
#######################################################
#                                                     #
#                        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   52 (  208),  selected   52 , name T0311AL381_3
# Molecule2: number of CA atoms   87 (  672),  selected   87 , name T0311.pdb
# PARAMETERS: T0311AL381_3.T0311.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R       8           -
LGA    -       -      P       9           -
LGA    -       -      G      10           -
LGA    -       -      D      11           -
LGA    -       -      I      12           -
LGA    I      13      I      13          3.746
LGA    Q      14      Q      14          3.236
LGA    E      15      E      15          2.690
LGA    S      16      S      16          2.246
LGA    L      17      L      17          2.009
LGA    D      18      D      18          3.634
LGA    E      19      E      19          3.407
LGA    L      20      L      20          2.161
LGA    N      21      N      21          3.089
LGA    V      22      V      22          1.431
LGA    S      23      S      23          1.626
LGA    L      24      L      24          1.457
LGA    R      25      R      25          0.819
LGA    E      26      E      26          0.891
LGA    F      27      F      27          1.329
LGA    A      28      A      28          0.809
LGA    R      29      R      29          0.788
LGA    A      30      A      30          1.480
LGA    M      31      M      31          2.264
LGA    E      32      E      32          2.110
LGA    I      33      I      33          1.802
LGA    A      34      A      34          1.783
LGA    P      35      P      35          1.441
LGA    S      36      S      36          1.156
LGA    T      37      T      37          0.758
LGA    A      38      A      38          0.610
LGA    S      39      S      39          0.960
LGA    R      40      R      40          0.779
LGA    L      41      L      41          1.431
LGA    L      42      L      42          1.814
LGA    T      43      T      43          1.749
LGA    G      44      G      44          2.112
LGA    K      45      K      45          1.747
LGA    A      46      A      46          2.123
LGA    A      47      A      47          2.443
LGA    L      48      L      48          2.168
LGA    T      49      T      49          1.602
LGA    P      50      P      50          0.958
LGA    E      51      E      51          1.338
LGA    M      52      M      52          1.406
LGA    A      53      A      53          1.347
LGA    I      54      I      54          0.946
LGA    K      55      K      55          0.682
LGA    L      56      L      56          1.182
LGA    S      57      S      57          2.188
LGA    V      58      V      58          2.062
LGA    V      59      V      59          1.735
LGA    I      60      I      60          1.671
LGA    G      61      G      61          1.596
LGA    S      62      S      62          2.062
LGA    S      63      S      63          2.181
LGA    P      64      P      64          2.686
LGA    -       -      Q      65           -
LGA    -       -      M      66           -
LGA    -       -      W      67           -
LGA    -       -      L      68           -
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      Q      71           -
LGA    -       -      N      72           -
LGA    -       -      A      73           -
LGA    -       -      W      74           -
LGA    -       -      S      75           -
LGA    -       -      L      76           -
LGA    -       -      A      77           -
LGA    -       -      E      78           -
LGA    -       -      A      79           -
LGA    -       -      E      80           -
