    T      35      T      35           #
LGA    -       -      L      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Y      39           -
LGA    -       -      D      40           -
LGA    -       -      K      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      D      44           -
LGA    -       -      E      45           -
LGA    -       -      W      46           -
LGA    -       -      Y      47           -
LGA    -       -      K      48           -
LGA    -       -      V      49           -
LGA    -       -      E      50           -
LGA    -       -      E      51           -
LGA    -       -      A      52           -
LGA    -       -      P      53           -
LGA    -       -      N      54           -
LGA    -       -      V      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      63           -
LGA    L      36      W      64          2.892
LGA    A      37      A      65          2.924
LGA    -       -      I      66           -
LGA    -       -      E      67           -
LGA    I      38      V      68          1.751
LGA    Y      39      L      69          2.736
LGA    -       -      E      70           -
LGA    -       -      R      71           -
LGA    -       -      I      72           -
LGA    D      40      R      73          0.369
LGA    K      41      D      74          2.071
LGA    K      42      G      75           #
LGA    G      43      E      76           #
LGA    D      44      N      77          3.755
LGA    E      45      V      78          2.186
LGA    W      46      K      79          1.689
LGA    -       -      L      80           -
LGA    -       -      V      81           -
LGA    -       -      S      82           -
LGA    -       -      L      83           -
LGA    -       -      D      84           -
LGA    -       -      G      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      P      88           -
LGA    -       -      P      89           -
LGA    -       -      K      90           -
LGA    -       -      V      91           -
LGA    -       -      M      92           -
LGA    -       -      K      93           -
LGA    -       -      R      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      L      99           -
LGA    -       -      Q     100           -
LGA    -       -      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37   94    5.0     27    2.66    25.93     18.743     0.979

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.991391 * X  +   0.046547 * Y  +   0.122385 * Z  +  63.075203
  Y_new =  -0.129953 * X  +  -0.464194 * Y  +  -0.876148 * Z  +  43.980759
  Z_new =   0.016028 * X  +  -0.884510 * Y  +   0.466247 * Z  +  58.941723 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.085685    2.055907  [ DEG:   -62.2052    117.7948 ]
  Theta =  -0.016029   -3.125564  [ DEG:    -0.9184   -179.0816 ]
  Phi   =  -3.011254    0.130339  [ DEG:  -172.5321      7.4679 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0343AL381_2                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343AL381_2.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   94   5.0   27   2.66   25.93  18.743
REMARK  ---------------------------------------------------------- 
MOLECULE T0343AL381_2
REMARK Aligment from pdb entry: 1zoqA
ATOM      1  N   LYS     9      27.931   8.271  15.775  1.00  0.00              
ATOM      2  CA  LYS     9      27.450   9.634  15.929  1.00  0.00              
ATOM      3  C   LYS     9      26.918  10.185  14.616  1.00  0.00              
ATOM      4  O   LYS     9      27.248   9.687  13.545  1.00  0.00              
ATOM      5  N   GLU    10      26.090  11.220  14.716  1.00  0.00              
ATOM      6  CA  GLU    10      25.523  11.847  13.542  1.00  0.00              
ATOM      7  C   GLU    10      25.627  13.348  13.696  1.00  0.00              
