
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0306AL242_2
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306AL242_2.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D      31      M       1           -
LGA    P      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      -       -           -
LGA    N      35      -       -           -
LGA    P      36      -       -           -
LGA    D      37      -       -           -
LGA    G      38      -       -           -
LGA    Q      39      -       -           -
LGA    C      40      K       2           #
LGA    A      41      -       -           -
LGA    V      42      -       -           -
LGA    A      43      L       3          4.880
LGA    I      44      A       4          2.805
LGA    D      45      V       5          1.731
LGA    N      46      -       -           -
LGA    I      47      V       6          3.675
LGA    G      48      T       7          5.131
LGA    A      49      G       8          3.084
LGA    G      50      Q       9          2.625
LGA    T      51      -       -           -
LGA    G      52      I      10          2.213
LGA    E      53      V      11          1.664
LGA    W      54      C      12          2.754
LGA    V      55      -       -           -
LGA    L      56      T      13          3.996
LGA    L      57      V      14          1.416
LGA    V      58      R      15          1.356
LGA    S      59      H      16          2.273
LGA    G      60      H      17          4.569
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    S      61      H      21          4.119
LGA    S      62      D      22          3.055
LGA    A      63      K      23          3.921
LGA    -       -      L      24           -
LGA    -       -      L      25           -
LGA    -       -      M      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      M      29           -
LGA    -       -      I      30           -
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    -       -      C      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    -       -      I      44           -
LGA    -       -      D      45           -
LGA    -       -      N      46           -
LGA    R      64      I      47          2.072
LGA    Q      65      G      48          4.548
LGA    A      66      A      49          0.703
LGA    H      67      G      50          4.132
LGA    K      68      T      51           #
LGA    -       -      G      52           -
LGA    S      69      E      53          5.390
LGA    E      70      W      54           -
LGA    T      71      V      55           -
LGA    S      72      L      56           -
LGA    -       -      L      57           -
LGA    -       -      V      58           -
LGA    -       -      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    -       -      H      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    -       -      C      77           -
LGA    -       -      V      78           -
LGA    -       -      I      79           -
LGA    -       -      G      80           -
LGA    -       -      I      81           -
LGA    -       -      V      82           -
LGA    P      73      D      83          2.851
LGA    V      74      E      84          3.400
LGA    D      75      V      85          2.885
LGA    L      76      V      86          3.078
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   95    5.0     27    3.35     3.70     15.982     0.783

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.936002 * X  +   0.129022 * Y  +   0.327495 * Z  + -49.045914
  Y_new =   0.351793 * X  +  -0.374295 * Y  +  -0.857989 * Z  + 109.683754
  Z_new =   0.011880 * X  +   0.918290 * Y  +  -0.395730 * Z  + -60.242310 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.977690   -1.163903  [ DEG:   113.3133    -66.6867 ]
