
#######################################################
#                                                     #
#                        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   36 (  144),  selected   36 , name T0335AL257_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL257_3-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5           -
LGA    -       -      K       6           -
LGA    -       -      I       7           -
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    K       6      K      18          5.021
LGA    I       7      A      19          3.811
LGA    A       8      G      20          3.621
LGA    R       9      V      21          3.754
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      I      22          5.197
LGA    L      13      T      23          1.666
LGA    A      14      E      24          1.597
LGA    A      15      E      25          1.713
LGA    K      16      E      26          1.964
LGA    A      17      K      27          1.642
LGA    K      18      A      28          1.355
LGA    A      19      E      29          1.082
LGA    G      20      Q      30          0.940
LGA    V      21      Q      31          1.212
LGA    I      22      K      32          0.522
LGA    T      23      L      33          0.867
LGA    E      24      R      34          1.336
LGA    E      25      Q      35          1.461
LGA    E      26      E      36          1.129
LGA    K      27      Y      37          1.193
LGA    A      28      L      38          1.977
LGA    E      29      K      39          1.910
LGA    Q      30      G      40          1.520
LGA    Q      31      -       -           -
LGA    K      32      -       -           -
LGA    L      33      -       -           -
LGA    R      34      -       -           -
LGA    Q      35      -       -           -
LGA    E      36      -       -           -
LGA    Y      37      -       -           -
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     23    2.39     8.70     54.618     0.923

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.740505 * X  +   0.209076 * Y  +  -0.638701 * Z  + -19.926369
  Y_new =  -0.628314 * X  +   0.552627 * Y  +  -0.547563 * Z  + 122.938553
  Z_new =   0.238481 * X  +   0.806778 * Y  +   0.540588 * Z  +  69.979889 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.980449   -2.161143  [ DEG:    56.1756   -123.8244 ]
  Theta =  -0.240801   -2.900791  [ DEG:   -13.7969   -166.2031 ]
  Phi   =  -0.703619    2.437974  [ DEG:   -40.3144    139.6856 ]
 
# 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: T0335AL257_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL257_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   23   2.39    8.70  54.618
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL257_3-D1
REMARK Aligment from pdb entry: 1t11_A
ATOM     13  N   ALA     5     -16.911   2.761   8.414  1.00  0.00              
ATOM     14  CA  ALA     5     -16.141   1.529   8.542  1.00  0.00              
ATOM     15  C   ALA     5     -14.758   1.529   7.909  1.00  0.00              
ATOM     16  O   ALA     5     -13.833   0.880   8.412  1.00  0.00              
ATOM     17  N   LYS     6     -14.612   2.249   6.808  1.00  0.00              
ATOM     18  CA  LYS     6     -13.336   2.323   6.115  1.00  0.00              
ATOM     19  C   LYS     6     -12.258   2.959   6.996  1.00  0.00              
ATOM     20  O   LYS     6     -11.066   2.796   6.737  1.00  0.00              
ATOM     21  N   ILE     7     -12.675   3.651   8.051  1.00  0.00              
ATOM     22  CA  ILE     7     -11.723   4.327   8.926  1.00  0.00              