LGA    -       -      K      81           -
LGA    -       -      T      82           -
LGA    -       -      V      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      S      86           -
LGA    -       -      R      87           -
LGA    -       -      L      88           -
LGA    -       -      R      89           -
LGA    -       -      R      90           -
LGA    -       -      L      91           -
LGA    -       -      V      92           -
LGA    -       -      T      93           -
LGA    -       -      Q      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52   87    5.0     52    1.92   100.00     53.962     2.574

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.779820 * X  +  -0.576020 * Y  +   0.245116 * Z  +  37.045494
  Y_new =   0.576921 * X  +  -0.813279 * Y  +  -0.075760 * Z  + -23.476233
  Z_new =   0.242987 * X  +   0.082333 * Y  +   0.966529 * Z  + -11.363379 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.084979   -3.056613  [ DEG:     4.8690   -175.1310 ]
  Theta =  -0.245444   -2.896148  [ DEG:   -14.0629   -165.9371 ]
  Phi   =   2.504643   -0.636950  [ DEG:   143.5055    -36.4945 ]
 
# 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: T0311AL381_3                                  
REMARK     2: T0311.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311AL381_3.T0311.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   87   5.0   52   1.92  100.00  53.962
REMARK  ---------------------------------------------------------- 
MOLECULE T0311AL381_3
REMARK Aligment from pdb entry: 1lliA
ATOM      1  N   ILE    13      34.355   5.494  14.822  1.00  0.00              
ATOM      2  CA  ILE    13      33.225   6.310  14.425  1.00  0.00              
ATOM      3  C   ILE    13      31.966   5.748  15.013  1.00  0.00              
ATOM      4  O   ILE    13      31.125   6.511  15.476  1.00  0.00              
ATOM      5  N   GLN    14      31.616   3.960  17.869  1.00  0.00              
ATOM      6  CA  GLN    14      31.630   4.330  19.265  1.00  0.00              
ATOM      7  C   GLN    14      31.333   5.816  19.414  1.00  0.00              
ATOM      8  O   GLN    14      30.500   6.133  20.245  1.00  0.00              
ATOM      9  N   GLU    15      31.832   6.786  18.655  1.00  0.00              
ATOM     10  CA  GLU    15      31.391   8.170  18.782  1.00  0.00              
ATOM     11  C   GLU    15      29.916   8.402  18.410  1.00  0.00              
ATOM     12  O   GLU    15      29.243   9.282  18.966  1.00  0.00              
ATOM     13  N   SER    16      29.344   7.668  17.470  1.00  0.00              
ATOM     14  CA  SER    16      28.043   8.030  16.971  1.00  0.00              
ATOM     15  C   SER    16      26.968   7.116  17.408  1.00  0.00              
ATOM     16  O   SER    16      25.814   7.439  17.132  1.00  0.00              
ATOM     17  N   LEU    17      27.272   6.043  18.135  1.00  0.00              
ATOM     18  CA  LEU    17      26.238   5.062  18.409  1.00  0.00              
ATOM     19  C   LEU    17      25.071   5.565  19.225  1.00  0.00              
ATOM     20  O   LEU    17      23.926   5.213  18.929  1.00  0.00              
ATOM     21  N   ASP    18      25.299   6.422  20.222  1.00  0.00              
ATOM     22  CA  ASP    18      24.175   6.889  21.014  1.00  0.00              
ATOM     23  C   ASP    18      23.391   7.914  20.219  1.00  0.00              
ATOM     24  O   ASP    18      22.211   7.660  20.001  1.00  0.00              
ATOM     25  N   GLU    19      23.943   8.973  19.646  1.00  0.00              
ATOM     26  CA  GLU    19      23.161   9.875  18.820  1.00  0.00              