  Theta =  -0.011881   -3.129712  [ DEG:    -0.6807   -179.3193 ]
  Phi   =   0.359513   -2.782080  [ DEG:    20.5986   -159.4014 ]
 
# 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: T0306AL242_2                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306AL242_2.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   95   5.0   27   3.35    3.70  15.982
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL242_2
REMARK Aligment from pdb entry: 1jj2_1
ATOM      1  N   ASP    31      64.485  24.160  66.925  1.00  0.00              
ATOM      2  CA  ASP    31      64.378  25.584  66.675  1.00  0.00              
ATOM      3  C   ASP    31      64.108  26.380  67.941  1.00  0.00              
ATOM      4  O   ASP    31      63.786  25.813  68.982  1.00  0.00              
ATOM      5  N   PRO    32      64.246  27.696  67.855  1.00  0.00              
ATOM      6  CA  PRO    32      64.021  28.564  69.001  1.00  0.00              
ATOM      7  C   PRO    32      62.794  29.429  68.734  1.00  0.00              
ATOM      8  O   PRO    32      62.827  30.327  67.895  1.00  0.00              
ATOM      9  N   GLN    33      61.709  29.173  69.442  1.00  0.00              
ATOM     10  CA  GLN    33      60.515  29.964  69.205  1.00  0.00              
ATOM     11  C   GLN    33      60.452  31.227  70.070  1.00  0.00              
ATOM     12  O   GLN    33      60.951  31.263  71.188  1.00  0.00              
ATOM     13  N   GLY    34      59.856  32.276  69.527  1.00  0.00              
ATOM     14  CA  GLY    34      59.716  33.523  70.260  1.00  0.00              
ATOM     15  C   GLY    34      58.400  33.467  71.017  1.00  0.00              
ATOM     16  O   GLY    34      57.617  32.524  70.862  1.00  0.00              
ATOM     17  N   ASN    35      58.157  34.481  71.836  1.00  0.00              
ATOM     18  CA  ASN    35      56.931  34.562  72.618  1.00  0.00              
ATOM     19  C   ASN    35      55.704  34.638  71.709  1.00  0.00              
ATOM     20  O   ASN    35      54.691  34.007  71.974  1.00  0.00              
ATOM     21  N   PRO    36      55.792  35.414  70.636  1.00  0.00              
ATOM     22  CA  PRO    36      54.667  35.542  69.716  1.00  0.00              
ATOM     23  C   PRO    36      54.415  34.228  68.962  1.00  0.00              
ATOM     24  O   PRO    36      53.274  33.801  68.807  1.00  0.00              
ATOM     25  N   ASP    37      55.474  33.580  68.499  1.00  0.00              
ATOM     26  CA  ASP    37      55.289  32.331  67.790  1.00  0.00              
ATOM     27  C   ASP    37      54.631  31.330  68.715  1.00  0.00              
ATOM     28  O   ASP    37      53.721  30.599  68.319  1.00  0.00              
ATOM     29  N   GLY    38      55.091  31.310  69.960  1.00  0.00              
ATOM     30  CA  GLY    38      54.544  30.395  70.948  1.00  0.00              
ATOM     31  C   GLY    38      53.045  30.652  71.123  1.00  0.00              
ATOM     32  O   GLY    38      52.255  29.714  71.246  1.00  0.00              
ATOM     33  N   GLN    39      52.648  31.919  71.115  1.00  0.00              
ATOM     34  CA  GLN    39      51.240  32.245  71.265  1.00  0.00              
ATOM     35  C   GLN    39      50.451  31.684  70.094  1.00  0.00              
ATOM     36  O   GLN    39      49.414  31.049  70.288  1.00  0.00              
ATOM     37  N   CYS    40      50.950  31.896  68.878  1.00  0.00              
ATOM     38  CA  CYS    40      50.272  31.387  67.691  1.00  0.00              
ATOM     39  C   CYS    40      50.133  29.868  67.686  1.00  0.00              
ATOM     40  O   CYS    40      49.074  29.339  67.337  1.00  0.00              
ATOM     41  N   ALA    41      51.190  29.172  68.058  1.00  0.00              
ATOM     42  CA  ALA    41      51.072  27.710  68.081  1.00  0.00              
