
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   73 ( 1169),  selected   73 , name T0327.pdb
# PARAMETERS: T0327AL381_1.T0327.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K       5           -
LGA    -       -      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    -       -      N      24           -
LGA    -       -      D      25           -
LGA    I      26      I      26          0.599
LGA    G      27      G      27          2.820
LGA    V      28      V      28          2.037
LGA    T      29      T      29          1.789
LGA    E      30      E      30          1.547
LGA    D      31      D      31          1.149
LGA    Q      32      Q      32          1.169
LGA    F      33      F      33          0.635
LGA    D      34      D      34          0.624
LGA    D      35      D      35          0.746
LGA    A      36      A      36          1.322
LGA    V      37      V      37          1.356
LGA    N      38      N      38          1.657
LGA    F      39      F      39          1.704
LGA    L      40      L      40          1.414
LGA    K      41      K      41          1.611
LGA    R      42      R      42          1.763
LGA    E      43      E      43          1.460
LGA    G      44      G      44          0.810
LGA    Y      45      Y      45          0.950
LGA    I      46      I      46          1.389
LGA    I      47      I      47          1.755
LGA    G      48      G      48          3.465
LGA    V      49      V      49          2.862
LGA    H      50      H      50          2.555
LGA    Y      51      Y      51           -
LGA    S      52      -       -           -
LGA    D      53      -       -           -
LGA    D      54      -       -           -
LGA    R      55      -       -           -
LGA    P      56      -       -           -
LGA    H      57      S      52          6.377
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    -       -      R      55           -
LGA    -       -      P      56           -
LGA    L      58      H      57          2.397
LGA    Y      59      L      58          2.461
LGA    -       -      Y      59           -
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      G      62           -
LGA    K      60      P      63          3.692
LGA    E      64      E      64          3.227
LGA    L      65      L      65          2.249
LGA    T      66      T      66          1.896
LGA    E      67      E      67          2.567
LGA    K      68      K      68          2.007
LGA    G      69      G      69          0.544
LGA    E      70      E      70          0.628
LGA    N      71      N      71          1.356
LGA    Y      72      Y      72          1.923
LGA    L      73      L      73          1.477
LGA    K      74      K      74          0.693
LGA    E      75      E      75          2.664
LGA    T      85      N      76          3.010
LGA    I      86      G      77          2.505

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   49   73    5.0     43    2.17    86.05     46.205     1.898

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.677584 * X  +  -0.415908 * Y  +  -0.606547 * Z  + -24.645243
  Y_new =  -0.542289 * X  +   0.274560 * Y  +  -0.794065 * Z  +  12.780771
  Z_new =   0.496792 * X  +   0.866970 * Y  +  -0.039505 * Z  + -50.472073 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.616332   -1.525261  [ DEG:    92.6090    -87.3910 ]
  Theta =  -0.519898   -2.621694  [ DEG:   -29.7880   -150.2120 ]
  Phi   =  -0.674940    2.466653  [ DEG:   -38.6712    141.3288 ]
 
# 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_1                                  
REMARK     2: T0327.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0327AL381_1.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   43   2.17   86.05  46.205
REMARK  ---------------------------------------------------------- 
MOLECULE T0327AL381_1
REMARK Aligment from pdb entry: 1ub9A
