
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0327AL044_2
# Molecule2: number of CA atoms   73 ( 1169),  selected   73 , name T0327.pdb
# PARAMETERS: T0327AL044_2.T0327.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    K      41      -       -           -
LGA    Y      45      -       -           -
LGA    I      46      -       -           -
LGA    I      47      -       -           -
LGA    G      48      -       -           -
LGA    V      49      K       5           #
LGA    H      50      L       6          3.072
LGA    -       -      R       7           -
LGA    -       -      Y       8           -
LGA    -       -      A       9           -
LGA    -       -      I      10           -
LGA    Y      51      L      11          4.079
LGA    S      52      K      12          3.808
LGA    D      53      -       -           -
LGA    D      54      -       -           -
LGA    R      55      E      13          2.762
LGA    H      57      I      14          4.014
LGA    -       -      F      15           -
LGA    -       -      E      16           -
LGA    -       -      G      17           -
LGA    -       -      N      18           -
LGA    -       -      T      19           -
LGA    L      58      P      20          3.137
LGA    Y      59      L      21          3.605
LGA    K      60      S      22          4.786
LGA    L      61      E      23          2.352
LGA    -       -      N      24           -
LGA    G      62      D      25          1.749
LGA    P      63      I      26          2.844
LGA    E      64      G      27          3.787
LGA    L      65      V      28          1.743
LGA    T      66      T      29          1.173
LGA    E      67      E      30          3.107
LGA    -       -      D      31           -
LGA    -       -      Q      32           -
LGA    K      68      F      33          0.761
LGA    -       -      D      34           -
LGA    -       -      D      35           -
LGA    G      69      A      36          1.173
LGA    E      70      V      37          1.783
LGA    -       -      N      38           -
LGA    -       -      F      39           -
LGA    N      71      L      40          1.227
LGA    Y      72      K      41          1.993
LGA    -       -      R      42           -
LGA    -       -      E      43           -
LGA    -       -      G      44           -
LGA    -       -      Y      45           -
LGA    L      73      I      46          1.941
LGA    G      77      I      47          2.513
LGA    T      78      G      48          2.767
LGA    W      79      V      49          2.429
LGA    S      80      H      50          0.276
LGA    K      81      Y      51           #
LGA    -       -      S      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    -       -      R      55           -
LGA    A      82      P      56          4.912
LGA    Y      83      H      57          0.518
LGA    K      84      -       -           -
LGA    T      85      L      58          2.164
LGA    I      86      Y      59           #
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      G      62           -
LGA    -       -      P      63           -
LGA    -       -      E      64           -
LGA    -       -      L      65           -
LGA    -       -      T      66           -
LGA    -       -      E      67           -
LGA    -       -      K      68           -
LGA    -       -      G      69           -
LGA    -       -      E      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      E      75           -
LGA    -       -      N      76           -
LGA    -       -      G      77           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39   73    5.0     28    2.79     7.14     25.914     0.968

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.903615 * X  +   0.277247 * Y  +  -0.326518 * Z  + -27.504427
  Y_new =   0.403044 * X  +  -0.292213 * Y  +   0.867276 * Z  + -41.819542
  Z_new =   0.145037 * X  +  -0.915285 * Y  +  -0.375790 * Z  +  94.317787 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.960383    1.181209  [ DEG:  -112.3217     67.6783 ]
  Theta =  -0.145550   -2.996042  [ DEG:    -8.3394   -171.6606 ]
  Phi   =   0.419552   -2.722041  [ DEG:    24.0386   -155.9614 ]
 