ATOM     23  C   ILE     7     -11.691   3.890  10.393  1.00  0.00              
ATOM     24  O   ILE     7     -10.927   4.443  11.191  1.00  0.00              
ATOM     25  N   ALA     8     -12.503   2.901  10.762  1.00  0.00              
ATOM     26  CA  ALA     8     -12.542   2.449  12.150  1.00  0.00              
ATOM     27  C   ALA     8     -11.172   2.035  12.694  1.00  0.00              
ATOM     28  O   ALA     8     -10.758   2.500  13.758  1.00  0.00              
ATOM     29  N   ARG     9     -10.479   1.166  11.966  1.00  0.00              
ATOM     30  CA  ARG     9      -9.152   0.693  12.369  1.00  0.00              
ATOM     31  C   ARG     9      -8.159   1.837  12.615  1.00  0.00              
ATOM     32  O   ARG     9      -7.007   1.595  12.978  1.00  0.00              
ATOM     33  N   ILE    10      -8.601   3.075  12.430  1.00  0.00              
ATOM     34  CA  ILE    10      -7.730   4.226  12.618  1.00  0.00              
ATOM     35  C   ILE    10      -8.231   5.166  13.698  1.00  0.00              
ATOM     36  O   ILE    10      -7.628   6.224  13.950  1.00  0.00              
ATOM     37  N   ASN    11      -9.325   4.767  14.340  1.00  0.00              
ATOM     38  CA  ASN    11      -9.917   5.567  15.398  1.00  0.00              
ATOM     39  C   ASN    11      -8.962   5.885  16.531  1.00  0.00              
ATOM     40  O   ASN    11      -8.022   5.134  16.783  1.00  0.00              
ATOM     41  N   GLU    12      -1.279   4.356  13.248  1.00  0.00              
ATOM     42  CA  GLU    12      -1.639   3.159  12.523  1.00  0.00              
ATOM     43  C   GLU    12      -1.925   3.516  11.066  1.00  0.00              
ATOM     44  O   GLU    12      -1.544   2.788  10.145  1.00  0.00              
ATOM     45  N   LEU    13      -2.607   4.641  10.877  1.00  0.00              
ATOM     46  CA  LEU    13      -2.968   5.112   9.557  1.00  0.00              
ATOM     47  C   LEU    13      -1.730   5.518   8.789  1.00  0.00              
ATOM     48  O   LEU    13      -1.558   5.128   7.627  1.00  0.00              
ATOM     49  N   ALA    14      -0.871   6.303   9.432  1.00  0.00              
ATOM     50  CA  ALA    14       0.364   6.744   8.801  1.00  0.00              
ATOM     51  C   ALA    14       1.177   5.522   8.407  1.00  0.00              
ATOM     52  O   ALA    14       1.775   5.476   7.334  1.00  0.00              
ATOM     53  N   ALA    15       1.203   4.528   9.285  1.00  0.00              
ATOM     54  CA  ALA    15       1.944   3.321   9.016  1.00  0.00              
ATOM     55  C   ALA    15       1.387   2.674   7.763  1.00  0.00              
ATOM     56  O   ALA    15       2.138   2.219   6.900  1.00  0.00              
ATOM     57  N   LYS    16       0.059   2.650   7.656  1.00  0.00              
ATOM     58  CA  LYS    16      -0.602   2.037   6.508  1.00  0.00              
ATOM     59  C   LYS    16      -0.261   2.777   5.222  1.00  0.00              
ATOM     60  O   LYS    16       0.010   2.154   4.193  1.00  0.00              
ATOM     61  N   ALA    17      -0.262   4.101   5.276  1.00  0.00              
ATOM     62  CA  ALA    17       0.057   4.862   4.088  1.00  0.00              
ATOM     63  C   ALA    17       1.506   4.662   3.649  1.00  0.00              
ATOM     64  O   ALA    17       1.783   4.554   2.458  1.00  0.00              
ATOM     65  N   LYS    18       2.433   4.615   4.602  1.00  0.00              
ATOM     66  CA  LYS    18       3.834   4.407   4.259  1.00  0.00              