ATOM     43  C   ALA    41      50.093  27.238  69.159  1.00  0.00              
ATOM     44  O   ALA    41      49.389  26.269  68.973  1.00  0.00              
ATOM     45  N   VAL    42      50.071  27.977  70.253  1.00  0.00              
ATOM     46  CA  VAL    42      49.144  27.639  71.317  1.00  0.00              
ATOM     47  C   VAL    42      47.721  27.735  70.742  1.00  0.00              
ATOM     48  O   VAL    42      46.903  26.835  70.921  1.00  0.00              
ATOM     49  N   ALA    43      47.439  28.823  70.033  1.00  0.00              
ATOM     50  CA  ALA    43      46.124  29.023  69.436  1.00  0.00              
ATOM     51  C   ALA    43      45.766  27.894  68.453  1.00  0.00              
ATOM     52  O   ALA    43      44.642  27.378  68.471  1.00  0.00              
ATOM     53  N   ILE    44      46.721  27.519  67.600  1.00  0.00              
ATOM     54  CA  ILE    44      46.520  26.440  66.628  1.00  0.00              
ATOM     55  C   ILE    44      46.200  25.127  67.332  1.00  0.00              
ATOM     56  O   ILE    44      45.405  24.328  66.835  1.00  0.00              
ATOM     57  N   ASP    45      46.821  24.898  68.486  1.00  0.00              
ATOM     58  CA  ASP    45      46.559  23.673  69.233  1.00  0.00              
ATOM     59  C   ASP    45      45.139  23.732  69.751  1.00  0.00              
ATOM     60  O   ASP    45      44.413  22.739  69.732  1.00  0.00              
ATOM     61  N   ASN    46      44.742  24.913  70.212  1.00  0.00              
ATOM     62  CA  ASN    46      43.403  25.088  70.734  1.00  0.00              
ATOM     63  C   ASN    46      42.342  24.946  69.651  1.00  0.00              
ATOM     64  O   ASN    46      41.292  24.361  69.892  1.00  0.00              
ATOM     65  N   ILE    47      42.601  25.487  68.466  1.00  0.00              
ATOM     66  CA  ILE    47      41.635  25.378  67.372  1.00  0.00              
ATOM     67  C   ILE    47      41.504  23.934  66.929  1.00  0.00              
ATOM     68  O   ILE    47      40.585  23.569  66.198  1.00  0.00              
ATOM     69  N   GLY    48      42.439  23.116  67.382  1.00  0.00              
ATOM     70  CA  GLY    48      42.466  21.721  67.014  1.00  0.00              
ATOM     71  C   GLY    48      41.576  20.825  67.858  1.00  0.00              
ATOM     72  O   GLY    48      41.707  19.605  67.807  1.00  0.00              
ATOM     73  N   ALA    49      40.674  21.408  68.639  1.00  0.00              
ATOM     74  CA  ALA    49      39.789  20.590  69.459  1.00  0.00              
ATOM     75  C   ALA    49      38.542  20.239  68.653  1.00  0.00              
ATOM     76  O   ALA    49      38.336  20.750  67.554  1.00  0.00              
ATOM     77  N   GLY    50      37.707  19.368  69.202  1.00  0.00              
ATOM     78  CA  GLY    50      36.508  18.939  68.493  1.00  0.00              
ATOM     79  C   GLY    50      35.293  19.768  68.849  1.00  0.00              
ATOM     80  O   GLY    50      35.284  20.465  69.858  1.00  0.00              
ATOM     81  N   THR    51      34.272  19.707  68.004  1.00  0.00              
ATOM     82  CA  THR    51      33.048  20.434  68.279  1.00  0.00              
ATOM     83  C   THR    51      32.446  19.770  69.507  1.00  0.00              
ATOM     84  O   THR    51      32.138  18.580  69.482  1.00  0.00              
ATOM     85  N   GLY    52      32.284  20.521  70.604  1.00  0.00              
ATOM     86  CA  GLY    52      31.710  19.912  71.804  1.00  0.00              
ATOM     87  C   GLY    52      30.390  19.190  71.552  1.00  0.00              
ATOM     88  O   GLY    52      29.576  19.604  70.722  1.00  0.00              
ATOM     89  N   GLU    53      30.208  18.089  72.271  1.00  0.00              
