
#######################################################
#                                                     #
#                        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 (  188),  selected   46 , name T0363AL257_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL257_5-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11           -
LGA    Q      12      Q      12           -
LGA    I      13      I      13           -
LGA    N      14      N      14           -
LGA    I      15      I      15           -
LGA    E      16      E      16           -
LGA    I      17      I      17           -
LGA    A      18      A      18           #
LGA    Y      19      Y      19           #
LGA    A      20      A      20           #
LGA    F      21      F      21          2.582
LGA    P      22      P      22          1.405
LGA    E      23      E      23          2.263
LGA    R      24      R      24          2.663
LGA    Y      25      Y      25          1.685
LGA    Y      26      Y      26          3.414
LGA    L      27      L      27          1.964
LGA    K      28      K      28          0.806
LGA    S      29      S      29          3.463
LGA    F      30      F      30          3.289
LGA    Q      31      Q      31           #
LGA    V      32      V      32          4.784
LGA    D      33      D      33          2.272
LGA    E      34      E      34          1.582
LGA    G      35      G      35          1.801
LGA    I      36      I      36          2.010
LGA    T      37      T      37          1.475
LGA    -       -      V      38           -
LGA    -       -      Q      39           -
LGA    V      38      T      40          2.965
LGA    Q      39      A      41          1.070
LGA    -       -      I      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      S      45           -
LGA    T      40      G      46          5.404
LGA    A      41      I      47          5.884
LGA    I      42      L      48           -
LGA    T      43      -       -           -
LGA    Q      44      -       -           -
LGA    S      45      S      49           #
LGA    G      46      Q      50          2.313
LGA    I      47      F      51          3.361
LGA    L      48      P      52           -
LGA    S      49      E      53           -
LGA    Q      50      I      54           -
LGA    F      51      D      55           -
LGA    P      52      L      56           -
LGA    E      53      -       -           -
LGA    I      54      -       -           -
LGA    D      55      -       -           -
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   46    5.0     22    2.96    72.73     33.071     0.718

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.113016 * X  +  -0.711886 * Y  +   0.693142 * Z  +  26.126007
  Y_new =  -0.383187 * X  +   0.674873 * Y  +   0.630645 * Z  + -53.417297
  Z_new =  -0.916731 * X  +  -0.194330 * Y  +  -0.349057 * Z  +  65.741020 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.633597    0.507995  [ DEG:  -150.8940     29.1060 ]
  Theta =   1.159819    1.981774  [ DEG:    66.4527    113.5473 ]
  Phi   =  -1.857601    1.283992  [ DEG:  -106.4327     73.5673 ]
 
# 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: T0363AL257_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL257_5-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   46   5.0   22   2.96   72.73  33.071
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL257_5-D1
REMARK Aligment from pdb entry: 2aj7_A
ATOM     30  N   ASN    11      20.061   8.289  -9.864  1.00  0.00              
ATOM     31  CA AASN    11      21.319   8.872 -10.333  1.00  0.00              
ATOM     32  CA BASN    11      21.307   8.832 -10.361  1.00  0.00              