ATOM      1  N   ILE    26       0.189  11.201   0.966  1.00  0.00              
ATOM      2  CA  ILE    26      -1.201  10.918   1.325  1.00  0.00              
ATOM      3  C   ILE    26      -1.581  11.505   2.691  1.00  0.00              
ATOM      4  O   ILE    26      -2.652  11.210   3.230  1.00  0.00              
ATOM      5  N   GLY    27      -0.696  12.335   3.242  1.00  0.00              
ATOM      6  CA  GLY    27      -0.910  12.992   4.532  1.00  0.00              
ATOM      7  C   GLY    27      -1.424  12.049   5.620  1.00  0.00              
ATOM      8  O   GLY    27      -2.487  12.270   6.203  1.00  0.00              
ATOM      9  N   VAL    28      -0.652  10.999   5.876  1.00  0.00              
ATOM     10  CA  VAL    28      -0.980  10.000   6.883  1.00  0.00              
ATOM     11  C   VAL    28       0.132   9.983   7.925  1.00  0.00              
ATOM     12  O   VAL    28       1.286  10.287   7.622  1.00  0.00              
ATOM     13  N   THR    29      -0.210   9.628   9.152  1.00  0.00              
ATOM     14  CA  THR    29       0.798   9.544  10.192  1.00  0.00              
ATOM     15  C   THR    29       1.532   8.213   9.978  1.00  0.00              
ATOM     16  O   THR    29       0.960   7.256   9.447  1.00  0.00              
ATOM     17  N   GLU    30       2.809   8.137  10.376  1.00  0.00              
ATOM     18  CA  GLU    30       3.558   6.889  10.197  1.00  0.00              
ATOM     19  C   GLU    30       2.858   5.719  10.889  1.00  0.00              
ATOM     20  O   GLU    30       2.883   4.589  10.395  1.00  0.00              
ATOM     21  N   ASP    31       2.227   6.010  12.026  1.00  0.00              
ATOM     22  CA  ASP    31       1.522   4.992  12.795  1.00  0.00              
ATOM     23  C   ASP    31       0.296   4.407  12.111  1.00  0.00              
ATOM     24  O   ASP    31       0.098   3.188  12.113  1.00  0.00              
ATOM     25  N   GLN    32      -0.540   5.264  11.535  1.00  0.00              
ATOM     26  CA  GLN    32      -1.726   4.783  10.846  1.00  0.00              
ATOM     27  C   GLN    32      -1.353   4.044   9.572  1.00  0.00              
ATOM     28  O   GLN    32      -1.916   2.994   9.272  1.00  0.00              
ATOM     29  N   PHE    33      -0.412   4.604   8.822  1.00  0.00              
ATOM     30  CA  PHE    33       0.033   3.987   7.584  1.00  0.00              
ATOM     31  C   PHE    33       0.547   2.590   7.890  1.00  0.00              
ATOM     32  O   PHE    33       0.179   1.621   7.237  1.00  0.00              
ATOM     33  N   ASP    34       1.392   2.500   8.906  1.00  0.00              
ATOM     34  CA  ASP    34       1.971   1.228   9.310  1.00  0.00              
ATOM     35  C   ASP    34       0.905   0.162   9.568  1.00  0.00              
ATOM     36  O   ASP    34       1.012  -0.965   9.083  1.00  0.00              
ATOM     37  N   ASP    35      -0.132   0.519  10.319  1.00  0.00              
ATOM     38  CA  ASP    35      -1.194  -0.430  10.621  1.00  0.00              
ATOM     39  C   ASP    35      -1.946  -0.877   9.377  1.00  0.00              
ATOM     40  O   ASP    35      -2.244  -2.055   9.223  1.00  0.00              
ATOM     41  N   ALA    36      -2.260   0.059   8.491  1.00  0.00              
ATOM     42  CA  ALA    36      -2.967  -0.296   7.263  1.00  0.00              
ATOM     43  C   ALA    36      -2.108  -1.175   6.357  1.00  0.00              
ATOM     44  O   ALA    36      -2.611  -2.101   5.718  1.00  0.00              
ATOM     45  N   VAL    37      -0.813  -0.884   6.308  1.00  0.00              
ATOM     46  CA  VAL    37       0.116  -1.659   5.488  1.00  0.00              
ATOM     47  C   VAL    37       0.166  -3.112   5.966  1.00  0.00              
ATOM     48  O   VAL    37       0.198  -4.039   5.156  1.00  0.00              
ATOM     49  N   ASN    38       0.158  -3.301   7.286  1.00  0.00              
