
#######################################################
#                                                     #
#                        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   49 (  196),  selected   49 , name T0327AL381_2
# Molecule2: number of CA atoms   73 ( 1169),  selected   73 , name T0327.pdb
# PARAMETERS: T0327AL381_2.T0327.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D      25      K       5           -
LGA    I      26      L       6           -
LGA    -       -      R       7           -
LGA    -       -      Y       8           -
LGA    -       -      A       9           -
LGA    -       -      I      10           -
LGA    -       -      L      11           -
LGA    -       -      K      12           -
LGA    -       -      E      13           -
LGA    -       -      I      14           -
LGA    -       -      F      15           -
LGA    -       -      E      16           -
LGA    -       -      G      17           -
LGA    -       -      N      18           -
LGA    -       -      T      19           -
LGA    -       -      P      20           -
LGA    -       -      L      21           -
LGA    -       -      S      22           -
LGA    -       -      E      23           -
LGA    G      27      N      24          2.937
LGA    -       -      D      25           -
LGA    -       -      I      26           -
LGA    -       -      G      27           -
LGA    V      28      V      28          1.530
LGA    T      29      T      29          0.336
LGA    E      30      E      30          0.299
LGA    D      31      D      31          0.263
LGA    Q      32      Q      32          0.152
LGA    F      33      F      33          0.478
LGA    D      34      D      34          0.503
LGA    D      35      D      35          0.053
LGA    A      36      A      36          0.122
LGA    V      37      V      37          0.468
LGA    N      38      N      38          0.804
LGA    F      39      F      39          0.800
LGA    L      40      L      40          0.421
LGA    K      41      K      41          0.917
LGA    R      42      R      42          1.423
LGA    E      43      E      43          1.412
LGA    G      44      G      44          0.684
LGA    Y      45      Y      45          0.261
LGA    I      46      I      46          0.497
LGA    I      47      I      47          0.811
LGA    G      48      G      48          2.242
LGA    V      49      V      49          4.958
LGA    H      50      -       -           -
LGA    Y      51      -       -           -
LGA    S      52      -       -           -
LGA    R      55      -       -           -
LGA    P      56      -       -           -
LGA    H      57      -       -           -
LGA    L      58      -       -           -
LGA    Y      59      H      50          5.054
LGA    -       -      Y      51           -
LGA    -       -      S      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    -       -      R      55           -
LGA    -       -      P      56           -
LGA    -       -      H      57           -
LGA    -       -      L      58           -
LGA    -       -      Y      59           -
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      G      62           -
LGA    P      63      P      63          2.217
LGA    E      64      E      64          1.457
LGA    L      65      L      65          1.067
LGA    T      66      T      66          0.924
LGA    E      67      E      67          1.214
LGA    K      68      K      68          0.913
LGA    G      69      G      69          0.535
LGA    E      70      E      70          0.238
LGA    N      71      N      71          0.440
LGA    Y      72      Y      72          0.606
LGA    L      73      L      73          0.962
LGA    K      74      K      74          0.868
LGA    E      75      E      75          0.573
LGA    N      76      N      76          0.278
LGA    G      77      G      77          0.998
LGA    T      78      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   49   73    5.0     39    1.52    94.87     51.069     2.406

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.397622 * X  +   0.211925 * Y  +  -0.892740 * Z  +  -4.080672
