
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0306AL243_4
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306AL243_4.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    V       6      K       2          2.698
LGA    T       7      L       3          2.033
LGA    G       8      A       4          1.186
LGA    Q       9      V       5          0.754
LGA    I      10      V       6          0.537
LGA    V      11      T       7          0.563
LGA    C      12      G       8          0.733
LGA    T      13      Q       9          1.271
LGA    V      14      I      10          0.554
LGA    R      15      V      11          1.369
LGA    H      16      C      12          1.051
LGA    H      17      T      13          0.582
LGA    G      18      V      14          6.210
LGA    H      21      R      15          5.899
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    D      22      A      20          4.715
LGA    K      23      H      21          2.771
LGA    L      24      D      22          4.204
LGA    L      25      K      23          1.651
LGA    M      26      L      24          1.674
LGA    V      27      L      25          1.671
LGA    E      28      M      26          1.521
LGA    I      30      V      27          1.290
LGA    D      31      E      28          0.686
LGA    P      32      M      29          0.611
LGA    G      34      I      30          2.705
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    N      35      D      37          1.947
LGA    G      38      G      38          3.784
LGA    -       -      Q      39           -
LGA    Q      39      C      40          1.077
LGA    C      40      A      41          2.130
LGA    A      41      V      42          1.704
LGA    V      42      A      43          1.219
LGA    A      43      I      44          1.276
LGA    I      44      D      45          1.570
LGA    G      48      N      46          2.623
LGA    A      49      I      47          3.868
LGA    G      50      G      48           -
LGA    -       -      A      49           -
LGA    -       -      G      50           -
LGA    T      51      T      51          1.026
LGA    G      52      G      52          0.926
LGA    E      53      E      53          1.262
LGA    W      54      W      54          0.877
LGA    V      55      V      55          0.835
LGA    L      56      L      56          1.555
LGA    L      57      L      57          1.787
LGA    V      58      V      58          3.086
LGA    -       -      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    -       -      H      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    S      59      S      72          4.340
LGA    G      60      P      73          3.299
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    -       -      C      77           -
LGA    -       -      V      78           -
LGA    -       -      I      79           -
LGA    -       -      G      80           -
LGA    -       -      I      81           -
LGA    -       -      V      82           -
LGA    -       -      D      83           -
LGA    -       -      E      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   95    5.0     45    2.43    22.22     36.480     1.781

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.486887 * X  +   0.866573 * Y  +  -0.109504 * Z  +  74.274292
  Y_new =   0.873456 * X  +   0.482489 * Y  +  -0.065410 * Z  + -63.924683
  Z_new =  -0.003848 * X  +  -0.127494 * Y  +  -0.991832 * Z  +  80.304047 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.013750    0.127843  [ DEG:  -172.6751      7.3249 ]
  Theta =   0.003848    3.137744  [ DEG:     0.2205    179.7795 ]
  Phi   =   2.079323   -1.062269  [ DEG:   119.1364    -60.8636 ]
 