# 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: T0327AL044_2                                  
REMARK     2: T0327.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0327AL044_2.T0327.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39   73   5.0   28   2.79    7.14  25.914
REMARK  ---------------------------------------------------------- 
MOLECULE T0327AL044_2
REMARK Aligment from pdb entry: 1jph_A
ATOM      1  N   LYS    41      -7.592  16.662  17.280  1.00  0.00              
ATOM      2  CA  LYS    41      -7.578  15.748  16.138  1.00  0.00              
ATOM      3  C   LYS    41      -7.120  14.361  16.573  1.00  0.00              
ATOM      4  O   LYS    41      -6.457  14.202  17.598  1.00  0.00              
ATOM      5  N   TYR    45      -7.554  13.352  15.835  1.00  0.00              
ATOM      6  CA  TYR    45      -7.208  11.979  16.150  1.00  0.00              
ATOM      7  C   TYR    45      -6.251  11.454  15.093  1.00  0.00              
ATOM      8  O   TYR    45      -6.130  12.036  14.016  1.00  0.00              
ATOM      9  N   ILE    46      -5.503  10.389  15.411  1.00  0.00              
ATOM     10  CA  ILE    46      -4.582   9.861  14.404  1.00  0.00              
ATOM     11  C   ILE    46      -5.380   9.247  13.249  1.00  0.00              
ATOM     12  O   ILE    46      -6.386   8.567  13.465  1.00  0.00              
ATOM     13  N   ILE    47      -4.974   9.570  12.025  1.00  0.00              
ATOM     14  CA  ILE    47      -5.650   9.075  10.834  1.00  0.00              
ATOM     15  C   ILE    47      -4.789   8.092  10.028  1.00  0.00              
ATOM     16  O   ILE    47      -3.586   8.295   9.854  1.00  0.00              
ATOM     17  N   GLY    48      -5.423   7.009   9.579  1.00  0.00              
ATOM     18  CA  GLY    48      -4.769   5.944   8.822  1.00  0.00              
ATOM     19  C   GLY    48      -5.268   5.875   7.381  1.00  0.00              
ATOM     20  O   GLY    48      -6.471   5.985   7.122  1.00  0.00              
ATOM     21  N   VAL    49      -4.341   5.723   6.444  1.00  0.00              
ATOM     22  CA  VAL    49      -4.707   5.586   5.054  1.00  0.00              
ATOM     23  C   VAL    49      -4.266   4.208   4.585  1.00  0.00              
ATOM     24  O   VAL    49      -3.091   3.848   4.683  1.00  0.00              
ATOM     25  N   HIS    50      -5.252   3.397   4.210  1.00  0.00              
ATOM     26  CA  HIS    50      -4.999   2.046   3.733  1.00  0.00              
ATOM     27  C   HIS    50      -5.333   1.984   2.258  1.00  0.00              
ATOM     28  O   HIS    50      -6.472   2.216   1.865  1.00  0.00              
ATOM     29  N   TYR    51      -3.261  -2.862  -2.499  1.00  0.00              
ATOM     30  CA  TYR    51      -2.571  -2.971  -3.781  1.00  0.00              
ATOM     31  C   TYR    51      -2.023  -1.614  -4.226  1.00  0.00              
ATOM     32  O   TYR    51      -1.882  -1.363  -5.422  1.00  0.00              
ATOM     33  N   SER    52      -1.696  -0.756  -3.260  1.00  0.00              
ATOM     34  CA  SER    52      -1.185   0.570  -3.576  1.00  0.00              
ATOM     35  C   SER    52       0.314   0.766  -3.414  1.00  0.00              
ATOM     36  O   SER    52       0.760   1.861  -3.067  1.00  0.00              
ATOM     37  N   ASP    53       1.087  -0.278  -3.709  1.00  0.00              
ATOM     38  CA  ASP    53       2.546  -0.246  -3.612  1.00  0.00              
ATOM     39  C   ASP    53       3.172   0.965  -4.296  1.00  0.00              
ATOM     40  O   ASP    53       4.147   1.541  -3.801  1.00  0.00              
ATOM     41  N   ASP    54       2.605   1.330  -5.444  1.00  0.00              
ATOM     42  CA  ASP    54       3.070   2.441  -6.275  1.00  0.00              
ATOM     43  C   ASP    54       2.793   3.822  -5.716  1.00  0.00              
ATOM     44  O   ASP    54       3.286   4.816  -6.251  1.00  0.00              
ATOM     45  N   ARG    55       1.965   3.893  -4.680  1.00  0.00              
ATOM     46  CA  ARG    55       1.606   5.177  -4.107  1.00  0.00              
ATOM     47  C   ARG    55       2.077   5.387  -2.676  1.00  0.00              
ATOM     48  O   ARG    55       1.766   6.412  -2.077  1.00  0.00              
ATOM     49  N   HIS    57       2.853   4.448  -2.144  1.00  0.00              