ATOM     27  C   GLU    19      22.412   9.182  17.703  1.00  0.00              
ATOM     28  O   GLU    19      21.272   9.560  17.443  1.00  0.00              
ATOM     29  N   LEU    20      22.969   8.164  17.045  1.00  0.00              
ATOM     30  CA  LEU    20      22.241   7.497  15.978  1.00  0.00              
ATOM     31  C   LEU    20      21.418   6.301  16.441  1.00  0.00              
ATOM     32  O   LEU    20      20.752   5.661  15.622  1.00  0.00              
ATOM     33  N   ASN    21      21.422   5.972  17.734  1.00  0.00              
ATOM     34  CA  ASN    21      20.644   4.855  18.276  1.00  0.00              
ATOM     35  C   ASN    21      21.028   3.487  17.702  1.00  0.00              
ATOM     36  O   ASN    21      20.178   2.615  17.407  1.00  0.00              
ATOM     37  N   VAL    22      22.338   3.275  17.550  1.00  0.00              
ATOM     38  CA  VAL    22      22.810   2.043  16.907  1.00  0.00              
ATOM     39  C   VAL    22      23.339   1.015  17.882  1.00  0.00              
ATOM     40  O   VAL    22      23.649   1.314  19.044  1.00  0.00              
ATOM     41  N   SER    23      23.433  -0.222  17.433  1.00  0.00              
ATOM     42  CA  SER    23      24.201  -1.224  18.148  1.00  0.00              
ATOM     43  C   SER    23      24.694  -2.139  17.022  1.00  0.00              
ATOM     44  O   SER    23      24.250  -1.962  15.867  1.00  0.00              
ATOM     45  N   LEU    24      25.593  -3.101  17.310  1.00  0.00              
ATOM     46  CA  LEU    24      26.045  -4.108  16.334  1.00  0.00              
ATOM     47  C   LEU    24      24.888  -4.930  15.811  1.00  0.00              
ATOM     48  O   LEU    24      24.849  -5.161  14.599  1.00  0.00              
ATOM     49  N   ARG    25      23.896  -5.382  16.600  1.00  0.00              
ATOM     50  CA  ARG    25      22.747  -6.068  16.036  1.00  0.00              
ATOM     51  C   ARG    25      21.845  -5.203  15.120  1.00  0.00              
ATOM     52  O   ARG    25      21.366  -5.680  14.094  1.00  0.00              
ATOM     53  N   GLU    26      21.542  -3.933  15.317  1.00  0.00              
ATOM     54  CA  GLU    26      20.720  -3.175  14.379  1.00  0.00              
ATOM     55  C   GLU    26      21.453  -2.907  13.075  1.00  0.00              
ATOM     56  O   GLU    26      20.855  -2.997  12.001  1.00  0.00              
ATOM     57  N   PHE    27      22.740  -2.551  13.127  1.00  0.00              
ATOM     58  CA  PHE    27      23.572  -2.469  11.943  1.00  0.00              
ATOM     59  C   PHE    27      23.610  -3.809  11.198  1.00  0.00              
ATOM     60  O   PHE    27      23.576  -3.856   9.963  1.00  0.00              
ATOM     61  N   ALA    28      23.733  -4.925  11.921  1.00  0.00              
ATOM     62  CA  ALA    28      23.679  -6.234  11.340  1.00  0.00              
ATOM     63  C   ALA    28      22.431  -6.319  10.498  1.00  0.00              
ATOM     64  O   ALA    28      22.504  -6.574   9.297  1.00  0.00              
ATOM     65  N   ARG    29      21.270  -6.010  11.077  1.00  0.00              
ATOM     66  CA  ARG    29      19.995  -6.066  10.364  1.00  0.00              
ATOM     67  C   ARG    29      19.997  -5.185   9.126  1.00  0.00              
ATOM     68  O   ARG    29      19.691  -5.686   8.052  1.00  0.00              
ATOM     69  N   ALA    30      20.403  -3.917   9.162  1.00  0.00              
ATOM     70  CA  ALA    30      20.424  -3.063   7.974  1.00  0.00              
ATOM     71  C   ALA    30      21.325  -3.586   6.858  1.00  0.00              