# 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: T0306AL243_4                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306AL243_4.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   95   5.0   45   2.43   22.22  36.480
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL243_4
REMARK Aligment from pdb entry: 1pybA
ATOM      1  N   VAL     6      45.588  34.743  63.678  1.00  0.00              
ATOM      2  CA  VAL     6      46.445  34.048  64.618  1.00  0.00              
ATOM      3  C   VAL     6      46.323  32.548  64.443  1.00  0.00              
ATOM      4  O   VAL     6      45.242  32.027  64.171  1.00  0.00              
ATOM      5  N   THR     7      47.447  31.863  64.597  1.00  0.00              
ATOM      6  CA  THR     7      47.489  30.422  64.490  1.00  0.00              
ATOM      7  C   THR     7      47.258  29.847  65.881  1.00  0.00              
ATOM      8  O   THR     7      47.760  30.373  66.877  1.00  0.00              
ATOM      9  N   GLY     8      46.481  28.774  65.944  1.00  0.00              
ATOM     10  CA  GLY     8      46.179  28.132  67.214  1.00  0.00              
ATOM     11  C   GLY     8      46.031  26.628  67.053  1.00  0.00              
ATOM     12  O   GLY     8      45.621  26.132  65.999  1.00  0.00              
ATOM     13  N   GLN     9      46.373  25.900  68.107  1.00  0.00              
ATOM     14  CA  GLN     9      46.268  24.453  68.078  1.00  0.00              
ATOM     15  C   GLN     9      44.920  24.060  68.679  1.00  0.00              
ATOM     16  O   GLN     9      44.463  24.656  69.656  1.00  0.00              
ATOM     17  N   ILE    10      44.273  23.073  68.070  1.00  0.00              
ATOM     18  CA  ILE    10      42.983  22.595  68.548  1.00  0.00              
ATOM     19  C   ILE    10      43.254  21.625  69.682  1.00  0.00              
ATOM     20  O   ILE    10      43.665  20.490  69.449  1.00  0.00              
ATOM     21  N   VAL    11      43.022  22.081  70.910  1.00  0.00              
ATOM     22  CA  VAL    11      43.247  21.268  72.101  1.00  0.00              
ATOM     23  C   VAL    11      42.320  20.057  72.130  1.00  0.00              
ATOM     24  O   VAL    11      42.725  18.956  72.518  1.00  0.00              
ATOM     25  N   CYS    12      41.075  20.276  71.721  1.00  0.00              
ATOM     26  CA  CYS    12      40.077  19.224  71.706  1.00  0.00              
ATOM     27  C   CYS    12      38.846  19.631  70.903  1.00  0.00              
ATOM     28  O   CYS    12      38.744  20.772  70.439  1.00  0.00              
ATOM     29  N   THR    13      37.917  18.688  70.748  1.00  0.00              
ATOM     30  CA  THR    13      36.686  18.914  69.993  1.00  0.00              
ATOM     31  C   THR    13      35.452  18.370  70.713  1.00  0.00              
ATOM     32  O   THR    13      35.326  17.162  70.926  1.00  0.00              
ATOM     33  N   VAL    14      34.552  19.277  71.089  1.00  0.00              
ATOM     34  CA  VAL    14      33.318  18.898  71.767  1.00  0.00              
ATOM     35  C   VAL    14      32.329  18.426  70.699  1.00  0.00              
ATOM     36  O   VAL    14      32.545  18.639  69.501  1.00  0.00              
ATOM     37  N   ARG    15      31.262  17.760  71.134  1.00  0.00              
ATOM     38  CA  ARG    15      30.226  17.290  70.209  1.00  0.00              
ATOM     39  C   ARG    15      28.850  17.403  70.858  1.00  0.00              
ATOM     40  O   ARG    15      28.715  17.275  72.074  1.00  0.00              
ATOM     41  N   HIS    16      27.840  17.657  70.031  1.00  0.00              
ATOM     42  CA  HIS    16      26.461  17.790  70.475  1.00  0.00              
ATOM     43  C   HIS    16      25.714  16.524  70.101  1.00  0.00              
ATOM     44  O   HIS    16      26.232  15.690  69.364  1.00  0.00              