ATOM     50  CA  HIS    57       3.334   4.558  -0.771  1.00  0.00              
ATOM     51  C   HIS    57       4.077   5.856  -0.470  1.00  0.00              
ATOM     52  O   HIS    57       3.870   6.458   0.584  1.00  0.00              
ATOM     53  N   LEU    58       4.907   6.309  -1.405  1.00  0.00              
ATOM     54  CA  LEU    58       5.656   7.543  -1.203  1.00  0.00              
ATOM     55  C   LEU    58       4.739   8.769  -1.093  1.00  0.00              
ATOM     56  O   LEU    58       4.913   9.598  -0.200  1.00  0.00              
ATOM     57  N   TYR    59       3.755   8.879  -1.985  1.00  0.00              
ATOM     58  CA  TYR    59       2.827  10.012  -1.956  1.00  0.00              
ATOM     59  C   TYR    59       1.953   9.944  -0.701  1.00  0.00              
ATOM     60  O   TYR    59       1.684  10.965  -0.065  1.00  0.00              
ATOM     61  N   LYS    60       1.514   8.733  -0.357  1.00  0.00              
ATOM     62  CA  LYS    60       0.649   8.519   0.801  1.00  0.00              
ATOM     63  C   LYS    60       1.300   8.911   2.117  1.00  0.00              
ATOM     64  O   LYS    60       0.615   9.336   3.045  1.00  0.00              
ATOM     65  N   LEU    61       2.621   8.780   2.190  1.00  0.00              
ATOM     66  CA  LEU    61       3.367   9.136   3.393  1.00  0.00              
ATOM     67  C   LEU    61       3.447  10.652   3.564  1.00  0.00              
ATOM     68  O   LEU    61       3.886  11.137   4.605  1.00  0.00              
ATOM     69  N   GLY    62       3.016  11.389   2.544  1.00  0.00              
ATOM     70  CA  GLY    62       3.034  12.846   2.569  1.00  0.00              
ATOM     71  C   GLY    62       1.633  13.401   2.391  1.00  0.00              
ATOM     72  O   GLY    62       1.460  14.601   2.150  1.00  0.00              
ATOM     73  N   PRO    63       0.636  12.531   2.542  1.00  0.00              
ATOM     74  CA  PRO    63      -0.762  12.911   2.362  1.00  0.00              
ATOM     75  C   PRO    63      -1.450  13.485   3.603  1.00  0.00              
ATOM     76  O   PRO    63      -2.626  13.854   3.545  1.00  0.00              
ATOM     77  N   GLU    64      -0.724  13.557   4.713  1.00  0.00              
ATOM     78  CA  GLU    64      -1.289  14.118   5.928  1.00  0.00              
ATOM     79  C   GLU    64      -1.870  13.115   6.897  1.00  0.00              
ATOM     80  O   GLU    64      -2.709  13.476   7.721  1.00  0.00              
ATOM     81  N   LEU    65      -1.452  11.856   6.780  1.00  0.00              
ATOM     82  CA  LEU    65      -1.914  10.784   7.661  1.00  0.00              
ATOM     83  C   LEU    65      -0.753  10.325   8.524  1.00  0.00              
ATOM     84  O   LEU    65       0.392  10.256   8.060  1.00  0.00              
ATOM     85  N   THR    66      -1.060  10.013   9.781  1.00  0.00              
ATOM     86  CA  THR    66      -0.069   9.549  10.739  1.00  0.00              
ATOM     87  C   THR    66       0.354   8.122  10.448  1.00  0.00              
ATOM     88  O   THR    66       1.500   7.740  10.701  1.00  0.00              
ATOM     89  N   GLU    67      -0.581   7.335   9.922  1.00  0.00              
ATOM     90  CA  GLU    67      -0.332   5.931   9.622  1.00  0.00              
ATOM     91  C   GLU    67      -0.646   5.571   8.171  1.00  0.00              
ATOM     92  O   GLU    67      -1.576   6.113   7.575  1.00  0.00              
ATOM     93  N   LYS    68       0.163   4.674   7.607  1.00  0.00              
ATOM     94  CA  LYS    68      -0.025   4.182   6.243  1.00  0.00              
ATOM     95  C   LYS    68      -0.161   2.660   6.348  1.00  0.00              
ATOM     96  O   LYS    68       0.770   1.973   6.780  1.00  0.00              
ATOM     97  N   GLY    69      -1.352   2.152   6.030  1.00  0.00              
ATOM     98  CA  GLY    69      -1.607   0.719   6.092  1.00  0.00              
ATOM     99  C   GLY    69      -1.097   0.016   4.849  1.00  0.00              
ATOM    100  O   GLY    69      -1.203   0.545   3.749  1.00  0.00              
ATOM    101  N   GLU    70      -0.585  -1.196   5.012  1.00  0.00              
ATOM    102  CA  GLU    70      -0.024  -1.932   3.885  1.00  0.00              
ATOM    103  C   GLU    70      -0.677  -3.278   3.634  1.00  0.00              