ATOM     72  O   ALA    30      21.111  -3.275   5.688  1.00  0.00              
ATOM     73  N   MET    31      22.383  -4.351   7.124  1.00  0.00              
ATOM     74  CA  MET    31      23.210  -4.898   6.055  1.00  0.00              
ATOM     75  C   MET    31      22.813  -6.353   5.799  1.00  0.00              
ATOM     76  O   MET    31      23.547  -7.082   5.118  1.00  0.00              
ATOM     77  N   GLU    32      21.700  -6.797   6.404  1.00  0.00              
ATOM     78  CA  GLU    32      21.143  -8.132   6.256  1.00  0.00              
ATOM     79  C   GLU    32      22.126  -9.214   6.654  1.00  0.00              
ATOM     80  O   GLU    32      22.177 -10.284   6.044  1.00  0.00              
ATOM     81  N   ILE    33      22.865  -8.957   7.716  1.00  0.00              
ATOM     82  CA  ILE    33      23.956  -9.788   8.130  1.00  0.00              
ATOM     83  C   ILE    33      23.717 -10.045   9.619  1.00  0.00              
ATOM     84  O   ILE    33      22.764  -9.506  10.191  1.00  0.00              
ATOM     85  N   ALA    34      24.527 -10.846  10.319  1.00  0.00              
ATOM     86  CA  ALA    34      24.370 -11.108  11.747  1.00  0.00              
ATOM     87  C   ALA    34      25.303 -10.200  12.562  1.00  0.00              
ATOM     88  O   ALA    34      26.270  -9.616  12.031  1.00  0.00              
ATOM     89  N   PRO    35      25.050 -10.103  13.871  1.00  0.00              
ATOM     90  CA  PRO    35      25.870  -9.289  14.721  1.00  0.00              
ATOM     91  C   PRO    35      27.286  -9.789  14.666  1.00  0.00              
ATOM     92  O   PRO    35      28.152  -8.924  14.684  1.00  0.00              
ATOM     93  N   SER    36      27.587 -11.097  14.632  1.00  0.00              
ATOM     94  CA  SER    36      28.981 -11.542  14.636  1.00  0.00              
ATOM     95  C   SER    36      29.671 -11.200  13.336  1.00  0.00              
ATOM     96  O   SER    36      30.885 -10.971  13.388  1.00  0.00              
ATOM     97  N   THR    37      28.887 -11.058  12.245  1.00  0.00              
ATOM     98  CA  THR    37      29.382 -10.603  10.952  1.00  0.00              
ATOM     99  C   THR    37      29.858  -9.178  11.059  1.00  0.00              
ATOM    100  O   THR    37      30.923  -8.831  10.577  1.00  0.00              
ATOM    101  N   ALA    38      29.124  -8.300  11.737  1.00  0.00              
ATOM    102  CA  ALA    38      29.523  -6.919  12.006  1.00  0.00              
ATOM    103  C   ALA    38      30.695  -6.822  12.962  1.00  0.00              
ATOM    104  O   ALA    38      31.629  -6.027  12.754  1.00  0.00              
ATOM    105  N   SER    39      30.702  -7.586  14.032  1.00  0.00              
ATOM    106  CA  SER    39      31.833  -7.540  14.952  1.00  0.00              
ATOM    107  C   SER    39      33.155  -7.870  14.253  1.00  0.00              
ATOM    108  O   SER    39      34.196  -7.222  14.450  1.00  0.00              
ATOM    109  N   ARG    40      33.120  -8.865  13.366  1.00  0.00              
ATOM    110  CA  ARG    40      34.279  -9.261  12.574  1.00  0.00              
ATOM    111  C   ARG    40      34.755  -8.119  11.709  1.00  0.00              
ATOM    112  O   ARG    40      35.961  -7.895  11.641  1.00  0.00              
ATOM    113  N   LEU    41      33.870  -7.318  11.085  1.00  0.00              
ATOM    114  CA  LEU    41      34.309  -6.172  10.309  1.00  0.00              
ATOM    115  C   LEU    41      34.891  -5.125  11.253  1.00  0.00              
ATOM    116  O   LEU    41      36.045  -4.715  11.093  1.00  0.00              
ATOM    117  N   LEU    42      34.194  -4.750  12.333  1.00  0.00              
