
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0353AL243_5
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353AL243_5.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    Q       2      I       3          1.296
LGA    I       3      H       4          1.212
LGA    H       4      V       5          1.267
LGA    V       5      Y       6          1.598
LGA    Y       6      D       7          1.797
LGA    V      10      T       8          0.953
LGA    K      11      Y       9          1.949
LGA    A      12      V      10          1.653
LGA    K      13      K      11          1.969
LGA    D      14      A      12          1.712
LGA    -       -      K      13           -
LGA    -       -      D      14           -
LGA    -       -      G      15           -
LGA    -       -      H      16           -
LGA    G      15      V      17          1.123
LGA    H      16      M      18          1.076
LGA    V      17      H      19          1.899
LGA    M      18      F      20          1.840
LGA    H      19      D      21          1.506
LGA    F      20      V      22          0.715
LGA    D      21      F      23          0.929
LGA    V      22      T      24          1.445
LGA    F      23      D      25          2.656
LGA    T      24      V      26          5.326
LGA    D      25      R      27          3.515
LGA    V      26      -       -           -
LGA    K      31      D      28          2.280
LGA    A      32      D      29          2.275
LGA    I      33      K      30          2.887
LGA    E      34      K      31          1.930
LGA    F      35      A      32          1.526
LGA    A      36      I      33          1.148
LGA    K      37      E      34          1.313
LGA    Q      38      F      35          1.259
LGA    W      39      A      36          0.434
LGA    L      40      K      37          0.814
LGA    S      41      Q      38          1.465
LGA    S      42      W      39          1.104
LGA    I      43      L      40          1.267
LGA    G      44      S      41          3.108
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      E      45           -
LGA    -       -      E      46           -
LGA    E      45      G      47          5.097
LGA    T      49      A      48           -
LGA    V      50      -       -           -
LGA    T      51      -       -           -
LGA    S      52      T      49           #
LGA    -       -      V      50           -
LGA    -       -      T      51           -
LGA    -       -      S      52           -
LGA    -       -      E      53           -
LGA    -       -      E      54           -
LGA    -       -      C      55           -
LGA    -       -      R      56           -
LGA    -       -      F      57           -
LGA    -       -      C      58           -
LGA    -       -      H      59           -
LGA    -       -      S      60           -
LGA    -       -      Q      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    -       -      I      78           -
LGA    -       -      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -
LGA    -       -      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   85    5.0     36    2.10     2.78     37.371     1.637

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.822859 * X  +  -0.555128 * Y  +  -0.121392 * Z  +  -4.383746
  Y_new =   0.075624 * X  +   0.104744 * Y  +  -0.991620 * Z  +   5.097648
  Z_new =   0.563191 * X  +  -0.825143 * Y  +  -0.044208 * Z  +  -0.264480 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.624322    1.517271  [ DEG:   -93.0668     86.9332 ]
  Theta =  -0.598243   -2.543350  [ DEG:   -34.2768   -145.7232 ]
  Phi   =   3.049946   -0.091647  [ DEG:   174.7490     -5.2510 ]
 
# 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: T0353AL243_5                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353AL243_5.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   85   5.0   36   2.10    2.78  37.371
REMARK  ---------------------------------------------------------- 
MOLECULE T0353AL243_5
REMARK Aligment from pdb entry: 1u4aA
ATOM      1  N   GLN     2      10.210   2.747  -6.044  1.00  0.00              
ATOM      2  CA  GLN     2       8.853   2.502  -5.563  1.00  0.00              
ATOM      3  C   GLN     2       8.522   3.414  -4.384  1.00  0.00              