ATOM     50  CA  ASN    38       0.181  -4.642   7.876  1.00  0.00              
ATOM     51  C   ASN    38      -1.063  -5.437   7.474  1.00  0.00              
ATOM     52  O   ASN    38      -0.976  -6.609   7.127  1.00  0.00              
ATOM     53  N   PHE    39      -2.223  -4.792   7.521  1.00  0.00              
ATOM     54  CA  PHE    39      -3.471  -5.450   7.139  1.00  0.00              
ATOM     55  C   PHE    39      -3.383  -5.880   5.669  1.00  0.00              
ATOM     56  O   PHE    39      -3.733  -7.010   5.308  1.00  0.00              
ATOM     57  N   LEU    40      -2.922  -4.967   4.823  1.00  0.00              
ATOM     58  CA  LEU    40      -2.798  -5.247   3.400  1.00  0.00              
ATOM     59  C   LEU    40      -1.799  -6.362   3.122  1.00  0.00              
ATOM     60  O   LEU    40      -2.056  -7.228   2.287  1.00  0.00              
ATOM     61  N   LYS    41      -0.666  -6.351   3.823  1.00  0.00              
ATOM     62  CA  LYS    41       0.348  -7.376   3.591  1.00  0.00              
ATOM     63  C   LYS    41      -0.074  -8.759   4.096  1.00  0.00              
ATOM     64  O   LYS    41       0.249  -9.768   3.470  1.00  0.00              
ATOM     65  N   ARG    42      -0.801  -8.810   5.213  1.00  0.00              
ATOM     66  CA  ARG    42      -1.256 -10.094   5.742  1.00  0.00              
ATOM     67  C   ARG    42      -2.225 -10.734   4.762  1.00  0.00              
ATOM     68  O   ARG    42      -2.422 -11.948   4.772  1.00  0.00              
ATOM     69  N   GLU    43      -2.838  -9.912   3.915  1.00  0.00              
ATOM     70  CA  GLU    43      -3.787 -10.415   2.937  1.00  0.00              
ATOM     71  C   GLU    43      -3.197 -10.503   1.532  1.00  0.00              
ATOM     72  O   GLU    43      -3.929 -10.629   0.548  1.00  0.00              
ATOM     73  N   GLY    44      -1.866 -10.439   1.458  1.00  0.00              
ATOM     74  CA  GLY    44      -1.151 -10.543   0.196  1.00  0.00              
ATOM     75  C   GLY    44      -1.415  -9.487  -0.863  1.00  0.00              
ATOM     76  O   GLY    44      -1.136  -9.720  -2.042  1.00  0.00              
ATOM     77  N   TYR    45      -1.930  -8.327  -0.457  1.00  0.00              
ATOM     78  CA  TYR    45      -2.238  -7.241  -1.392  1.00  0.00              
ATOM     79  C   TYR    45      -1.018  -6.374  -1.690  1.00  0.00              
ATOM     80  O   TYR    45      -0.910  -5.768  -2.763  1.00  0.00              
ATOM     81  N   ILE    46      -0.109  -6.301  -0.725  1.00  0.00              
ATOM     82  CA  ILE    46       1.136  -5.568  -0.892  1.00  0.00              
ATOM     83  C   ILE    46       2.222  -6.393  -0.219  1.00  0.00              
ATOM     84  O   ILE    46       1.939  -7.400   0.438  1.00  0.00              
ATOM     85  N   ILE    47       3.463  -5.977  -0.407  1.00  0.00              
ATOM     86  CA  ILE    47       4.591  -6.652   0.205  1.00  0.00              
ATOM     87  C   ILE    47       5.523  -5.518   0.613  1.00  0.00              
ATOM     88  O   ILE    47       5.539  -4.466  -0.022  1.00  0.00              
ATOM     89  N   GLY    48       6.264  -5.711   1.693  1.00  0.00              
ATOM     90  CA  GLY    48       7.187  -4.684   2.150  1.00  0.00              
ATOM     91  C   GLY    48       8.542  -5.328   2.348  1.00  0.00              
ATOM     92  O   GLY    48       8.635  -6.526   2.607  1.00  0.00              
ATOM     93  N   VAL    49       9.591  -4.527   2.214  1.00  0.00              
ATOM     94  CA  VAL    49      10.948  -5.018   2.386  1.00  0.00              
ATOM     95  C   VAL    49      11.875  -3.838   2.606  1.00  0.00              
ATOM     96  O   VAL    49      11.647  -2.749   2.074  1.00  0.00              
ATOM     97  N   HIS    50      12.908  -4.057   3.409  1.00  0.00              
ATOM     98  CA  HIS    50      13.868  -3.012   3.711  1.00  0.00              