ATOM     33  C   ASN    11      22.486   7.969  -9.892  1.00  0.00              
ATOM     34  O   ASN    11      22.488   7.459  -8.779  1.00  0.00              
ATOM     35  N   GLN    12      23.458   7.787 -10.775  1.00  0.00              
ATOM     36  CA  GLN    12      24.690   7.082 -10.444  1.00  0.00              
ATOM     37  C   GLN    12      25.748   8.093 -10.032  1.00  0.00              
ATOM     38  O   GLN    12      26.087   8.996 -10.803  1.00  0.00              
ATOM     39  N   ILE    13      26.295   7.924  -8.835  1.00  0.00              
ATOM     40  CA  ILE    13      27.381   8.794  -8.381  1.00  0.00              
ATOM     41  C   ILE    13      28.588   8.016  -7.843  1.00  0.00              
ATOM     42  O   ILE    13      28.436   6.945  -7.249  1.00  0.00              
ATOM     43  N   ASN    14      29.782   8.530  -8.103  1.00  0.00              
ATOM     44  CA  ASN    14      31.000   7.974  -7.572  1.00  0.00              
ATOM     45  C   ASN    14      31.227   8.572  -6.172  1.00  0.00              
ATOM     46  O   ASN    14      31.271   9.794  -6.013  1.00  0.00              
ATOM     47  N   ILE    15      27.455   4.267  -6.556  1.00  0.00              
ATOM     48  CA  ILE    15      26.176   4.077  -5.850  1.00  0.00              
ATOM     49  C   ILE    15      25.076   4.657  -6.742  1.00  0.00              
ATOM     50  O   ILE    15      25.331   5.573  -7.509  1.00  0.00              
ATOM     51  N   GLU    16      23.868   4.115  -6.649  1.00  0.00              
ATOM     52  CA  GLU    16      22.687   4.756  -7.229  1.00  0.00              
ATOM     53  C   GLU    16      21.992   5.514  -6.117  1.00  0.00              
ATOM     54  O   GLU    16      21.799   4.962  -5.029  1.00  0.00              
ATOM     55  N   ILE    17      21.612   6.767  -6.394  1.00  0.00              
ATOM     56  CA AILE    17      20.871   7.576  -5.418  1.00  0.00              
ATOM     57  CA BILE    17      20.889   7.593  -5.431  1.00  0.00              
ATOM     58  C   ILE    17      19.615   8.159  -6.045  1.00  0.00              
ATOM     59  O   ILE    17      19.657   8.678  -7.166  1.00  0.00              
ATOM     60  N   ALA    18      29.261  25.386   0.253  1.00  0.00              
ATOM     61  CA  ALA    18      29.749  25.304   1.633  1.00  0.00              
ATOM     62  C   ALA    18      30.985  26.245   1.639  1.00  0.00              
ATOM     63  O   ALA    18      31.677  26.353   0.625  1.00  0.00              
ATOM     64  N   TYR    19      31.227  26.955   2.746  1.00  0.00              
ATOM     65  CA  TYR    19      32.394  27.823   2.854  1.00  0.00              
ATOM     66  C   TYR    19      33.691  27.099   2.472  1.00  0.00              
ATOM     67  O   TYR    19      33.917  25.968   2.978  1.00  0.00              
ATOM     68  N   ALA    20      34.468  27.727   1.591  1.00  0.00              
ATOM     69  CA  ALA    20      35.689  27.170   1.006  1.00  0.00              
ATOM     70  C   ALA    20      35.423  26.150  -0.123  1.00  0.00              
ATOM     71  O   ALA    20      36.359  25.748  -0.820  1.00  0.00              
ATOM     72  N   PHE    21      34.161  25.875  -0.386  1.00  0.00              
ATOM     73  CA  PHE    21      33.698  24.969  -1.438  1.00  0.00              
ATOM     74  C   PHE    21      32.384  25.545  -2.029  1.00  0.00              
ATOM     75  O   PHE    21      31.380  24.870  -2.196  1.00  0.00              
ATOM     76  N   PRO    22      32.408  26.830  -2.356  1.00  0.00              
ATOM     77  CA  PRO    22      31.175  27.540  -2.652  1.00  0.00              
ATOM     78  C   PRO    22      30.563  27.104  -3.999  1.00  0.00              