  Y_new =  -0.909995 * X  +  -0.033507 * Y  +  -0.413262 * Z  +  31.087450
  Z_new =  -0.117493 * X  +   0.976711 * Y  +   0.179527 * Z  + -37.950909 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.389017   -1.752575  [ DEG:    79.5848   -100.4152 ]
  Theta =   0.117765    3.023828  [ DEG:     6.7474    173.2526 ]
  Phi   =  -1.158848    1.982745  [ DEG:   -66.3971    113.6029 ]
 
# 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: T0327AL381_2                                  
REMARK     2: T0327.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0327AL381_2.T0327.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   49   73   5.0   39   1.52   94.87  51.069
REMARK  ---------------------------------------------------------- 
MOLECULE T0327AL381_2
REMARK Aligment from pdb entry: 1xmaA
ATOM      1  N   ASP    25      -4.399  18.213   1.049  1.00  0.00              
ATOM      2  CA  ASP    25      -5.777  17.896   1.437  1.00  0.00              
ATOM      3  C   ASP    25      -5.843  16.618   2.281  1.00  0.00              
ATOM      4  O   ASP    25      -6.580  16.568   3.258  1.00  0.00              
ATOM      5  N   ILE    26      -5.052  15.606   1.911  1.00  0.00              
ATOM      6  CA  ILE    26      -4.824  14.445   2.773  1.00  0.00              
ATOM      7  C   ILE    26      -3.334  14.223   3.174  1.00  0.00              
ATOM      8  O   ILE    26      -2.440  14.132   2.312  1.00  0.00              
ATOM      9  N   GLY    27      -3.084  14.167   4.485  1.00  0.00              
ATOM     10  CA  GLY    27      -1.773  13.764   5.008  1.00  0.00              
ATOM     11  C   GLY    27      -1.932  12.553   5.952  1.00  0.00              
ATOM     12  O   GLY    27      -2.458  12.664   7.077  1.00  0.00              
ATOM     13  N   VAL    28      -1.515  11.393   5.454  1.00  0.00              
ATOM     14  CA  VAL    28      -1.638  10.137   6.202  1.00  0.00              
ATOM     15  C   VAL    28      -0.803  10.178   7.487  1.00  0.00              
ATOM     16  O   VAL    28       0.341  10.664   7.483  1.00  0.00              
ATOM     17  N   THR    29      -1.378   9.672   8.577  1.00  0.00              
ATOM     18  CA  THR    29      -0.675   9.584   9.860  1.00  0.00              
ATOM     19  C   THR    29       0.285   8.399   9.865  1.00  0.00              
ATOM     20  O   THR    29      -0.031   7.356   9.318  1.00  0.00              
ATOM     21  N   GLU    30       1.456   8.572  10.486  1.00  0.00              
ATOM     22  CA  GLU    30       2.453   7.496  10.621  1.00  0.00              
ATOM     23  C   GLU    30       1.879   6.158  11.130  1.00  0.00              
ATOM     24  O   GLU    30       2.306   5.104  10.668  1.00  0.00              
ATOM     25  N   ASP    31       0.923   6.191  12.060  1.00  0.00              
ATOM     26  CA  ASP    31       0.392   4.934  12.612  1.00  0.00              
ATOM     27  C   ASP    31      -0.515   4.262  11.581  1.00  0.00              
ATOM     28  O   ASP    31      -0.414   3.071  11.347  1.00  0.00              
ATOM     29  N   GLN    32      -1.381   5.060  10.961  1.00  0.00              
ATOM     30  CA  GLN    32      -2.258   4.620   9.877  1.00  0.00              
ATOM     31  C   GLN    32      -1.503   3.985   8.719  1.00  0.00              
ATOM     32  O   GLN    32      -1.950   2.987   8.148  1.00  0.00              
ATOM     33  N   PHE    33      -0.359   4.562   8.385  1.00  0.00              
ATOM     34  CA  PHE    33       0.407   4.108   7.245  1.00  0.00              
ATOM     35  C   PHE    33       1.100   2.762   7.537  1.00  0.00              
ATOM     36  O   PHE    33       1.134   1.875   6.694  1.00  0.00              
ATOM     37  N   ASP    34       1.630   2.608   8.740  1.00  0.00              
ATOM     38  CA  ASP    34       2.327   1.373   9.071  1.00  0.00              
ATOM     39  C   ASP    34       1.364   0.209   9.343  1.00  0.00              
ATOM     40  O   ASP    34       1.690  -0.951   9.063  1.00  0.00              
ATOM     41  N   ASP    35       0.162   0.545   9.822  1.00  0.00              