ATOM      8  O   GLU    10      25.548  13.844  14.813  1.00  0.00              
ATOM      9  N   GLY    11      25.830  14.070  12.593  1.00  0.00              
ATOM     10  CA  GLY    11      25.920  15.520  12.656  1.00  0.00              
ATOM     11  C   GLY    11      24.548  16.155  12.790  1.00  0.00              
ATOM     12  O   GLY    11      23.624  15.820  12.041  1.00  0.00              
ATOM     13  N   PHE    12      24.403  17.076  13.736  1.00  0.00              
ATOM     14  CA  PHE    12      23.112  17.739  13.951  1.00  0.00              
ATOM     15  C   PHE    12      23.141  19.245  13.734  1.00  0.00              
ATOM     16  O   PHE    12      22.093  19.898  13.734  1.00  0.00              
ATOM     17  N   LEU    13      24.339  19.795  13.556  1.00  0.00              
ATOM     18  CA  LEU    13      24.494  21.225  13.340  1.00  0.00              
ATOM     19  C   LEU    13      25.808  21.571  12.633  1.00  0.00              
ATOM     20  O   LEU    13      26.889  21.196  13.084  1.00  0.00              
ATOM     21  N   ASP    14      25.703  22.326  11.546  1.00  0.00              
ATOM     22  CA  ASP    14      26.860  22.736  10.754  1.00  0.00              
ATOM     23  C   ASP    14      27.144  24.235  10.939  1.00  0.00              
ATOM     24  O   ASP    14      26.336  25.073  10.570  1.00  0.00              
ATOM     25  N   LEU    15      28.297  24.565  11.513  1.00  0.00              
ATOM     26  CA  LEU    15      28.679  25.966  11.737  1.00  0.00              
ATOM     27  C   LEU    15      28.897  26.760  10.444  1.00  0.00              
ATOM     28  O   LEU    15      28.697  27.985  10.420  1.00  0.00              
ATOM     29  N   GLY    16      29.296  26.067   9.375  1.00  0.00              
ATOM     30  CA  GLY    16      29.527  26.732   8.102  1.00  0.00              
ATOM     31  C   GLY    16      28.329  27.522   7.610  1.00  0.00              
ATOM     32  O   GLY    16      28.411  28.741   7.441  1.00  0.00              
ATOM     33  N   GLU    17      27.197  26.855   7.352  1.00  0.00              
ATOM     34  CA  GLU    17      26.011  27.579   6.876  1.00  0.00              
ATOM     35  C   GLU    17      25.564  28.684   7.854  1.00  0.00              
ATOM     36  O   GLU    17      25.074  29.735   7.436  1.00  0.00              
ATOM     37  N   PHE    18      25.736  28.434   9.151  1.00  0.00              
ATOM     38  CA  PHE    18      25.358  29.391  10.190  1.00  0.00              
ATOM     39  C   PHE    18      26.076  30.732  10.033  1.00  0.00              
ATOM     40  O   PHE    18      25.456  31.794  10.141  1.00  0.00              
ATOM     41  N   ILE    19      27.387  30.686   9.799  1.00  0.00              
ATOM     42  CA  ILE    19      28.164  31.909   9.646  1.00  0.00              
ATOM     43  C   ILE    19      27.851  32.615   8.331  1.00  0.00              
ATOM     44  O   ILE    19      27.802  33.853   8.275  1.00  0.00              
ATOM     45  N   VAL    20      27.611  31.834   7.281  1.00  0.00              
ATOM     46  CA  VAL    20      27.263  32.403   5.989  1.00  0.00              
ATOM     47  C   VAL    20      25.997  33.253   6.147  1.00  0.00              
ATOM     48  O   VAL    20      25.943  34.400   5.691  1.00  0.00              
ATOM     49  N   GLU    21      24.994  32.710   6.829  1.00  0.00              
ATOM     50  CA  GLU    21      23.741  33.432   7.027  1.00  0.00              
ATOM     51  C   GLU    21      23.804  34.498   8.132  1.00  0.00              
ATOM     52  O   GLU    21      22.966  35.400   8.181  1.00  0.00              
ATOM     53  N   LEU    22      24.778  34.390   9.029  1.00  0.00              
ATOM     54  CA  LEU    22      24.935  35.384  10.078  1.00  0.00              