ATOM      4  O   GLN     2       9.394   3.740  -3.576  1.00  0.00              
ATOM      5  N   ILE     3       7.258   3.823  -4.292  1.00  0.00              
ATOM      6  CA  ILE     3       6.816   4.698  -3.211  1.00  0.00              
ATOM      7  C   ILE     3       6.263   3.892  -2.038  1.00  0.00              
ATOM      8  O   ILE     3       5.367   3.061  -2.204  1.00  0.00              
ATOM      9  N   HIS     4       6.815   4.141  -0.853  1.00  0.00              
ATOM     10  CA  HIS     4       6.396   3.444   0.359  1.00  0.00              
ATOM     11  C   HIS     4       5.333   4.246   1.108  1.00  0.00              
ATOM     12  O   HIS     4       5.653   5.067   1.973  1.00  0.00              
ATOM     13  N   VAL     5       4.068   4.007   0.771  1.00  0.00              
ATOM     14  CA  VAL     5       2.957   4.709   1.409  1.00  0.00              
ATOM     15  C   VAL     5       2.461   3.956   2.639  1.00  0.00              
ATOM     16  O   VAL     5       2.083   2.785   2.552  1.00  0.00              
ATOM     17  N   TYR     6       2.457   4.638   3.782  1.00  0.00              
ATOM     18  CA  TYR     6       1.997   4.045   5.035  1.00  0.00              
ATOM     19  C   TYR     6       0.614   4.583   5.398  1.00  0.00              
ATOM     20  O   TYR     6       0.493   5.635   6.033  1.00  0.00              
ATOM     21  N   VAL    10      -0.429   3.861   4.984  1.00  0.00              
ATOM     22  CA  VAL    10      -1.806   4.270   5.256  1.00  0.00              
ATOM     23  C   VAL    10      -2.266   3.782   6.631  1.00  0.00              
ATOM     24  O   VAL    10      -2.199   2.586   6.930  1.00  0.00              
ATOM     25  N   LYS    11      -2.736   4.715   7.458  1.00  0.00              
ATOM     26  CA  LYS    11      -3.212   4.392   8.798  1.00  0.00              
ATOM     27  C   LYS    11      -4.737   4.448   8.863  1.00  0.00              
ATOM     28  O   LYS    11      -5.339   5.504   8.656  1.00  0.00              
ATOM     29  N   ALA    12      -5.354   3.303   9.149  1.00  0.00              
ATOM     30  CA  ALA    12      -6.802   3.232   9.237  1.00  0.00              
ATOM     31  C   ALA    12      -7.328   3.678  10.588  1.00  0.00              
ATOM     32  O   ALA    12      -6.654   3.518  11.608  1.00  0.00              
ATOM     33  N   LYS    13      -8.539   4.236  10.593  1.00  0.00              
ATOM     34  CA  LYS    13      -9.171   4.712  11.827  1.00  0.00              
ATOM     35  C   LYS    13      -9.361   3.582  12.850  1.00  0.00              
ATOM     36  O   LYS    13      -9.535   3.847  14.041  1.00  0.00              
ATOM     37  N   ASP    14      -9.331   2.329  12.387  1.00  0.00              
ATOM     38  CA  ASP    14      -9.505   1.178  13.275  1.00  0.00              
ATOM     39  C   ASP    14      -8.162   0.685  13.834  1.00  0.00              
ATOM     40  O   ASP    14      -7.989  -0.510  14.085  1.00  0.00              
ATOM     41  N   GLY    15      -7.214   1.609  14.030  1.00  0.00              
ATOM     42  CA  GLY    15      -5.907   1.244  14.560  1.00  0.00              
ATOM     43  C   GLY    15      -5.188   0.215  13.701  1.00  0.00              
ATOM     44  O   GLY    15      -4.572  -0.715  14.224  1.00  0.00              
ATOM     45  N   HIS    16      -5.274   0.378  12.380  1.00  0.00              
ATOM     46  CA  HIS    16      -4.634  -0.545  11.444  1.00  0.00              
ATOM     47  C   HIS    16      -3.544   0.158  10.637  1.00  0.00              
ATOM     48  O   HIS    16      -3.790   1.199  10.022  1.00  0.00              
ATOM     49  N   VAL    17      -2.340  -0.419  10.640  1.00  0.00              
ATOM     50  CA  VAL    17      -1.208   0.149   9.903  1.00  0.00              
ATOM     51  C   VAL    17      -0.729  -0.805   8.809  1.00  0.00              
ATOM     52  O   VAL    17      -0.249  -1.905   9.096  1.00  0.00              
ATOM     53  N   MET    18      -0.869  -0.377   7.554  1.00  0.00              
ATOM     54  CA  MET    18      -0.456  -1.190   6.411  1.00  0.00              
ATOM     55  C   MET    18       0.276  -0.347   5.366  1.00  0.00              
ATOM     56  O   MET    18      -0.173   0.746   5.011  1.00  0.00              
ATOM     57  N   HIS    19       1.402  -0.868   4.874  1.00  0.00              