ATOM     79  O   PRO    22      29.371  27.309  -4.232  1.00  0.00              
ATOM     80  N   GLU    23      31.389  26.521  -4.858  1.00  0.00              
ATOM     81  CA  GLU    23      30.915  25.942  -6.130  1.00  0.00              
ATOM     82  C   GLU    23      30.246  24.542  -6.042  1.00  0.00              
ATOM     83  O   GLU    23      29.677  24.050  -7.033  1.00  0.00              
ATOM     84  N   ARG    24      30.297  23.905  -4.881  1.00  0.00              
ATOM     85  CA  ARG    24      29.748  22.564  -4.700  1.00  0.00              
ATOM     86  C   ARG    24      28.311  22.752  -4.250  1.00  0.00              
ATOM     87  O   ARG    24      28.039  22.962  -3.058  1.00  0.00              
ATOM     88  N   TYR    25      27.377  22.659  -5.214  1.00  0.00              
ATOM     89  CA  TYR    25      25.994  23.026  -4.992  1.00  0.00              
ATOM     90  C   TYR    25      25.114  21.813  -4.730  1.00  0.00              
ATOM     91  O   TYR    25      23.903  21.976  -4.607  1.00  0.00              
ATOM     92  N   TYR    26      25.666  20.587  -4.705  1.00  0.00              
ATOM     93  CA  TYR    26      24.820  19.414  -4.487  1.00  0.00              
ATOM     94  C   TYR    26      25.585  18.296  -3.772  1.00  0.00              
ATOM     95  O   TYR    26      26.699  17.884  -4.176  1.00  0.00              
ATOM     96  N   LEU    27      24.935  17.796  -2.725  1.00  0.00              
ATOM     97  CA  LEU    27      25.470  16.771  -1.826  1.00  0.00              
ATOM     98  C   LEU    27      24.383  15.742  -1.574  1.00  0.00              
ATOM     99  O   LEU    27      23.189  16.030  -1.706  1.00  0.00              
ATOM    100  N   LYS    28      24.832  14.543  -1.217  1.00  0.00              
ATOM    101  CA  LYS    28      23.948  13.510  -0.719  1.00  0.00              
ATOM    102  C   LYS    28      24.413  13.067   0.686  1.00  0.00              
ATOM    103  O   LYS    28      25.596  12.921   0.956  1.00  0.00              
ATOM    104  N   SER    29      23.443  12.792   1.566  1.00  0.00              
ATOM    105  CA  SER    29      23.766  12.376   2.904  1.00  0.00              
ATOM    106  C   SER    29      23.776  10.860   2.914  1.00  0.00              
ATOM    107  O   SER    29      22.787  10.247   2.535  1.00  0.00              
ATOM    108  N   PHE    30      24.893  10.271   3.324  1.00  0.00              
ATOM    109  CA  PHE    30      25.066   8.830   3.350  1.00  0.00              
ATOM    110  C   PHE    30      25.258   8.377   4.804  1.00  0.00              
ATOM    111  O   PHE    30      26.337   8.530   5.360  1.00  0.00              
ATOM    112  N   GLN    31      24.186   7.885   5.456  1.00  0.00              
ATOM    113  CA  GLN    31      24.322   7.442   6.846  1.00  0.00              
ATOM    114  C   GLN    31      25.147   6.125   6.955  1.00  0.00              
ATOM    115  O   GLN    31      25.115   5.292   6.062  1.00  0.00              
ATOM    116  N   VAL    32      25.916   6.008   8.024  1.00  0.00              
ATOM    117  CA  VAL    32      26.639   4.776   8.324  1.00  0.00              
ATOM    118  C   VAL    32      25.691   3.609   8.608  1.00  0.00              
ATOM    119  O   VAL    32      25.722   2.523   7.946  1.00  0.00              
ATOM    120  N   ASP    33      24.853   3.807   9.620  1.00  0.00              
ATOM    121  CA  ASP    33      23.974   2.711  10.066  1.00  0.00              
ATOM    122  C   ASP    33      22.908   3.251  10.978  1.00  0.00              
ATOM    123  O   ASP    33      23.189   4.108  11.836  1.00  0.00              
ATOM    124  N   GLU    34      21.690   2.782  10.789  1.00  0.00              
ATOM    125  CA  GLU    34      20.579   3.193  11.615  1.00  0.00              