ATOM     67  C   LYS    18       3.950   3.027   3.629  1.00  0.00              
ATOM     68  O   LYS    18       4.538   2.868   2.556  1.00  0.00              
ATOM     69  N   ALA    19       3.370   2.037   4.307  1.00  0.00              
ATOM     70  CA  ALA    19       3.382   0.655   3.839  1.00  0.00              
ATOM     71  C   ALA    19       2.982   0.564   2.381  1.00  0.00              
ATOM     72  O   ALA    19       3.561  -0.216   1.625  1.00  0.00              
ATOM     73  N   GLY    20       1.983   1.352   1.985  1.00  0.00              
ATOM     74  CA  GLY    20       1.516   1.344   0.607  1.00  0.00              
ATOM     75  C   GLY    20       2.462   2.112  -0.288  1.00  0.00              
ATOM     76  O   GLY    20       2.803   1.652  -1.386  1.00  0.00              
ATOM     77  N   VAL    21       2.883   3.279   0.183  1.00  0.00              
ATOM     78  CA  VAL    21       3.784   4.107  -0.597  1.00  0.00              
ATOM     79  C   VAL    21       5.088   3.422  -0.940  1.00  0.00              
ATOM     80  O   VAL    21       5.654   3.691  -1.998  1.00  0.00              
ATOM     81  N   ILE    22       5.579   2.561  -0.046  1.00  0.00              
ATOM     82  CA  ILE    22       6.824   1.842  -0.298  1.00  0.00              
ATOM     83  C   ILE    22       6.664   1.050  -1.584  1.00  0.00              
ATOM     84  O   ILE    22       7.534   1.068  -2.452  1.00  0.00              
ATOM     85  N   THR    23       5.529   0.364  -1.698  1.00  0.00              
ATOM     86  CA  THR    23       5.234  -0.428  -2.870  1.00  0.00              
ATOM     87  C   THR    23       5.150   0.480  -4.080  1.00  0.00              
ATOM     88  O   THR    23       5.838   0.253  -5.070  1.00  0.00              
ATOM     89  N   GLU    24       4.322   1.519  -4.000  1.00  0.00              
ATOM     90  CA  GLU    24       4.179   2.433  -5.126  1.00  0.00              
ATOM     91  C   GLU    24       5.534   2.963  -5.583  1.00  0.00              
ATOM     92  O   GLU    24       5.846   2.977  -6.778  1.00  0.00              
ATOM     93  N   GLU    25       6.350   3.385  -4.626  1.00  0.00              
ATOM     94  CA  GLU    25       7.663   3.905  -4.963  1.00  0.00              
ATOM     95  C   GLU    25       8.465   2.864  -5.723  1.00  0.00              
ATOM     96  O   GLU    25       9.048   3.163  -6.761  1.00  0.00              
ATOM     97  N   GLU    26       8.498   1.634  -5.212  1.00  0.00              
ATOM     98  CA  GLU    26       9.248   0.583  -5.888  1.00  0.00              
ATOM     99  C   GLU    26       8.740   0.443  -7.326  1.00  0.00              
ATOM    100  O   GLU    26       9.521   0.318  -8.267  1.00  0.00              
ATOM    101  N   LYS    27       7.426   0.488  -7.490  1.00  0.00              
ATOM    102  CA  LYS    27       6.837   0.380  -8.816  1.00  0.00              
ATOM    103  C   LYS    27       7.213   1.598  -9.642  1.00  0.00              
ATOM    104  O   LYS    27       7.612   1.469 -10.800  1.00  0.00              
ATOM    105  N   ALA    28       7.090   2.781  -9.050  1.00  0.00              
ATOM    106  CA  ALA    28       7.438   4.008  -9.751  1.00  0.00              
ATOM    107  C   ALA    28       8.896   3.991 -10.221  1.00  0.00              
ATOM    108  O   ALA    28       9.207   4.441 -11.318  1.00  0.00              
ATOM    109  N   GLU    29       9.798   3.473  -9.397  1.00  0.00              
ATOM    110  CA  GLU    29      11.192   3.425  -9.794  1.00  0.00              
ATOM    111  C   GLU    29      11.389   2.425 -10.935  1.00  0.00              