ATOM     45  N   HIS    17      24.491  16.382  70.603  1.00  0.00              
ATOM     46  CA  HIS    17      23.699  15.193  70.314  1.00  0.00              
ATOM     47  C   HIS    17      22.936  15.276  68.985  1.00  0.00              
ATOM     48  O   HIS    17      21.962  16.023  68.856  1.00  0.00              
ATOM     49  N   GLY    18      23.395  14.504  68.002  1.00  0.00              
ATOM     50  CA  GLY    18      22.749  14.474  66.699  1.00  0.00              
ATOM     51  C   GLY    18      23.178  15.528  65.686  1.00  0.00              
ATOM     52  O   GLY    18      23.706  15.200  64.620  1.00  0.00              
ATOM     53  N   HIS    21      22.947  16.798  66.015  1.00  0.00              
ATOM     54  CA  HIS    21      23.291  17.907  65.128  1.00  0.00              
ATOM     55  C   HIS    21      24.705  17.827  64.551  1.00  0.00              
ATOM     56  O   HIS    21      25.697  17.807  65.283  1.00  0.00              
ATOM     57  N   ASP    22      24.774  17.774  63.222  1.00  0.00              
ATOM     58  CA  ASP    22      26.044  17.689  62.504  1.00  0.00              
ATOM     59  C   ASP    22      26.817  18.992  62.635  1.00  0.00              
ATOM     60  O   ASP    22      26.308  19.960  63.200  1.00  0.00              
ATOM     61  N   LYS    23      28.044  19.011  62.118  1.00  0.00              
ATOM     62  CA  LYS    23      28.877  20.205  62.199  1.00  0.00              
ATOM     63  C   LYS    23      29.082  20.552  63.670  1.00  0.00              
ATOM     64  O   LYS    23      29.259  21.718  64.033  1.00  0.00              
ATOM     65  N   LEU    24      29.054  19.527  64.515  1.00  0.00              
ATOM     66  CA  LEU    24      29.217  19.708  65.953  1.00  0.00              
ATOM     67  C   LEU    24      30.659  19.934  66.402  1.00  0.00              
ATOM     68  O   LEU    24      30.939  19.974  67.595  1.00  0.00              
ATOM     69  N   LEU    25      31.561  20.108  65.445  1.00  0.00              
ATOM     70  CA  LEU    25      32.974  20.314  65.736  1.00  0.00              
ATOM     71  C   LEU    25      33.302  21.572  66.545  1.00  0.00              
ATOM     72  O   LEU    25      33.784  22.564  65.995  1.00  0.00              
ATOM     73  N   MET    26      33.032  21.529  67.848  1.00  0.00              
ATOM     74  CA  MET    26      33.333  22.654  68.730  1.00  0.00              
ATOM     75  C   MET    26      34.821  22.591  69.057  1.00  0.00              
ATOM     76  O   MET    26      35.232  21.985  70.050  1.00  0.00              
ATOM     77  N   VAL    27      35.625  23.212  68.200  1.00  0.00              
ATOM     78  CA  VAL    27      37.066  23.215  68.365  1.00  0.00              
ATOM     79  C   VAL    27      37.554  24.204  69.415  1.00  0.00              
ATOM     80  O   VAL    27      37.291  25.402  69.323  1.00  0.00              
ATOM     81  N   GLU    28      38.263  23.691  70.416  1.00  0.00              
ATOM     82  CA  GLU    28      38.827  24.541  71.458  1.00  0.00              
ATOM     83  C   GLU    28      40.207  25.004  71.014  1.00  0.00              
ATOM     84  O   GLU    28      41.202  24.315  71.209  1.00  0.00              
ATOM     85  N   ILE    30      40.241  26.174  70.387  1.00  0.00              
ATOM     86  CA  ILE    30      41.471  26.767  69.892  1.00  0.00              
ATOM     87  C   ILE    30      42.249  27.404  71.037  1.00  0.00              
ATOM     88  O   ILE    30      41.690  28.111  71.876  1.00  0.00              
ATOM     89  N   ASP    31      43.549  27.149  71.065  1.00  0.00              
ATOM     90  CA  ASP    31      44.397  27.711  72.095  1.00  0.00              