ATOM     58  CA  HIS    19       2.200  -0.173   3.862  1.00  0.00              
ATOM     59  C   HIS    19       2.031  -0.820   2.486  1.00  0.00              
ATOM     60  O   HIS    19       1.713  -2.007   2.384  1.00  0.00              
ATOM     61  N   PHE    20       2.249  -0.030   1.432  1.00  0.00              
ATOM     62  CA  PHE    20       2.126  -0.521   0.059  1.00  0.00              
ATOM     63  C   PHE    20       3.292  -0.036  -0.804  1.00  0.00              
ATOM     64  O   PHE    20       3.802   1.069  -0.610  1.00  0.00              
ATOM     65  N   ASP    21       3.706  -0.874  -1.758  1.00  0.00              
ATOM     66  CA  ASP    21       4.812  -0.540  -2.655  1.00  0.00              
ATOM     67  C   ASP    21       4.350  -0.510  -4.112  1.00  0.00              
ATOM     68  O   ASP    21       4.015  -1.550  -4.686  1.00  0.00              
ATOM     69  N   VAL    22       4.342   0.685  -4.704  1.00  0.00              
ATOM     70  CA  VAL    22       3.925   0.858  -6.097  1.00  0.00              
ATOM     71  C   VAL    22       4.724   1.971  -6.779  1.00  0.00              
ATOM     72  O   VAL    22       5.572   2.611  -6.154  1.00  0.00              
ATOM     73  N   PHE    23       4.442   2.200  -8.063  1.00  0.00              
ATOM     74  CA  PHE    23       5.127   3.242  -8.827  1.00  0.00              
ATOM     75  C   PHE    23       4.416   4.586  -8.669  1.00  0.00              
ATOM     76  O   PHE    23       3.240   4.636  -8.305  1.00  0.00              
ATOM     77  N   THR    24       5.134   5.673  -8.953  1.00  0.00              
ATOM     78  CA  THR    24       4.567   7.020  -8.849  1.00  0.00              
ATOM     79  C   THR    24       4.098   7.535 -10.215  1.00  0.00              
ATOM     80  O   THR    24       4.140   8.739 -10.484  1.00  0.00              
ATOM     81  N   ASP    25       3.646   6.619 -11.075  1.00  0.00              
ATOM     82  CA  ASP    25       3.166   6.978 -12.407  1.00  0.00              
ATOM     83  C   ASP    25       1.774   6.387 -12.671  1.00  0.00              
ATOM     84  O   ASP    25       1.434   6.060 -13.811  1.00  0.00              
ATOM     85  N   VAL    26       0.970   6.255 -11.613  1.00  0.00              
ATOM     86  CA  VAL    26      -0.383   5.706 -11.732  1.00  0.00              
ATOM     87  C   VAL    26      -1.320   6.337 -10.699  1.00  0.00              
ATOM     88  O   VAL    26      -0.865   6.860  -9.680  1.00  0.00              
ATOM     89  N   LYS    31      -2.646   6.300 -10.951  1.00  0.00              
ATOM     90  CA  LYS    31      -3.643   6.877 -10.037  1.00  0.00              
ATOM     91  C   LYS    31      -3.792   6.073  -8.746  1.00  0.00              
ATOM     92  O   LYS    31      -3.371   4.916  -8.672  1.00  0.00              
ATOM     93  N   ALA    32      -4.400   6.693  -7.732  1.00  0.00              
ATOM     94  CA  ALA    32      -4.610   6.035  -6.440  1.00  0.00              
ATOM     95  C   ALA    32      -5.584   4.857  -6.553  1.00  0.00              
ATOM     96  O   ALA    32      -5.689   4.053  -5.631  1.00  0.00              
ATOM     97  N   ILE    33      -6.290   4.760  -7.683  1.00  0.00              
ATOM     98  CA  ILE    33      -7.248   3.678  -7.908  1.00  0.00              
ATOM     99  C   ILE    33      -6.614   2.310  -7.639  1.00  0.00              
ATOM    100  O   ILE    33      -7.283   1.394  -7.166  1.00  0.00              
ATOM    101  N   GLU    34      -5.319   2.183  -7.939  1.00  0.00              
ATOM    102  CA  GLU    34      -4.598   0.928  -7.721  1.00  0.00              
ATOM    103  C   GLU    34      -4.356   0.687  -6.230  1.00  0.00              
ATOM    104  O   GLU    34      -4.756  -0.345  -5.691  1.00  0.00              
ATOM    105  N   PHE    35      -3.705   1.647  -5.571  1.00  0.00              
ATOM    106  CA  PHE    35      -3.413   1.540  -4.139  1.00  0.00              
ATOM    107  C   PHE    35      -4.702   1.459  -3.319  1.00  0.00              
ATOM    108  O   PHE    35      -4.825   0.614  -2.431  1.00  0.00              
ATOM    109  N   ALA    36      -5.656   2.339  -3.624  1.00  0.00              
ATOM    110  CA  ALA    36      -6.934   2.367  -2.914  1.00  0.00              