ATOM    112  O   GLU    29      12.164   2.674 -11.862  1.00  0.00              
ATOM    113  N   GLN    30      10.683   1.296 -10.870  1.00  0.00              
ATOM    114  CA  GLN    30      10.787   0.274 -11.905  1.00  0.00              
ATOM    115  C   GLN    30      10.170   0.806 -13.186  1.00  0.00              
ATOM    116  O   GLN    30      10.648   0.517 -14.285  1.00  0.00              
ATOM    117  N   GLN    31       9.114   1.596 -13.044  1.00  0.00              
ATOM    118  CA  GLN    31       8.460   2.176 -14.202  1.00  0.00              
ATOM    119  C   GLN    31       9.291   3.323 -14.744  1.00  0.00              
ATOM    120  O   GLN    31       9.212   3.626 -15.920  1.00  0.00              
ATOM    121  N   LYS    32      10.093   3.959 -13.893  1.00  0.00              
ATOM    122  CA  LYS    32      10.951   5.069 -14.333  1.00  0.00              
ATOM    123  C   LYS    32      11.859   4.605 -15.460  1.00  0.00              
ATOM    124  O   LYS    32      11.927   5.215 -16.524  1.00  0.00              
ATOM    125  N   LEU    33      12.568   3.514 -15.185  1.00  0.00              
ATOM    126  CA  LEU    33      13.503   2.920 -16.120  1.00  0.00              
ATOM    127  C   LEU    33      12.869   2.600 -17.471  1.00  0.00              
ATOM    128  O   LEU    33      13.268   3.156 -18.491  1.00  0.00              
ATOM    129  N   ARG    34      11.878   1.715 -17.486  1.00  0.00              
ATOM    130  CA  ARG    34      11.221   1.329 -18.733  1.00  0.00              
ATOM    131  C   ARG    34      10.863   2.512 -19.624  1.00  0.00              
ATOM    132  O   ARG    34      10.967   2.437 -20.848  1.00  0.00              
ATOM    133  N   GLN    35      10.452   3.616 -19.015  1.00  0.00              
ATOM    134  CA  GLN    35      10.055   4.781 -19.779  1.00  0.00              
ATOM    135  C   GLN    35      11.196   5.680 -20.198  1.00  0.00              
ATOM    136  O   GLN    35      10.986   6.658 -20.918  1.00  0.00              
ATOM    137  N   GLU    36      12.409   5.365 -19.760  1.00  0.00              
ATOM    138  CA  GLU    36      13.549   6.195 -20.137  1.00  0.00              
ATOM    139  C   GLU    36      13.686   6.137 -21.655  1.00  0.00              
ATOM    140  O   GLU    36      13.437   5.105 -22.280  1.00  0.00              
ATOM    141  N   TYR    37      14.068   7.254 -22.253  1.00  0.00              
ATOM    142  CA  TYR    37      14.240   7.289 -23.696  1.00  0.00              
ATOM    143  C   TYR    37      13.039   6.739 -24.454  1.00  0.00              
ATOM    144  O   TYR    37      13.182   5.852 -25.299  1.00  0.00              
ATOM    145  N   LEU    38      11.857   7.242 -24.113  1.00  0.00              
ATOM    146  CA  LEU    38      10.624   6.887 -24.806  1.00  0.00              
ATOM    147  C   LEU    38      10.047   8.240 -25.201  1.00  0.00              
ATOM    148  O   LEU    38       9.140   8.743 -24.548  1.00  0.00              
ATOM    149  N   LYS    39      10.598   8.836 -26.251  1.00  0.00              
ATOM    150  CA  LYS    39      10.139  10.140 -26.709  1.00  0.00              
ATOM    151  C   LYS    39       8.615  10.170 -26.819  1.00  0.00              
ATOM    152  O   LYS    39       7.986   9.173 -27.164  1.00  0.00              
ATOM    153  N   GLY    40       8.026  11.320 -26.510  1.00  0.00              
ATOM    154  CA  GLY    40       6.579  11.435 -26.554  1.00  0.00              
ATOM    155  C   GLY    40       6.078  11.664 -25.144  1.00  0.00              
ATOM    156  O   GLY    40       5.090  12.359 -24.915  1.00  0.00              
END