ATOM     91  C   ASP    31      45.257  28.801  71.464  1.00  0.00              
ATOM     92  O   ASP    31      46.285  28.513  70.853  1.00  0.00              
ATOM     93  N   PRO    32      44.825  30.051  71.591  1.00  0.00              
ATOM     94  CA  PRO    32      45.577  31.173  71.036  1.00  0.00              
ATOM     95  C   PRO    32      46.642  31.602  72.040  1.00  0.00              
ATOM     96  O   PRO    32      46.554  32.675  72.630  1.00  0.00              
ATOM     97  N   GLY    34      47.635  30.737  72.238  1.00  0.00              
ATOM     98  CA  GLY    34      48.710  31.024  73.172  1.00  0.00              
ATOM     99  C   GLY    34      48.280  30.970  74.625  1.00  0.00              
ATOM    100  O   GLY    34      48.358  29.921  75.260  1.00  0.00              
ATOM    101  N   ASN    35      47.836  32.112  75.145  1.00  0.00              
ATOM    102  CA  ASN    35      47.385  32.243  76.527  1.00  0.00              
ATOM    103  C   ASN    35      45.855  32.259  76.536  1.00  0.00              
ATOM    104  O   ASN    35      45.215  31.915  77.526  1.00  0.00              
ATOM    105  N   GLY    38      45.280  32.676  75.416  1.00  0.00              
ATOM    106  CA  GLY    38      43.837  32.727  75.279  1.00  0.00              
ATOM    107  C   GLY    38      43.285  31.394  74.770  1.00  0.00              
ATOM    108  O   GLY    38      43.975  30.636  74.069  1.00  0.00              
ATOM    109  N   GLN    39      42.040  31.112  75.149  1.00  0.00              
ATOM    110  CA  GLN    39      41.350  29.889  74.755  1.00  0.00              
ATOM    111  C   GLN    39      39.952  30.288  74.299  1.00  0.00              
ATOM    112  O   GLN    39      39.207  30.931  75.036  1.00  0.00              
ATOM    113  N   CYS    40      39.605  29.920  73.072  1.00  0.00              
ATOM    114  CA  CYS    40      38.298  30.251  72.513  1.00  0.00              
ATOM    115  C   CYS    40      37.648  29.080  71.790  1.00  0.00              
ATOM    116  O   CYS    40      38.327  28.213  71.251  1.00  0.00              
ATOM    117  N   ALA    41      36.320  29.062  71.777  1.00  0.00              
ATOM    118  CA  ALA    41      35.592  27.988  71.105  1.00  0.00              
ATOM    119  C   ALA    41      35.053  28.460  69.767  1.00  0.00              
ATOM    120  O   ALA    41      34.520  29.561  69.650  1.00  0.00              
ATOM    121  N   VAL    42      35.213  27.620  68.754  1.00  0.00              
ATOM    122  CA  VAL    42      34.736  27.932  67.413  1.00  0.00              
ATOM    123  C   VAL    42      34.177  26.640  66.855  1.00  0.00              
ATOM    124  O   VAL    42      34.847  25.611  66.887  1.00  0.00              
ATOM    125  N   ALA    43      32.944  26.691  66.366  1.00  0.00              
ATOM    126  CA  ALA    43      32.307  25.520  65.781  1.00  0.00              
ATOM    127  C   ALA    43      32.623  25.457  64.297  1.00  0.00              
ATOM    128  O   ALA    43      32.398  26.421  63.564  1.00  0.00              
ATOM    129  N   ILE    44      33.113  24.304  63.857  1.00  0.00              
ATOM    130  CA  ILE    44      33.475  24.093  62.462  1.00  0.00              
ATOM    131  C   ILE    44      32.505  23.166  61.734  1.00  0.00              
ATOM    132  O   ILE    44      32.165  22.101  62.245  1.00  0.00              
ATOM    133  N   GLY    48      32.060  23.568  60.545  1.00  0.00              
ATOM    134  CA  GLY    48      31.162  22.716  59.784  1.00  0.00              
ATOM    135  C   GLY    48      31.867  21.450  59.300  1.00  0.00              
ATOM    136  O   GLY    48      31.681  20.375  59.872  1.00  0.00              
ATOM    137  N   ALA    49      32.677  21.586  58.249  1.00  0.00              