ATOM     42  CA  ASP    35      -0.941  -0.408   9.975  1.00  0.00              
ATOM     43  C   ASP    35      -1.398  -0.945   8.631  1.00  0.00              
ATOM     44  O   ASP    35      -1.691  -2.113   8.496  1.00  0.00              
ATOM     45  N   ALA    36      -1.492  -0.065   7.657  1.00  0.00              
ATOM     46  CA  ALA    36      -1.961  -0.415   6.343  1.00  0.00              
ATOM     47  C   ALA    36      -0.929  -1.270   5.573  1.00  0.00              
ATOM     48  O   ALA    36      -1.311  -2.220   4.878  1.00  0.00              
ATOM     49  N   VAL    37       0.361  -0.930   5.705  1.00  0.00              
ATOM     50  CA  VAL    37       1.455  -1.775   5.185  1.00  0.00              
ATOM     51  C   VAL    37       1.353  -3.171   5.705  1.00  0.00              
ATOM     52  O   VAL    37       1.543  -4.134   4.961  1.00  0.00              
ATOM     53  N   ASN    38       1.043  -3.266   6.993  1.00  0.00              
ATOM     54  CA  ASN    38       1.046  -4.526   7.715  1.00  0.00              
ATOM     55  C   ASN    38      -0.132  -5.394   7.314  1.00  0.00              
ATOM     56  O   ASN    38       0.009  -6.624   7.171  1.00  0.00              
ATOM     57  N   PHE    39      -1.294  -4.749   7.151  1.00  0.00              
ATOM     58  CA  PHE    39      -2.533  -5.419   6.716  1.00  0.00              
ATOM     59  C   PHE    39      -2.448  -5.820   5.243  1.00  0.00              
ATOM     60  O   PHE    39      -2.860  -6.912   4.863  1.00  0.00              
ATOM     61  N   LEU    40      -1.912  -4.941   4.411  1.00  0.00              
ATOM     62  CA  LEU    40      -1.747  -5.247   2.979  1.00  0.00              
ATOM     63  C   LEU    40      -0.843  -6.448   2.751  1.00  0.00              
ATOM     64  O   LEU    40      -1.108  -7.269   1.878  1.00  0.00              
ATOM     65  N   LYS    41       0.219  -6.534   3.558  1.00  0.00              
ATOM     66  CA  LYS    41       1.162  -7.640   3.503  1.00  0.00              
ATOM     67  C   LYS    41       0.593  -8.945   4.086  1.00  0.00              
ATOM     68  O   LYS    41       0.766 -10.013   3.502  1.00  0.00              
ATOM     69  N   ARG    42      -0.093  -8.839   5.219  1.00  0.00              
ATOM     70  CA  ARG    42      -0.931  -9.920   5.757  1.00  0.00              
ATOM     71  C   ARG    42      -1.899 -10.467   4.674  1.00  0.00              
ATOM     72  O   ARG    42      -2.012 -11.682   4.463  1.00  0.00              
ATOM     73  N   GLU    43      -2.574  -9.566   3.973  1.00  0.00              
ATOM     74  CA  GLU    43      -3.559  -9.971   2.978  1.00  0.00              
ATOM     75  C   GLU    43      -2.979 -10.490   1.649  1.00  0.00              
ATOM     76  O   GLU    43      -3.724 -10.923   0.789  1.00  0.00              
ATOM     77  N   GLY    44      -1.651 -10.479   1.516  1.00  0.00              
ATOM     78  CA  GLY    44      -0.979 -10.900   0.279  1.00  0.00              
ATOM     79  C   GLY    44      -1.108  -9.894  -0.858  1.00  0.00              
ATOM     80  O   GLY    44      -1.112 -10.279  -2.029  1.00  0.00              
ATOM     81  N   TYR    45      -1.211  -8.601  -0.532  1.00  0.00              
ATOM     82  CA  TYR    45      -1.442  -7.589  -1.567  1.00  0.00              
ATOM     83  C   TYR    45      -0.167  -6.843  -1.937  1.00  0.00              
ATOM     84  O   TYR    45      -0.087  -6.225  -3.009  1.00  0.00              
ATOM     85  N   ILE    46       0.816  -6.889  -1.033  1.00  0.00              
ATOM     86  CA  ILE    46       2.156  -6.329  -1.254  1.00  0.00              
ATOM     87  C   ILE    46       3.190  -7.270  -0.656  1.00  0.00              
ATOM     88  O   ILE    46       2.873  -8.021   0.285  1.00  0.00              
ATOM     89  N   ILE    47       4.421  -7.206  -1.189  1.00  0.00              
ATOM     90  CA  ILE    47       5.597  -7.862  -0.586  1.00  0.00              
ATOM     91  C   ILE    47       6.682  -6.855  -0.172  1.00  0.00              
ATOM     92  O   ILE    47       7.015  -5.914  -0.914  1.00  0.00              
ATOM     93  N   GLY    48       7.259  -7.061   0.995  1.00  0.00              