ATOM     99  C   HIS    50      14.966  -3.008   2.667  1.00  0.00              
ATOM    100  O   HIS    50      15.498  -4.054   2.305  1.00  0.00              
ATOM    101  N   TYR    51      15.282  -1.824   2.164  1.00  0.00              
ATOM    102  CA  TYR    51      16.347  -1.675   1.190  1.00  0.00              
ATOM    103  C   TYR    51      17.478  -1.023   1.973  1.00  0.00              
ATOM    104  O   TYR    51      17.459   0.187   2.213  1.00  0.00              
ATOM    105  N   SER    52      18.442  -1.839   2.396  1.00  0.00              
ATOM    106  CA  SER    52      19.570  -1.346   3.176  1.00  0.00              
ATOM    107  C   SER    52      20.817  -1.164   2.323  1.00  0.00              
ATOM    108  O   SER    52      21.938  -1.376   2.792  1.00  0.00              
ATOM    109  N   ASP    53      20.618  -0.763   1.070  1.00  0.00              
ATOM    110  CA  ASP    53      21.731  -0.534   0.157  1.00  0.00              
ATOM    111  C   ASP    53      22.475   0.711   0.608  1.00  0.00              
ATOM    112  O   ASP    53      23.056   1.435  -0.195  1.00  0.00              
ATOM    113  N   ASP    54      22.421   0.952   1.913  1.00  0.00              
ATOM    114  CA  ASP    54      23.085   2.079   2.563  1.00  0.00              
ATOM    115  C   ASP    54      22.409   3.447   2.410  1.00  0.00              
ATOM    116  O   ASP    54      23.039   4.463   2.127  1.00  0.00              
ATOM    117  N   ARG    55      21.101   3.401   2.612  1.00  0.00              
ATOM    118  CA  ARG    55      20.179   4.520   2.633  1.00  0.00              
ATOM    119  C   ARG    55      18.947   3.779   3.103  1.00  0.00              
ATOM    120  O   ARG    55      18.053   3.535   2.304  1.00  0.00              
ATOM    121  N   PRO    56      18.912   3.345   4.379  1.00  0.00              
ATOM    122  CA  PRO    56      17.795   2.623   5.004  1.00  0.00              
ATOM    123  C   PRO    56      16.416   3.177   4.606  1.00  0.00              
ATOM    124  O   PRO    56      16.095   4.344   4.876  1.00  0.00              
ATOM    125  N   HIS    57      15.605   2.321   3.991  1.00  0.00              
ATOM    126  CA  HIS    57      14.269   2.690   3.558  1.00  0.00              
ATOM    127  C   HIS    57      13.394   1.460   3.411  1.00  0.00              
ATOM    128  O   HIS    57      13.834   0.403   2.949  1.00  0.00              
ATOM    129  N   LEU    58      12.155   1.606   3.850  1.00  0.00              
ATOM    130  CA  LEU    58      11.188   0.540   3.741  1.00  0.00              
ATOM    131  C   LEU    58      10.386   0.867   2.491  1.00  0.00              
ATOM    132  O   LEU    58       9.884   1.984   2.336  1.00  0.00              
ATOM    133  N   TYR    59      10.287  -0.100   1.589  1.00  0.00              
ATOM    134  CA  TYR    59       9.540   0.095   0.358  1.00  0.00              
ATOM    135  C   TYR    59       8.234  -0.696   0.418  1.00  0.00              
ATOM    136  O   TYR    59       8.191  -1.811   0.949  1.00  0.00              
ATOM    137  N   LYS    60       7.165  -0.093  -0.097  1.00  0.00              
ATOM    138  CA  LYS    60       5.865  -0.747  -0.142  1.00  0.00              
ATOM    139  C   LYS    60       5.604  -1.050  -1.608  1.00  0.00              
ATOM    140  O   LYS    60       5.672  -0.163  -2.449  1.00  0.00              
ATOM    141  N   GLU    64       5.316  -2.307  -1.917  1.00  0.00              
ATOM    142  CA  GLU    64       5.069  -2.695  -3.294  1.00  0.00              
ATOM    143  C   GLU    64       3.745  -3.426  -3.405  1.00  0.00              
ATOM    144  O   GLU    64       3.435  -4.287  -2.584  1.00  0.00              
ATOM    145  N   LEU    65       2.956  -3.075  -4.414  1.00  0.00              
ATOM    146  CA  LEU    65       1.678  -3.738  -4.628  1.00  0.00              
ATOM    147  C   LEU    65       1.998  -5.043  -5.358  1.00  0.00              