ATOM    118  CA  LEU    42      34.691  -3.719  13.266  1.00  0.00              
ATOM    119  C   LEU    42      36.003  -4.002  13.928  1.00  0.00              
ATOM    120  O   LEU    42      36.811  -3.122  14.259  1.00  0.00              
ATOM    121  N   THR    43      36.149  -5.298  14.150  1.00  0.00              
ATOM    122  CA  THR    43      37.342  -5.777  14.826  1.00  0.00              
ATOM    123  C   THR    43      38.480  -6.268  13.945  1.00  0.00              
ATOM    124  O   THR    43      39.362  -6.953  14.444  1.00  0.00              
ATOM    125  N   GLY    44      38.526  -5.948  12.653  1.00  0.00              
ATOM    126  CA  GLY    44      39.669  -6.309  11.832  1.00  0.00              
ATOM    127  C   GLY    44      39.892  -7.822  11.718  1.00  0.00              
ATOM    128  O   GLY    44      41.037  -8.273  11.646  1.00  0.00              
ATOM    129  N   LYS    45      38.839  -8.633  11.692  1.00  0.00              
ATOM    130  CA  LYS    45      38.939 -10.072  11.535  1.00  0.00              
ATOM    131  C   LYS    45      38.616 -10.346  10.068  1.00  0.00              
ATOM    132  O   LYS    45      39.334 -11.118   9.431  1.00  0.00              
ATOM    133  N   ALA    46      37.520  -9.785   9.524  1.00  0.00              
ATOM    134  CA  ALA    46      37.098 -10.001   8.143  1.00  0.00              
ATOM    135  C   ALA    46      37.302  -8.705   7.420  1.00  0.00              
ATOM    136  O   ALA    46      37.147  -7.625   7.986  1.00  0.00              
ATOM    137  N   ALA    47      37.684  -8.784   6.157  1.00  0.00              
ATOM    138  CA  ALA    47      37.999  -7.600   5.410  1.00  0.00              
ATOM    139  C   ALA    47      36.740  -6.901   4.992  1.00  0.00              
ATOM    140  O   ALA    47      35.749  -7.573   4.687  1.00  0.00              
ATOM    141  N   LEU    48      36.821  -5.568   4.981  1.00  0.00              
ATOM    142  CA  LEU    48      35.808  -4.716   4.403  1.00  0.00              
ATOM    143  C   LEU    48      35.902  -4.756   2.886  1.00  0.00              
ATOM    144  O   LEU    48      36.998  -4.870   2.311  1.00  0.00              
ATOM    145  N   THR    49      34.759  -4.644   2.237  1.00  0.00              
ATOM    146  CA  THR    49      34.752  -4.539   0.806  1.00  0.00              
ATOM    147  C   THR    49      34.041  -3.231   0.482  1.00  0.00              
ATOM    148  O   THR    49      33.517  -2.605   1.401  1.00  0.00              
ATOM    149  N   PRO    50      34.036  -2.799  -0.776  1.00  0.00              
ATOM    150  CA  PRO    50      33.476  -1.552  -1.237  1.00  0.00              
ATOM    151  C   PRO    50      31.969  -1.428  -0.971  1.00  0.00              
ATOM    152  O   PRO    50      31.517  -0.343  -0.588  1.00  0.00              
ATOM    153  N   GLU    51      31.154  -2.488  -1.028  1.00  0.00              
ATOM    154  CA  GLU    51      29.705  -2.415  -0.837  1.00  0.00              
ATOM    155  C   GLU    51      29.271  -2.265   0.610  1.00  0.00              
ATOM    156  O   GLU    51      28.387  -1.494   0.968  1.00  0.00              
ATOM    157  N   MET    52      29.887  -3.082   1.447  1.00  0.00              
ATOM    158  CA  MET    52      29.759  -3.086   2.910  1.00  0.00              
ATOM    159  C   MET    52      30.247  -1.760   3.424  1.00  0.00              
ATOM    160  O   MET    52      29.551  -1.167   4.215  1.00  0.00              
ATOM    161  N   ALA    53      31.413  -1.259   3.034  1.00  0.00              
ATOM    162  CA  ALA    53      31.875   0.017   3.461  1.00  0.00              
ATOM    163  C   ALA    53      30.933   1.129   3.049  1.00  0.00              