ATOM     55  C   LEU    22      25.458  36.639   9.376  1.00  0.00              
ATOM     56  O   LEU    22      25.032  37.769   9.668  1.00  0.00              
ATOM     57  N   VAL    23      26.367  36.434   8.423  1.00  0.00              
ATOM     58  CA  VAL    23      26.938  37.564   7.695  1.00  0.00              
ATOM     59  C   VAL    23      25.878  38.293   6.851  1.00  0.00              
ATOM     60  O   VAL    23      25.843  39.523   6.867  1.00  0.00              
ATOM     61  N   TYR    24      25.012  37.566   6.131  1.00  0.00              
ATOM     62  CA  TYR    24      23.976  38.236   5.315  1.00  0.00              
ATOM     63  C   TYR    24      22.929  38.876   6.224  1.00  0.00              
ATOM     64  O   TYR    24      22.248  39.828   5.833  1.00  0.00              
ATOM     65  N   ILE    25      22.797  38.345   7.437  1.00  0.00              
ATOM     66  CA  ILE    25      21.842  38.892   8.389  1.00  0.00              
ATOM     67  C   ILE    25      22.301  40.297   8.770  1.00  0.00              
ATOM     68  O   ILE    25      21.491  41.215   8.858  1.00  0.00              
ATOM     69  N   ASP    26      23.604  40.457   8.993  1.00  0.00              
ATOM     70  CA  ASP    26      24.167  41.760   9.340  1.00  0.00              
ATOM     71  C   ASP    26      24.019  42.710   8.143  1.00  0.00              
ATOM     72  O   ASP    26      23.959  43.924   8.311  1.00  0.00              
ATOM     73  N   CYS    27      23.954  42.147   6.937  1.00  0.00              
ATOM     74  CA  CYS    27      23.818  42.952   5.725  1.00  0.00              
ATOM     75  C   CYS    27      22.380  43.407   5.510  1.00  0.00              
ATOM     76  O   CYS    27      22.145  44.402   4.838  1.00  0.00              
ATOM     77  N   PRO    28      21.420  42.677   6.074  1.00  0.00              
ATOM     78  CA  PRO    28      20.023  43.057   5.930  1.00  0.00              
ATOM     79  C   PRO    28      19.057  42.014   5.395  1.00  0.00              
ATOM     80  O   PRO    28      17.921  42.349   5.074  1.00  0.00              
ATOM     81  N   GLU    30      19.484  40.757   5.298  1.00  0.00              
ATOM     82  CA  GLU    30      18.616  39.686   4.792  1.00  0.00              
ATOM     83  C   GLU    30      17.337  39.568   5.626  1.00  0.00              
ATOM     84  O   GLU    30      16.346  38.993   5.173  1.00  0.00              
ATOM     85  N   PRO    31      17.373  40.107   6.843  1.00  0.00              
ATOM     86  CA  PRO    31      16.216  40.050   7.718  1.00  0.00              
ATOM     87  C   PRO    31      15.895  38.675   8.281  1.00  0.00              
ATOM     88  O   PRO    31      14.833  38.491   8.871  1.00  0.00              
ATOM     89  N   ILE    32      16.790  37.704   8.108  1.00  0.00              
ATOM     90  CA  ILE    32      16.542  36.358   8.622  1.00  0.00              
ATOM     91  C   ILE    32      17.649  35.897   9.580  1.00  0.00              
ATOM     92  O   ILE    32      18.763  35.546   9.168  1.00  0.00              
ATOM     93  N   PRO    33      17.326  35.909  10.867  1.00  0.00              
ATOM     94  CA  PRO    33      18.262  35.497  11.899  1.00  0.00              
ATOM     95  C   PRO    33      18.498  33.992  11.810  1.00  0.00              
ATOM     96  O   PRO    33      17.546  33.221  11.751  1.00  0.00              
ATOM     97  N   PRO    34      19.771  33.558  11.796  1.00  0.00              
ATOM     98  CA  PRO    34      20.106  32.128  11.715  1.00  0.00              
ATOM     99  C   PRO    34      19.824  31.353  13.017  1.00  0.00              
ATOM    100  O   PRO    34      20.132  31.821  14.115  1.00  0.00              
ATOM    101  N   THR    35      19.239  30.166  12.886  1.00  0.00              