ATOM    148  O   LEU    65       2.849  -5.069  -6.251  1.00  0.00              
ATOM    149  N   THR    66       1.354  -6.135  -4.951  1.00  0.00              
ATOM    150  CA  THR    66       1.598  -7.428  -5.574  1.00  0.00              
ATOM    151  C   THR    66       0.700  -7.586  -6.786  1.00  0.00              
ATOM    152  O   THR    66      -0.226  -6.801  -6.983  1.00  0.00              
ATOM    153  N   GLU    67       0.980  -8.597  -7.602  1.00  0.00              
ATOM    154  CA  GLU    67       0.166  -8.852  -8.782  1.00  0.00              
ATOM    155  C   GLU    67      -1.266  -9.152  -8.348  1.00  0.00              
ATOM    156  O   GLU    67      -2.223  -8.715  -8.990  1.00  0.00              
ATOM    157  N   LYS    68      -1.412  -9.877  -7.242  1.00  0.00              
ATOM    158  CA  LYS    68      -2.738 -10.188  -6.719  1.00  0.00              
ATOM    159  C   LYS    68      -3.390  -8.871  -6.279  1.00  0.00              
ATOM    160  O   LYS    68      -4.558  -8.616  -6.571  1.00  0.00              
ATOM    161  N   GLY    69      -2.622  -8.044  -5.573  1.00  0.00              
ATOM    162  CA  GLY    69      -3.139  -6.763  -5.119  1.00  0.00              
ATOM    163  C   GLY    69      -3.678  -5.940  -6.276  1.00  0.00              
ATOM    164  O   GLY    69      -4.769  -5.380  -6.194  1.00  0.00              
ATOM    165  N   GLU    70      -2.919  -5.867  -7.365  1.00  0.00              
ATOM    166  CA  GLU    70      -3.363  -5.110  -8.533  1.00  0.00              
ATOM    167  C   GLU    70      -4.694  -5.631  -9.081  1.00  0.00              
ATOM    168  O   GLU    70      -5.595  -4.849  -9.384  1.00  0.00              
ATOM    169  N   ASN    71      -4.824  -6.948  -9.212  1.00  0.00              
ATOM    170  CA  ASN    71      -6.063  -7.522  -9.735  1.00  0.00              
ATOM    171  C   ASN    71      -7.260  -7.361  -8.801  1.00  0.00              
ATOM    172  O   ASN    71      -8.365  -7.058  -9.254  1.00  0.00              
ATOM    173  N   TYR    72      -7.046  -7.564  -7.506  1.00  0.00              
ATOM    174  CA  TYR    72      -8.122  -7.418  -6.528  1.00  0.00              
ATOM    175  C   TYR    72      -8.622  -5.983  -6.517  1.00  0.00              
ATOM    176  O   TYR    72      -9.825  -5.738  -6.476  1.00  0.00              
ATOM    177  N   LEU    73      -7.689  -5.034  -6.546  1.00  0.00              
ATOM    178  CA  LEU    73      -8.045  -3.621  -6.542  1.00  0.00              
ATOM    179  C   LEU    73      -8.870  -3.291  -7.778  1.00  0.00              
ATOM    180  O   LEU    73      -9.883  -2.598  -7.683  1.00  0.00              
ATOM    181  N   LYS    74      -8.433  -3.784  -8.936  1.00  0.00              
ATOM    182  CA  LYS    74      -9.157  -3.535 -10.180  1.00  0.00              
ATOM    183  C   LYS    74     -10.556  -4.133 -10.119  1.00  0.00              
ATOM    184  O   LYS    74     -11.521  -3.501 -10.549  1.00  0.00              
ATOM    185  N   GLU    75     -10.666  -5.348  -9.583  1.00  0.00              
ATOM    186  CA  GLU    75     -11.969  -6.000  -9.458  1.00  0.00              
ATOM    187  C   GLU    75     -12.873  -5.152  -8.570  1.00  0.00              
ATOM    188  O   GLU    75     -14.022  -4.874  -8.909  1.00  0.00              
ATOM    189  N   THR    85     -12.357  -4.761  -7.413  1.00  0.00              
ATOM    190  CA  THR    85     -13.143  -3.949  -6.500  1.00  0.00              
ATOM    191  C   THR    85     -13.513  -2.602  -7.122  1.00  0.00              
ATOM    192  O   THR    85     -14.645  -2.142  -6.988  1.00  0.00              
ATOM    193  N   ILE    86     -12.562  -1.961  -7.791  1.00  0.00              
ATOM    194  CA  ILE    86     -12.843  -0.666  -8.403  1.00  0.00              
ATOM    195  C   ILE    86     -13.868  -0.782  -9.525  1.00  0.00              
ATOM    196  O   ILE    86     -14.646   0.139  -9.760  1.00  0.00              
END