ATOM    164  O   ALA    53      30.659   2.003   3.873  1.00  0.00              
ATOM    165  N   ILE    54      30.427   1.153   1.813  1.00  0.00              
ATOM    166  CA  ILE    54      29.474   2.145   1.325  1.00  0.00              
ATOM    167  C   ILE    54      28.171   2.143   2.116  1.00  0.00              
ATOM    168  O   ILE    54      27.645   3.203   2.466  1.00  0.00              
ATOM    169  N   LYS    55      27.630   0.979   2.418  1.00  0.00              
ATOM    170  CA  LYS    55      26.478   0.859   3.289  1.00  0.00              
ATOM    171  C   LYS    55      26.743   1.304   4.725  1.00  0.00              
ATOM    172  O   LYS    55      25.932   2.008   5.328  1.00  0.00              
ATOM    173  N   LEU    56      27.857   0.922   5.334  1.00  0.00              
ATOM    174  CA  LEU    56      28.193   1.397   6.637  1.00  0.00              
ATOM    175  C   LEU    56      28.392   2.897   6.615  1.00  0.00              
ATOM    176  O   LEU    56      27.900   3.518   7.556  1.00  0.00              
ATOM    177  N   SER    57      28.988   3.546   5.600  1.00  0.00              
ATOM    178  CA  SER    57      29.218   4.971   5.577  1.00  0.00              
ATOM    179  C   SER    57      27.916   5.726   5.519  1.00  0.00              
ATOM    180  O   SER    57      27.725   6.742   6.203  1.00  0.00              
ATOM    181  N   VAL    58      26.989   5.222   4.714  1.00  0.00              
ATOM    182  CA  VAL    58      25.644   5.775   4.694  1.00  0.00              
ATOM    183  C   VAL    58      24.942   5.671   6.031  1.00  0.00              
ATOM    184  O   VAL    58      24.381   6.666   6.463  1.00  0.00              
ATOM    185  N   VAL    59      24.958   4.546   6.753  1.00  0.00              
ATOM    186  CA  VAL    59      24.264   4.445   8.026  1.00  0.00              
ATOM    187  C   VAL    59      24.858   5.346   9.082  1.00  0.00              
ATOM    188  O   VAL    59      24.167   5.854   9.937  1.00  0.00              
ATOM    189  N   ILE    60      26.167   5.466   9.080  1.00  0.00              
ATOM    190  CA  ILE    60      26.891   6.182  10.085  1.00  0.00              
ATOM    191  C   ILE    60      27.011   7.642   9.743  1.00  0.00              
ATOM    192  O   ILE    60      27.595   8.378  10.521  1.00  0.00              
ATOM    193  N   GLY    61      26.565   8.081   8.572  1.00  0.00              
ATOM    194  CA  GLY    61      26.529   9.476   8.175  1.00  0.00              
ATOM    195  C   GLY    61      27.932  10.010   7.986  1.00  0.00              
ATOM    196  O   GLY    61      28.233  11.164   8.305  1.00  0.00              
ATOM    197  N   SER    62      28.865   9.208   7.453  1.00  0.00              
ATOM    198  CA  SER    62      30.208   9.715   7.227  1.00  0.00              
ATOM    199  C   SER    62      30.528   9.340   5.795  1.00  0.00              
ATOM    200  O   SER    62      29.765   8.615   5.141  1.00  0.00              
ATOM    201  N   SER    63      31.623   9.856   5.269  1.00  0.00              
ATOM    202  CA  SER    63      32.060   9.466   3.954  1.00  0.00              
ATOM    203  C   SER    63      32.919   8.201   4.118  1.00  0.00              
ATOM    204  O   SER    63      33.530   8.020   5.163  1.00  0.00              
ATOM    205  N   PRO    64      33.041   7.303   3.131  1.00  0.00              
ATOM    206  CA  PRO    64      33.864   6.095   3.190  1.00  0.00              
ATOM    207  C   PRO    64      35.293   6.473   3.437  1.00  0.00              
ATOM    208  O   PRO    64      35.991   5.865   4.231  1.00  0.00              
END