ATOM     90  CA  GLU    53      29.020  17.259  72.155  1.00  0.00              
ATOM     91  C   GLU    53      27.731  18.059  72.323  1.00  0.00              
ATOM     92  O   GLU    53      26.788  17.905  71.545  1.00  0.00              
ATOM     93  N   TRP    54      27.683  18.928  73.327  1.00  0.00              
ATOM     94  CA  TRP    54      26.511  19.714  73.610  1.00  0.00              
ATOM     95  C   TRP    54      26.117  20.541  72.403  1.00  0.00              
ATOM     96  O   TRP    54      24.925  20.835  72.208  1.00  0.00              
ATOM     97  N   VAL    55      27.075  20.954  71.583  1.00  0.00              
ATOM     98  CA  VAL    55      26.769  21.769  70.416  1.00  0.00              
ATOM     99  C   VAL    55      26.013  20.971  69.368  1.00  0.00              
ATOM    100  O   VAL    55      25.288  21.533  68.555  1.00  0.00              
ATOM    101  N   LEU    56      26.182  19.656  69.395  1.00  0.00              
ATOM    102  CA  LEU    56      25.494  18.783  68.452  1.00  0.00              
ATOM    103  C   LEU    56      24.011  18.745  68.803  1.00  0.00              
ATOM    104  O   LEU    56      23.148  18.844  67.930  1.00  0.00              
ATOM    105  N   LEU    57      23.731  18.602  70.095  1.00  0.00              
ATOM    106  CA  LEU    57      22.366  18.550  70.596  1.00  0.00              
ATOM    107  C   LEU    57      21.674  19.895  70.417  1.00  0.00              
ATOM    108  O   LEU    57      20.496  19.956  70.065  1.00  0.00              
ATOM    109  N   VAL    58      22.413  20.973  70.661  1.00  0.00              
ATOM    110  CA  VAL    58      21.869  22.317  70.545  1.00  0.00              
ATOM    111  C   VAL    58      21.585  22.703  69.102  1.00  0.00              
ATOM    112  O   VAL    58      20.756  23.570  68.841  1.00  0.00              
ATOM    113  N   SER    59      22.264  22.052  68.165  1.00  0.00              
ATOM    114  CA  SER    59      22.080  22.360  66.753  1.00  0.00              
ATOM    115  C   SER    59      21.361  21.252  65.998  1.00  0.00              
ATOM    116  O   SER    59      21.154  21.353  64.789  1.00  0.00              
ATOM    117  N   GLY    60      20.976  20.201  66.715  1.00  0.00              
ATOM    118  CA  GLY    60      20.301  19.064  66.100  1.00  0.00              
ATOM    119  C   GLY    60      21.121  18.543  64.929  1.00  0.00              
ATOM    120  O   GLY    60      20.565  18.064  63.940  1.00  0.00              
ATOM    121  N   SER    61      22.443  18.654  65.051  1.00  0.00              
ATOM    122  CA  SER    61      23.376  18.198  64.021  1.00  0.00              
ATOM    123  C   SER    61      23.334  19.083  62.780  1.00  0.00              
ATOM    124  O   SER    61      23.768  20.233  62.815  1.00  0.00              
ATOM    125  N   SER    62      31.266  18.233  62.770  1.00  0.00              
ATOM    126  CA  SER    62      32.458  18.330  61.930  1.00  0.00              
ATOM    127  C   SER    62      33.300  19.588  62.161  1.00  0.00              
ATOM    128  O   SER    62      32.785  20.708  62.146  1.00  0.00              
ATOM    129  N   ALA    63      34.597  19.389  62.365  1.00  0.00              
ATOM    130  CA  ALA    63      35.539  20.487  62.550  1.00  0.00              
ATOM    131  C   ALA    63      36.401  20.466  61.289  1.00  0.00              
ATOM    132  O   ALA    63      37.301  19.637  61.150  1.00  0.00              
ATOM    133  N   ARG    64      36.122  21.372  60.364  1.00  0.00              
ATOM    134  CA  ARG    64      36.858  21.409  59.109  1.00  0.00              
ATOM    135  C   ARG    64      38.272  21.968  59.215  1.00  0.00              
ATOM    136  O   ARG    64      39.025  21.958  58.241  1.00  0.00              
ATOM    137  N   GLN    65      38.638  22.440  60.400  1.00  0.00              