ATOM    111  C   ALA    36      -7.661   1.029  -3.037  1.00  0.00              
ATOM    112  O   ALA    36      -8.119   0.473  -2.038  1.00  0.00              
ATOM    113  N   LYS    37      -7.759   0.512  -4.263  1.00  0.00              
ATOM    114  CA  LYS    37      -8.430  -0.766  -4.501  1.00  0.00              
ATOM    115  C   LYS    37      -7.721  -1.899  -3.764  1.00  0.00              
ATOM    116  O   LYS    37      -8.343  -2.628  -2.993  1.00  0.00              
ATOM    117  N   GLN    38      -6.415  -2.036  -4.002  1.00  0.00              
ATOM    118  CA  GLN    38      -5.617  -3.080  -3.355  1.00  0.00              
ATOM    119  C   GLN    38      -5.705  -2.987  -1.830  1.00  0.00              
ATOM    120  O   GLN    38      -5.690  -4.004  -1.139  1.00  0.00              
ATOM    121  N   TRP    39      -5.797  -1.761  -1.313  1.00  0.00              
ATOM    122  CA  TRP    39      -5.892  -1.536   0.127  1.00  0.00              
ATOM    123  C   TRP    39      -7.285  -1.895   0.647  1.00  0.00              
ATOM    124  O   TRP    39      -7.421  -2.699   1.567  1.00  0.00              
ATOM    125  N   LEU    40      -8.316  -1.292   0.049  1.00  0.00              
ATOM    126  CA  LEU    40      -9.703  -1.548   0.450  1.00  0.00              
ATOM    127  C   LEU    40     -10.065  -3.026   0.288  1.00  0.00              
ATOM    128  O   LEU    40     -10.739  -3.606   1.144  1.00  0.00              
ATOM    129  N   SER    41      -9.613  -3.624  -0.814  1.00  0.00              
ATOM    130  CA  SER    41      -9.883  -5.033  -1.100  1.00  0.00              
ATOM    131  C   SER    41      -9.144  -5.950  -0.122  1.00  0.00              
ATOM    132  O   SER    41      -9.669  -6.990   0.281  1.00  0.00              
ATOM    133  N   SER    42      -7.925  -5.561   0.250  1.00  0.00              
ATOM    134  CA  SER    42      -7.116  -6.348   1.178  1.00  0.00              
ATOM    135  C   SER    42      -7.578  -6.160   2.625  1.00  0.00              
ATOM    136  O   SER    42      -7.605  -7.116   3.400  1.00  0.00              
ATOM    137  N   ILE    43      -7.934  -4.924   2.985  1.00  0.00              
ATOM    138  CA  ILE    43      -8.385  -4.616   4.342  1.00  0.00              
ATOM    139  C   ILE    43      -9.727  -5.283   4.647  1.00  0.00              
ATOM    140  O   ILE    43      -9.810  -6.149   5.519  1.00  0.00              
ATOM    141  N   GLY    44     -10.776  -4.871   3.931  1.00  0.00              
ATOM    142  CA  GLY    44     -12.095  -5.438   4.150  1.00  0.00              
ATOM    143  C   GLY    44     -13.187  -4.392   4.050  1.00  0.00              
ATOM    144  O   GLY    44     -14.071  -4.323   4.906  1.00  0.00              
ATOM    145  N   GLU    45     -13.119  -3.576   3.000  1.00  0.00              
ATOM    146  CA  GLU    45     -14.099  -2.522   2.777  1.00  0.00              
ATOM    147  C   GLU    45     -14.769  -2.702   1.416  1.00  0.00              
ATOM    148  O   GLU    45     -14.721  -3.787   0.830  1.00  0.00              
ATOM    149  N   THR    49     -15.387  -1.636   0.915  1.00  0.00              
ATOM    150  CA  THR    49     -16.064  -1.675  -0.379  1.00  0.00              
ATOM    151  C   THR    49     -15.514  -0.601  -1.314  1.00  0.00              
ATOM    152  O   THR    49     -14.803   0.308  -0.882  1.00  0.00              
ATOM    153  N   VAL    50     -15.853  -0.707  -2.597  1.00  0.00              
ATOM    154  CA  VAL    50     -15.397   0.261  -3.592  1.00  0.00              
ATOM    155  C   VAL    50     -16.450   1.345  -3.839  1.00  0.00              
ATOM    156  O   VAL    50     -16.475   1.965  -4.905  1.00  0.00              
ATOM    157  N   THR    51     -17.318   1.571  -2.850  1.00  0.00              
ATOM    158  CA  THR    51     -18.367   2.582  -2.962  1.00  0.00              
ATOM    159  C   THR    51     -18.496   3.403  -1.672  1.00  0.00              
ATOM    160  O   THR    51     -19.467   4.144  -1.499  1.00  0.00              
ATOM    161  N   SER    52     -17.512   3.284  -0.772  1.00  0.00              
ATOM    162  CA  SER    52     -17.523   4.029   0.478  1.00  0.00              
ATOM    163  C   SER    52     -16.120   4.082   1.075  1.00  0.00              
ATOM    164  O   SER    52     -15.799   3.350   2.015  1.00  0.00              
END