ATOM    126  C   GLU    34      20.932   3.079  13.099  1.00  0.00              
ATOM    127  O   GLU    34      21.502   2.093  13.532  1.00  0.00              
ATOM    128  N   GLY    35      20.607   4.116  13.866  1.00  0.00              
ATOM    129  CA  GLY    35      20.797   4.062  15.303  1.00  0.00              
ATOM    130  C   GLY    35      22.128   4.669  15.704  1.00  0.00              
ATOM    131  O   GLY    35      22.399   4.868  16.895  1.00  0.00              
ATOM    132  N   ILE    36      22.994   4.969  14.733  1.00  0.00              
ATOM    133  CA  ILE    36      24.296   5.577  14.991  1.00  0.00              
ATOM    134  C   ILE    36      24.388   7.010  14.470  1.00  0.00              
ATOM    135  O   ILE    36      23.639   7.356  13.566  1.00  0.00              
ATOM    136  N   THR    37      25.243   7.836  15.081  1.00  0.00              
ATOM    137  CA  THR    37      25.268   9.236  14.672  1.00  0.00              
ATOM    138  C   THR    37      26.226   9.649  13.563  1.00  0.00              
ATOM    139  O   THR    37      26.505  10.823  13.421  1.00  0.00              
ATOM    140  N   VAL    38      26.733   8.684  12.807  1.00  0.00              
ATOM    141  CA  VAL    38      27.776   8.900  11.821  1.00  0.00              
ATOM    142  C   VAL    38      27.200   8.926  10.387  1.00  0.00              
ATOM    143  O   VAL    38      26.370   8.087  10.005  1.00  0.00              
ATOM    144  N   GLN    39      27.692   9.848   9.594  1.00  0.00              
ATOM    145  CA  GLN    39      27.270  10.070   8.223  1.00  0.00              
ATOM    146  C   GLN    39      28.473  10.602   7.442  1.00  0.00              
ATOM    147  O   GLN    39      29.425  11.160   7.984  1.00  0.00              
ATOM    148  N   THR    40      28.497  13.719   0.876  1.00  0.00              
ATOM    149  CA  THR    40      29.232  13.388  -0.344  1.00  0.00              
ATOM    150  C   THR    40      28.831  14.324  -1.474  1.00  0.00              
ATOM    151  O   THR    40      27.657  14.425  -1.796  1.00  0.00              
ATOM    152  N   ALA    41      29.814  15.010  -2.071  1.00  0.00              
ATOM    153  CA  ALA    41      29.595  15.796  -3.290  1.00  0.00              
ATOM    154  C   ALA    41      29.124  14.845  -4.391  1.00  0.00              
ATOM    155  O   ALA    41      29.718  13.790  -4.577  1.00  0.00              
ATOM    156  N   ILE    42      28.117  15.245  -5.144  1.00  0.00              
ATOM    157  CA  ILE    42      27.659  14.430  -6.287  1.00  0.00              
ATOM    158  C   ILE    42      28.418  14.719  -7.584  1.00  0.00              
ATOM    159  O   ILE    42      28.170  14.045  -8.593  1.00  0.00              
ATOM    160  N   THR    43      29.311  15.710  -7.543  1.00  0.00              
ATOM    161  CA  THR    43      30.122  16.116  -8.681  1.00  0.00              
ATOM    162  C   THR    43      31.598  15.829  -8.484  1.00  0.00              
ATOM    163  O   THR    43      32.331  15.723  -9.461  1.00  0.00              
ATOM    164  N   GLN    44      32.044  15.722  -7.237  1.00  0.00              
ATOM    165  CA  GLN    44      33.457  15.610  -6.928  1.00  0.00              
ATOM    166  C   GLN    44      33.662  14.407  -6.036  1.00  0.00              
ATOM    167  O   GLN    44      33.320  14.442  -4.862  1.00  0.00              
ATOM    168  N   SER    45      34.222  13.338  -6.598  1.00  0.00              
ATOM    169  CA ASER    45      34.260  12.078  -5.862  1.00  0.00              
ATOM    170  CA BSER    45      34.298  12.062  -5.864  1.00  0.00              
ATOM    171  C   SER    45      35.029  12.195  -4.547  1.00  0.00              