ATOM     94  CA  GLY    48       8.390  -6.236   1.418  1.00  0.00              
ATOM     95  C   GLY    48       9.715  -6.800   0.918  1.00  0.00              
ATOM     96  O   GLY    48       9.891  -8.022   0.807  1.00  0.00              
ATOM     97  N   VAL    49      10.644  -5.890   0.618  1.00  0.00              
ATOM     98  CA  VAL    49      12.052  -6.259   0.447  1.00  0.00              
ATOM     99  C   VAL    49      12.963  -5.181   1.020  1.00  0.00              
ATOM    100  O   VAL    49      12.495  -4.121   1.429  1.00  0.00              
ATOM    101  N   HIS    50      14.257  -5.465   1.074  1.00  0.00              
ATOM    102  CA  HIS    50      15.187  -4.604   1.801  1.00  0.00              
ATOM    103  C   HIS    50      16.296  -4.013   0.953  1.00  0.00              
ATOM    104  O   HIS    50      16.903  -4.686   0.118  1.00  0.00              
ATOM    105  N   TYR    51      16.558  -2.739   1.177  1.00  0.00              
ATOM    106  CA  TYR    51      17.715  -2.089   0.573  1.00  0.00              
ATOM    107  C   TYR    51      19.002  -2.418   1.315  1.00  0.00              
ATOM    108  O   TYR    51      19.035  -3.260   2.223  1.00  0.00              
ATOM    109  N   SER    52      22.457   1.120   5.289  1.00  0.00              
ATOM    110  CA  SER    52      23.156   2.400   5.442  1.00  0.00              
ATOM    111  C   SER    52      22.864   3.066   6.793  1.00  0.00              
ATOM    112  O   SER    52      21.712   3.139   7.216  1.00  0.00              
ATOM    113  N   ARG    55      20.909   0.692   9.542  1.00  0.00              
ATOM    114  CA  ARG    55      19.549   0.345   9.087  1.00  0.00              
ATOM    115  C   ARG    55      19.350   0.118   7.569  1.00  0.00              
ATOM    116  O   ARG    55      20.111   0.598   6.750  1.00  0.00              
ATOM    117  N   PRO    56      18.311  -0.636   7.227  1.00  0.00              
ATOM    118  CA  PRO    56      17.954  -0.933   5.838  1.00  0.00              
ATOM    119  C   PRO    56      16.558  -0.450   5.570  1.00  0.00              
ATOM    120  O   PRO    56      15.631  -0.696   6.371  1.00  0.00              
ATOM    121  N   HIS    57      16.397   0.195   4.422  1.00  0.00              
ATOM    122  CA  HIS    57      15.095   0.665   3.958  1.00  0.00              
ATOM    123  C   HIS    57      14.182  -0.500   3.560  1.00  0.00              
ATOM    124  O   HIS    57      14.637  -1.458   2.961  1.00  0.00              
ATOM    125  N   LEU    58      12.892  -0.387   3.886  1.00  0.00              
ATOM    126  CA  LEU    58      11.914  -1.428   3.589  1.00  0.00              
ATOM    127  C   LEU    58      11.061  -1.006   2.394  1.00  0.00              
ATOM    128  O   LEU    58      10.246  -0.067   2.494  1.00  0.00              
ATOM    129  N   TYR    59      11.253  -1.702   1.268  1.00  0.00              
ATOM    130  CA  TYR    59      10.465  -1.441   0.081  1.00  0.00              
ATOM    131  C   TYR    59       9.270  -2.374   0.035  1.00  0.00              
ATOM    132  O   TYR    59       9.298  -3.456   0.635  1.00  0.00              
ATOM    133  N   PRO    63       8.222  -1.925  -0.649  1.00  0.00              
ATOM    134  CA  PRO    63       7.050  -2.745  -0.963  1.00  0.00              
ATOM    135  C   PRO    63       6.794  -2.796  -2.463  1.00  0.00              
ATOM    136  O   PRO    63       6.958  -1.791  -3.173  1.00  0.00              
ATOM    137  N   GLU    64       6.408  -3.973  -2.935  1.00  0.00              
ATOM    138  CA  GLU    64       6.010  -4.191  -4.324  1.00  0.00              
ATOM    139  C   GLU    64       4.619  -4.816  -4.319  1.00  0.00              
ATOM    140  O   GLU    64       4.373  -5.784  -3.589  1.00  0.00              
ATOM    141  N   LEU    65       3.714  -4.247  -5.111  1.00  0.00              
ATOM    142  CA  LEU    65       2.359  -4.768  -5.271  1.00  0.00              
ATOM    143  C   LEU    65       2.392  -6.195  -5.886  1.00  0.00              
ATOM    144  O   LEU    65       3.261  -6.506  -6.720  1.00  0.00              
ATOM    145  N   THR    66       1.492  -7.064  -5.433  1.00  0.00              