ATOM    102  CA  THR    35      18.903  29.340  14.041  1.00  0.00              
ATOM    103  C   THR    35      20.093  28.568  14.620  1.00  0.00              
ATOM    104  O   THR    35      20.964  28.112  13.890  1.00  0.00              
ATOM    105  N   LEU    36      20.110  28.419  15.941  1.00  0.00              
ATOM    106  CA  LEU    36      21.197  27.733  16.633  1.00  0.00              
ATOM    107  C   LEU    36      20.738  26.866  17.805  1.00  0.00              
ATOM    108  O   LEU    36      21.550  26.197  18.433  1.00  0.00              
ATOM    109  N   ALA    37      19.441  26.860  18.089  1.00  0.00              
ATOM    110  CA  ALA    37      18.923  26.065  19.202  1.00  0.00              
ATOM    111  C   ALA    37      18.542  24.642  18.811  1.00  0.00              
ATOM    112  O   ALA    37      17.756  24.426  17.898  1.00  0.00              
ATOM    113  N   ILE    38      19.114  23.675  19.521  1.00  0.00              
ATOM    114  CA  ILE    38      18.838  22.259  19.284  1.00  0.00              
ATOM    115  C   ILE    38      17.776  21.754  20.233  1.00  0.00              
ATOM    116  O   ILE    38      17.886  21.927  21.444  1.00  0.00              
ATOM    117  N   TYR    39      16.744  21.133  19.680  1.00  0.00              
ATOM    118  CA  TYR    39      15.667  20.594  20.490  1.00  0.00              
ATOM    119  C   TYR    39      15.598  19.095  20.339  1.00  0.00              
ATOM    120  O   TYR    39      15.574  18.574  19.214  1.00  0.00              
ATOM    121  N   ASP    40      15.536  18.408  21.477  1.00  0.00              
ATOM    122  CA  ASP    40      15.472  16.951  21.492  1.00  0.00              
ATOM    123  C   ASP    40      14.201  16.404  22.148  1.00  0.00              
ATOM    124  O   ASP    40      13.855  16.811  23.252  1.00  0.00              
ATOM    125  N   LYS    41      13.508  15.500  21.458  1.00  0.00              
ATOM    126  CA  LYS    41      12.337  14.839  22.020  1.00  0.00              
ATOM    127  C   LYS    41      12.881  13.476  22.473  1.00  0.00              
ATOM    128  O   LYS    41      13.318  12.659  21.654  1.00  0.00              
ATOM    129  N   LYS    42      12.870  13.258  23.783  1.00  0.00              
ATOM    130  CA  LYS    42      13.400  12.040  24.389  1.00  0.00              
ATOM    131  C   LYS    42      12.349  11.013  24.816  1.00  0.00              
ATOM    132  O   LYS    42      11.509  11.293  25.668  1.00  0.00              
ATOM    133  N   GLY    43      12.409   9.827  24.213  1.00  0.00              
ATOM    134  CA  GLY    43      11.502   8.745  24.564  1.00  0.00              
ATOM    135  C   GLY    43      10.209   8.590  23.786  1.00  0.00              
ATOM    136  O   GLY    43       9.530   7.573  23.918  1.00  0.00              
ATOM    137  N   ASP    44       9.851   9.587  22.987  1.00  0.00              
ATOM    138  CA  ASP    44       8.621   9.529  22.207  1.00  0.00              
ATOM    139  C   ASP    44       8.901  10.036  20.816  1.00  0.00              
ATOM    140  O   ASP    44       9.932  10.668  20.577  1.00  0.00              
ATOM    141  N   GLU    45       7.988   9.766  19.894  1.00  0.00              
ATOM    142  CA  GLU    45       8.149  10.243  18.532  1.00  0.00              
ATOM    143  C   GLU    45       8.154  11.780  18.594  1.00  0.00              
ATOM    144  O   GLU    45       7.760  12.369  19.597  1.00  0.00              
ATOM    145  N   TRP    46       8.612  12.427  17.528  1.00  0.00              
ATOM    146  CA  TRP    46       8.637  13.888  17.487  1.00  0.00              
ATOM    147  C   TRP    46       7.193  14.422  17.444  1.00  0.00              
ATOM    148  O   TRP    46       6.359  13.906  16.699  1.00  0.00              
END