ATOM    172  O   SER    45      34.604  11.665  -3.533  1.00  0.00              
ATOM    173  N   GLY    46      36.135  12.928  -4.543  1.00  0.00              
ATOM    174  CA  GLY    46      36.953  12.978  -3.342  1.00  0.00              
ATOM    175  C   GLY    46      36.533  13.987  -2.272  1.00  0.00              
ATOM    176  O   GLY    46      37.222  14.167  -1.245  1.00  0.00              
ATOM    177  N   ILE    47      35.397  14.641  -2.473  1.00  0.00              
ATOM    178  CA  ILE    47      34.897  15.604  -1.496  1.00  0.00              
ATOM    179  C   ILE    47      33.730  14.961  -0.740  1.00  0.00              
ATOM    180  O   ILE    47      32.608  14.894  -1.224  1.00  0.00              
ATOM    181  N   LEU    48      24.077  16.194  18.680  1.00  0.00              
ATOM    182  CA  LEU    48      23.250  15.987  19.860  1.00  0.00              
ATOM    183  C   LEU    48      23.478  14.606  20.497  1.00  0.00              
ATOM    184  O   LEU    48      23.242  14.438  21.717  1.00  0.00              
ATOM    185  N   SER    49      23.959  13.640  19.710  1.00  0.00              
ATOM    186  CA ASER    49      24.264  12.313  20.231  1.00  0.00              
ATOM    187  CA BSER    49      24.277  12.313  20.239  1.00  0.00              
ATOM    188  C   SER    49      25.507  12.348  21.141  1.00  0.00              
ATOM    189  O   SER    49      25.701  11.465  21.976  1.00  0.00              
ATOM    190  N   GLN    50      26.328  13.362  20.978  1.00  0.00              
ATOM    191  CA  GLN    50      27.579  13.502  21.724  1.00  0.00              
ATOM    192  C   GLN    50      27.487  14.604  22.788  1.00  0.00              
ATOM    193  O   GLN    50      28.186  14.533  23.789  1.00  0.00              
ATOM    194  N   PHE    51      26.665  15.625  22.522  1.00  0.00              
ATOM    195  CA  PHE    51      26.556  16.836  23.370  1.00  0.00              
ATOM    196  C   PHE    51      25.087  17.108  23.565  1.00  0.00              
ATOM    197  O   PHE    51      24.466  17.894  22.854  1.00  0.00              
ATOM    198  N   PRO    52      24.494  16.422  24.536  1.00  0.00              
ATOM    199  CA  PRO    52      23.077  16.570  24.848  1.00  0.00              
ATOM    200  C   PRO    52      22.574  18.005  25.095  1.00  0.00              
ATOM    201  O   PRO    52      21.433  18.294  24.748  1.00  0.00              
ATOM    202  N   GLU    53      23.425  18.869  25.648  1.00  0.00              
ATOM    203  CA  GLU    53      23.088  20.264  25.937  1.00  0.00              
ATOM    204  C   GLU    53      23.334  21.238  24.770  1.00  0.00              
ATOM    205  O   GLU    53      23.030  22.419  24.896  1.00  0.00              
ATOM    206  N   ILE    54      23.873  20.759  23.643  1.00  0.00              
ATOM    207  CA  ILE    54      24.095  21.601  22.458  1.00  0.00              
ATOM    208  C   ILE    54      22.777  22.217  21.985  1.00  0.00              
ATOM    209  O   ILE    54      21.714  21.569  22.057  1.00  0.00              
ATOM    210  N   ASP    55      22.841  23.469  21.550  1.00  0.00              
ATOM    211  CA  ASP    55      21.673  24.191  21.060  1.00  0.00              
ATOM    212  C   ASP    55      22.103  25.018  19.867  1.00  0.00              
ATOM    213  O   ASP    55      23.155  25.681  19.913  1.00  0.00              
ATOM    214  N   LEU    56      21.301  24.972  18.809  1.00  0.00              
ATOM    215  CA  LEU    56      21.569  25.714  17.575  1.00  0.00              
ATOM    216  C   LEU    56      20.444  26.698  17.274  1.00  0.00              
ATOM    217  O   LEU    56      19.313  26.307  17.086  1.00  0.00              
END