ATOM    146  CA  THR    66       1.408  -8.431  -5.967  1.00  0.00              
ATOM    147  C   THR    66       0.303  -8.486  -7.044  1.00  0.00              
ATOM    148  O   THR    66      -0.495  -7.530  -7.169  1.00  0.00              
ATOM    149  N   GLU    67       0.251  -9.585  -7.844  1.00  0.00              
ATOM    150  CA  GLU    67      -0.905  -9.729  -8.746  1.00  0.00              
ATOM    151  C   GLU    67      -2.276  -9.701  -8.025  1.00  0.00              
ATOM    152  O   GLU    67      -3.217  -9.127  -8.556  1.00  0.00              
ATOM    153  N   LYS    68      -2.370 -10.311  -6.837  1.00  0.00              
ATOM    154  CA  LYS    68      -3.563 -10.211  -5.989  1.00  0.00              
ATOM    155  C   LYS    68      -3.850  -8.787  -5.493  1.00  0.00              
ATOM    156  O   LYS    68      -5.021  -8.387  -5.385  1.00  0.00              
ATOM    157  N   GLY    69      -2.787  -8.032  -5.187  1.00  0.00              
ATOM    158  CA  GLY    69      -2.926  -6.607  -4.814  1.00  0.00              
ATOM    159  C   GLY    69      -3.568  -5.782  -5.911  1.00  0.00              
ATOM    160  O   GLY    69      -4.435  -4.948  -5.639  1.00  0.00              
ATOM    161  N   GLU    70      -3.142  -6.029  -7.157  1.00  0.00              
ATOM    162  CA  GLU    70      -3.762  -5.430  -8.364  1.00  0.00              
ATOM    163  C   GLU    70      -5.248  -5.851  -8.554  1.00  0.00              
ATOM    164  O   GLU    70      -6.105  -5.022  -8.868  1.00  0.00              
ATOM    165  N   ASN    71      -5.545  -7.129  -8.356  1.00  0.00              
ATOM    166  CA  ASN    71      -6.938  -7.608  -8.371  1.00  0.00              
ATOM    167  C   ASN    71      -7.823  -6.870  -7.344  1.00  0.00              
ATOM    168  O   ASN    71      -8.911  -6.387  -7.671  1.00  0.00              
ATOM    169  N   TYR    72      -7.343  -6.782  -6.106  1.00  0.00              
ATOM    170  CA  TYR    72      -8.047  -6.045  -5.036  1.00  0.00              
ATOM    171  C   TYR    72      -8.192  -4.555  -5.353  1.00  0.00              
ATOM    172  O   TYR    72      -9.256  -3.962  -5.156  1.00  0.00              
ATOM    173  N   LEU    73      -7.114  -3.949  -5.829  1.00  0.00              
ATOM    174  CA  LEU    73      -7.165  -2.562  -6.279  1.00  0.00              
ATOM    175  C   LEU    73      -8.331  -2.303  -7.275  1.00  0.00              
ATOM    176  O   LEU    73      -9.106  -1.367  -7.114  1.00  0.00              
ATOM    177  N   LYS    74      -8.449  -3.154  -8.285  1.00  0.00              
ATOM    178  CA  LYS    74      -9.446  -2.952  -9.334  1.00  0.00              
ATOM    179  C   LYS    74     -10.886  -3.270  -8.902  1.00  0.00              
ATOM    180  O   LYS    74     -11.843  -2.723  -9.460  1.00  0.00              
ATOM    181  N   GLU    75     -11.043  -4.126  -7.905  1.00  0.00              
ATOM    182  CA  GLU    75     -12.365  -4.316  -7.321  1.00  0.00              
ATOM    183  C   GLU    75     -12.752  -3.104  -6.443  1.00  0.00              
ATOM    184  O   GLU    75     -13.908  -2.712  -6.392  1.00  0.00              
ATOM    185  N   ASN    76     -11.780  -2.515  -5.768  1.00  0.00              
ATOM    186  CA  ASN    76     -12.040  -1.322  -4.993  1.00  0.00              
ATOM    187  C   ASN    76     -12.319  -0.076  -5.846  1.00  0.00              
ATOM    188  O   ASN    76     -13.077   0.791  -5.423  1.00  0.00              
ATOM    189  N   GLY    77     -11.742   0.003  -7.044  1.00  0.00              
ATOM    190  CA  GLY    77     -12.098   1.078  -8.002  1.00  0.00              
ATOM    191  C   GLY    77     -13.569   0.996  -8.435  1.00  0.00              
ATOM    192  O   GLY    77     -14.265   1.989  -8.435  1.00  0.00              
ATOM    193  N   THR    78     -14.028  -0.199  -8.789  1.00  0.00              
ATOM    194  CA  THR    78     -15.439  -0.436  -9.126  1.00  0.00              
ATOM    195  C   THR    78     -16.366  -0.063  -7.985  1.00  0.00              
ATOM    196  O   THR    78     -17.373   0.609  -8.201  1.00  0.00              
END