ATOM    104  O   GLU    70      -1.102  -3.954   4.571  1.00  0.00              
ATOM    105  N   ASN    71      -0.745  -3.673   2.365  1.00  0.00              
ATOM    106  CA  ASN    71      -1.271  -4.986   2.034  1.00  0.00              
ATOM    107  C   ASN    71      -0.061  -5.919   2.179  1.00  0.00              
ATOM    108  O   ASN    71       1.064  -5.447   2.370  1.00  0.00              
ATOM    109  N   TYR    72      -0.279  -7.227   2.090  1.00  0.00              
ATOM    110  CA  TYR    72       0.796  -8.199   2.263  1.00  0.00              
ATOM    111  C   TYR    72       1.803  -8.373   1.118  1.00  0.00              
ATOM    112  O   TYR    72       2.790  -9.092   1.279  1.00  0.00              
ATOM    113  N   LEU    73       1.568  -7.736  -0.026  1.00  0.00              
ATOM    114  CA  LEU    73       2.482  -7.890  -1.160  1.00  0.00              
ATOM    115  C   LEU    73       3.706  -6.984  -1.104  1.00  0.00              
ATOM    116  O   LEU    73       4.667  -7.184  -1.846  1.00  0.00              
ATOM    117  N   GLY    77       3.662  -5.984  -0.234  1.00  0.00              
ATOM    118  CA  GLY    77       4.772  -5.060  -0.075  1.00  0.00              
ATOM    119  C   GLY    77       5.656  -5.552   1.068  1.00  0.00              
ATOM    120  O   GLY    77       5.167  -5.791   2.177  1.00  0.00              
ATOM    121  N   THR    78       6.935  -5.775   0.777  1.00  0.00              
ATOM    122  CA  THR    78       7.890  -6.215   1.795  1.00  0.00              
ATOM    123  C   THR    78       8.017  -5.059   2.795  1.00  0.00              
ATOM    124  O   THR    78       8.153  -3.898   2.388  1.00  0.00              
ATOM    125  N   TRP    79       7.933  -5.353   4.111  1.00  0.00              
ATOM    126  CA  TRP    79       8.031  -4.340   5.174  1.00  0.00              
ATOM    127  C   TRP    79       9.204  -3.367   5.029  1.00  0.00              
ATOM    128  O   TRP    79       9.015  -2.151   5.055  1.00  0.00              
ATOM    129  N   SER    80      10.405  -3.900   4.819  1.00  0.00              
ATOM    130  CA  SER    80      11.590  -3.064   4.660  1.00  0.00              
ATOM    131  C   SER    80      11.497  -2.108   3.475  1.00  0.00              
ATOM    132  O   SER    80      11.906  -0.951   3.581  1.00  0.00              
ATOM    133  N   LYS    81      10.950  -2.582   2.356  1.00  0.00              
ATOM    134  CA  LYS    81      10.789  -1.744   1.167  1.00  0.00              
ATOM    135  C   LYS    81       9.738  -0.671   1.430  1.00  0.00              
ATOM    136  O   LYS    81       9.852   0.456   0.947  1.00  0.00              
ATOM    137  N   ALA    82       8.701  -1.032   2.182  1.00  0.00              
ATOM    138  CA  ALA    82       7.650  -0.082   2.518  1.00  0.00              
ATOM    139  C   ALA    82       8.270   1.019   3.366  1.00  0.00              
ATOM    140  O   ALA    82       7.994   2.202   3.159  1.00  0.00              
ATOM    141  N   TYR    83       9.142   0.621   4.292  1.00  0.00              
ATOM    142  CA  TYR    83       9.816   1.567   5.173  1.00  0.00              
ATOM    143  C   TYR    83      10.646   2.535   4.327  1.00  0.00              
ATOM    144  O   TYR    83      10.652   3.746   4.582  1.00  0.00              
ATOM    145  N   LYS    84      11.295   2.006   3.290  1.00  0.00              
ATOM    146  CA  LYS    84      12.095   2.826   2.384  1.00  0.00              
ATOM    147  C   LYS    84      11.209   3.860   1.705  1.00  0.00              
ATOM    148  O   LYS    84      11.510   5.050   1.730  1.00  0.00              
ATOM    149  N   THR    85      10.101   3.398   1.129  1.00  0.00              
ATOM    150  CA  THR    85       9.163   4.273   0.423  1.00  0.00              
ATOM    151  C   THR    85       8.523   5.363   1.273  1.00  0.00              
ATOM    152  O   THR    85       8.436   6.516   0.849  1.00  0.00              
ATOM    153  N   ILE    86       8.068   4.996   2.466  1.00  0.00              
ATOM    154  CA  ILE    86       7.396   5.946   3.345  1.00  0.00              
ATOM    155  C   ILE    86       8.308   6.902   4.096  1.00  0.00              
ATOM    156  O   ILE    86       7.936   8.045   4.339  1.00  0.00              
END