ATOM    138  CA  ALA    49      33.447  20.486  57.645  1.00  0.00              
ATOM    139  C   ALA    49      32.657  19.191  57.487  1.00  0.00              
ATOM    140  O   ALA    49      32.851  18.234  58.242  1.00  0.00              
ATOM    141  N   GLY    50      31.797  19.166  56.472  1.00  0.00              
ATOM    142  CA  GLY    50      30.939  18.015  56.172  1.00  0.00              
ATOM    143  C   GLY    50      31.631  16.655  56.060  1.00  0.00              
ATOM    144  O   GLY    50      31.978  16.217  54.958  1.00  0.00              
ATOM    145  N   THR    51      42.396  17.152  66.636  1.00  0.00              
ATOM    146  CA  THR    51      43.054  17.283  67.923  1.00  0.00              
ATOM    147  C   THR    51      44.553  17.396  67.711  1.00  0.00              
ATOM    148  O   THR    51      45.223  16.420  67.374  1.00  0.00              
ATOM    149  N   GLY    52      45.075  18.595  67.922  1.00  0.00              
ATOM    150  CA  GLY    52      46.496  18.814  67.744  1.00  0.00              
ATOM    151  C   GLY    52      46.773  19.563  66.457  1.00  0.00              
ATOM    152  O   GLY    52      47.900  19.992  66.231  1.00  0.00              
ATOM    153  N   GLU    53      45.752  19.720  65.613  1.00  0.00              
ATOM    154  CA  GLU    53      45.916  20.431  64.351  1.00  0.00              
ATOM    155  C   GLU    53      46.015  21.934  64.585  1.00  0.00              
ATOM    156  O   GLU    53      45.212  22.522  65.316  1.00  0.00              
ATOM    157  N   TRP    54      47.024  22.532  63.953  1.00  0.00              
ATOM    158  CA  TRP    54      47.308  23.960  64.053  1.00  0.00              
ATOM    159  C   TRP    54      46.667  24.688  62.876  1.00  0.00              
ATOM    160  O   TRP    54      47.124  24.573  61.736  1.00  0.00              
ATOM    161  N   VAL    55      45.620  25.456  63.165  1.00  0.00              
ATOM    162  CA  VAL    55      44.884  26.181  62.135  1.00  0.00              
ATOM    163  C   VAL    55      44.992  27.688  62.322  1.00  0.00              
ATOM    164  O   VAL    55      45.262  28.180  63.413  1.00  0.00              
ATOM    165  N   LEU    56      44.766  28.419  61.241  1.00  0.00              
ATOM    166  CA  LEU    56      44.802  29.871  61.279  1.00  0.00              
ATOM    167  C   LEU    56      43.370  30.380  61.405  1.00  0.00              
ATOM    168  O   LEU    56      42.501  30.025  60.604  1.00  0.00              
ATOM    169  N   LEU    57      43.136  31.217  62.409  1.00  0.00              
ATOM    170  CA  LEU    57      41.812  31.783  62.662  1.00  0.00              
ATOM    171  C   LEU    57      41.843  33.293  62.836  1.00  0.00              
ATOM    172  O   LEU    57      42.785  33.851  63.407  1.00  0.00              
ATOM    173  N   VAL    58      40.789  33.940  62.351  1.00  0.00              
ATOM    174  CA  VAL    58      40.632  35.384  62.458  1.00  0.00              
ATOM    175  C   VAL    58      40.174  35.681  63.884  1.00  0.00              
ATOM    176  O   VAL    58      38.996  35.532  64.214  1.00  0.00              
ATOM    177  N   SER    59      23.686  33.508  65.738  1.00  0.00              
ATOM    178  CA  SER    59      22.862  32.309  65.657  1.00  0.00              
ATOM    179  C   SER    59      23.179  31.296  66.746  1.00  0.00              
ATOM    180  O   SER    59      22.975  30.098  66.566  1.00  0.00              
ATOM    181  N   GLY    60      23.673  31.785  67.879  1.00  0.00              
ATOM    182  CA  GLY    60      23.997  30.907  68.988  1.00  0.00              
ATOM    183  C   GLY    60      25.235  30.044  68.795  1.00  0.00              
ATOM    184  O   GLY    60      25.857  29.628  69.779  1.00  0.00              
END