ATOM    138  CA  GLN    65      39.969  22.992  60.601  1.00  0.00              
ATOM    139  C   GLN    65      40.891  22.057  61.378  1.00  0.00              
ATOM    140  O   GLN    65      41.888  22.496  61.955  1.00  0.00              
ATOM    141  N   ALA    66      40.550  20.768  61.390  1.00  0.00              
ATOM    142  CA  ALA    66      41.362  19.768  62.076  1.00  0.00              
ATOM    143  C   ALA    66      42.725  19.705  61.392  1.00  0.00              
ATOM    144  O   ALA    66      42.814  19.618  60.168  1.00  0.00              
ATOM    145  N   HIS    67      43.784  19.756  62.191  1.00  0.00              
ATOM    146  CA  HIS    67      45.137  19.746  61.659  1.00  0.00              
ATOM    147  C   HIS    67      46.059  18.780  62.393  1.00  0.00              
ATOM    148  O   HIS    67      46.339  18.962  63.572  1.00  0.00              
ATOM    149  N   LYS    68      46.531  17.755  61.695  1.00  0.00              
ATOM    150  CA  LYS    68      47.450  16.807  62.307  1.00  0.00              
ATOM    151  C   LYS    68      48.863  17.372  62.182  1.00  0.00              
ATOM    152  O   LYS    68      49.200  18.004  61.184  1.00  0.00              
ATOM    153  N   SER    69      49.690  17.149  63.194  1.00  0.00              
ATOM    154  CA  SER    69      51.051  17.667  63.176  1.00  0.00              
ATOM    155  C   SER    69      51.917  17.073  62.063  1.00  0.00              
ATOM    156  O   SER    69      52.802  17.742  61.523  1.00  0.00              
ATOM    157  N   GLU    70      51.648  15.820  61.714  1.00  0.00              
ATOM    158  CA  GLU    70      52.428  15.124  60.701  1.00  0.00              
ATOM    159  C   GLU    70      51.908  15.323  59.286  1.00  0.00              
ATOM    160  O   GLU    70      52.677  15.642  58.380  1.00  0.00              
ATOM    161  N   THR    71      50.606  15.125  59.101  1.00  0.00              
ATOM    162  CA  THR    71      49.983  15.273  57.787  1.00  0.00              
ATOM    163  C   THR    71      49.843  16.717  57.318  1.00  0.00              
ATOM    164  O   THR    71      49.856  16.984  56.118  1.00  0.00              
ATOM    165  N   SER    72      49.718  17.647  58.258  1.00  0.00              
ATOM    166  CA  SER    72      49.563  19.050  57.900  1.00  0.00              
ATOM    167  C   SER    72      50.784  19.894  58.215  1.00  0.00              
ATOM    168  O   SER    72      51.742  19.429  58.836  1.00  0.00              
ATOM    169  N   PRO    73      50.737  21.142  57.771  1.00  0.00              
ATOM    170  CA  PRO    73      51.826  22.082  57.979  1.00  0.00              
ATOM    171  C   PRO    73      51.206  23.395  58.452  1.00  0.00              
ATOM    172  O   PRO    73      50.211  23.839  57.889  1.00  0.00              
ATOM    173  N   VAL    74      51.766  23.988  59.504  1.00  0.00              
ATOM    174  CA  VAL    74      51.266  25.261  60.024  1.00  0.00              
ATOM    175  C   VAL    74      52.006  26.379  59.274  1.00  0.00              
ATOM    176  O   VAL    74      52.865  26.095  58.438  1.00  0.00              
ATOM    177  N   ASP    75      51.686  27.641  59.557  1.00  0.00              
ATOM    178  CA  ASP    75      52.362  28.742  58.871  1.00  0.00              
ATOM    179  C   ASP    75      53.635  29.227  59.569  1.00  0.00              
ATOM    180  O   ASP    75      54.012  28.714  60.623  1.00  0.00              
ATOM    181  N   LEU    76      54.288  30.213  58.946  1.00  0.00              
ATOM    182  CA  LEU    76      55.544  30.831  59.412  1.00  0.00              
ATOM    183  C   LEU    76      56.788  30.102  58.878  1.00  0.00              
ATOM    184  O   LEU    76      56.875  28.866  58.892  1.00  0.00              
END
