
#######################################################
#                                                     #
#                        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   38 (  186),  selected   38 , name T0306TS239_4_2
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS239_4_2.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    K       2      K       2           -
LGA    L       3      L       3           -
LGA    A       4      A       4           -
LGA    -       -      V       5           -
LGA    -       -      V       6           -
LGA    -       -      T       7           -
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
LGA    -       -      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    V       5      H      17          4.963
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    V       6      A      20          2.195
LGA    T       7      H      21          2.026
LGA    G       8      D      22          3.969
LGA    Q       9      K      23          1.974
LGA    I      10      L      24          1.357
LGA    V      11      L      25          2.038
LGA    C      12      M      26          2.725
LGA    T      13      V      27          1.728
LGA    V      14      E      28          2.005
LGA    R      15      M      29          1.854
LGA    H      16      I      30          1.971
LGA    H      17      D      31          1.794
LGA    -       -      P      32           -
LGA    G      18      Q      33          3.588
LGA    L      19      G      34          3.655
LGA    A      20      N      35           -
LGA    H      21      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    -       -      C      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    -       -      I      44           -
LGA    -       -      D      45           -
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    D      22      A      49           #
LGA    K      23      -       -           -
LGA    L      24      -       -           -
LGA    L      25      G      50           #
LGA    M      26      T      51          1.670
LGA    V      27      G      52          3.561
LGA    E      28      E      53          3.843
LGA    M      29      W      54          3.134
LGA    I      30      -       -           -
LGA    D      31      V      55           #
LGA    P      32      L      56          2.938
LGA    Q      33      L      57          2.576
LGA    -       -      V      58           -
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      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    -       -      C      77           -
LGA    -       -      V      78           -
LGA    G      34      I      79          3.228
LGA    N      35      G      80          3.548
LGA    P      36      I      81           -
LGA    D      37      V      82           -
LGA    G      38      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)   38   95    5.0     23    2.86     4.35     16.427     0.776

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.075466 * X  +   0.144238 * Y  +   0.986661 * Z  + -82.866508
  Y_new =  -0.512145 * X  +   0.843394 * Y  +  -0.162466 * Z  +  -5.381821
  Z_new =  -0.855578 * X  +  -0.517574 * Y  +   0.010223 * Z  + 189.613831 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.551046    1.590546  [ DEG:   -88.8684     91.1316 ]
  Theta =   1.026665    2.114927  [ DEG:    58.8236    121.1764 ]
  Phi   =  -1.717096    1.424497  [ DEG:   -98.3824     81.6176 ]
 
# 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: T0306TS239_4_2                                
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS239_4_2.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38   95   5.0   23   2.86    4.35  16.427
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS239_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0306
PARENT 1qk3_A
ATOM      1  N   MET     1      14.932  17.162  64.386  1.00  9.99
ATOM      2  CA  MET     1      15.245  17.451  62.992  1.00  9.99
ATOM      3  C   MET     1      16.644  16.940  62.651  1.00  9.99
ATOM      4  O   MET     1      17.421  17.668  62.035  1.00  9.99
ATOM      5  CB  MET     1      15.168  18.968  62.745  1.00  9.99
ATOM      6  N   LYS     2      16.963  15.713  63.061  1.00  9.99
ATOM      7  CA  LYS     2      18.260  15.088  62.896  1.00  9.99
ATOM      8  C   LYS     2      18.699  14.788  61.469  1.00  9.99
ATOM      9  O   LYS     2      19.857  14.393  61.260  1.00  9.99
ATOM     10  CB  LYS     2      18.329  13.790  63.720  1.00  9.99
ATOM     11  N   LEU     3      17.801  14.885  60.488  1.00  9.99
ATOM     12  CA  LEU     3      18.186  14.661  59.102  1.00  9.99
ATOM     13  C   LEU     3      18.298  15.978  58.333  1.00  9.99
ATOM     14  O   LEU     3      18.835  15.965  57.216  1.00  9.99
ATOM     15  CB  LEU     3      17.198  13.722  58.406  1.00  9.99
ATOM     16  N   ALA     4      17.812  17.081  58.888  1.00  9.99
ATOM     17  CA  ALA     4      17.794  18.346  58.168  1.00  9.99
ATOM     18  C   ALA     4      18.666  19.455  58.698  1.00  9.99
ATOM     19  O   ALA     4      18.526  20.609  58.264  1.00  9.99
ATOM     20  CB  ALA     4      16.325  18.827  58.097  1.00  9.99
ATOM     21  N   VAL     5      19.537  19.220  59.683  1.00  9.99
ATOM     22  CA  VAL     5      20.433  20.266  60.201  1.00  9.99
ATOM     23  C   VAL     5      21.850  19.694  60.351  1.00  9.99
ATOM     24  O   VAL     5      21.962  18.528  60.773  1.00  9.99
ATOM     25  CB  VAL     5      19.934  20.835  61.533  1.00  9.99
ATOM     26  N   VAL     6      22.895  20.403  59.991  1.00  9.99
ATOM     27  CA  VAL     6      24.277  19.941  60.119  1.00  9.99
ATOM     28  C   VAL     6      24.793  19.905  61.538  1.00  9.99
ATOM     29  O   VAL     6      24.630  20.841  62.321  1.00  9.99
ATOM     30  CB  VAL     6      25.041  20.951  59.262  1.00  9.99
ATOM     31  N   THR     7      25.357  18.771  62.008  1.00  9.99
ATOM     32  CA  THR     7      25.799  18.663  63.395  1.00  9.99
ATOM     33  C   THR     7      26.950  19.631  63.668  1.00  9.99
ATOM     34  O   THR     7      27.703  19.987  62.751  1.00  9.99
ATOM     35  CB  THR     7      26.213  17.212  63.562  1.00  9.99
ATOM     36  N   GLY     8      27.128  20.078  64.907  1.00  9.99
ATOM     37  CA  GLY     8      28.167  21.038  65.263  1.00  9.99
ATOM     38  C   GLY     8      29.576  20.497  65.073  1.00  9.99
ATOM     39  O   GLY     8      29.790  19.267  65.027  1.00  9.99
ATOM     40  N   GLN     9      30.531  21.422  64.952  1.00  9.99
ATOM     41  CA  GLN     9      31.941  21.076  64.812  1.00  9.99
ATOM     42  C   GLN     9      32.713  21.552  66.051  1.00  9.99
ATOM     43  O   GLN     9      32.447  22.606  66.652  1.00  9.99
ATOM     44  CB  GLN     9      32.560  21.855  63.608  1.00  9.99
ATOM     45  N   ILE    10      33.630  20.711  66.543  1.00  9.99
ATOM     46  CA  ILE    10      34.480  21.027  67.673  1.00  9.99
ATOM     47  C   ILE    10      35.919  21.374  67.207  1.00  9.99
ATOM     48  O   ILE    10      36.453  20.632  66.354  1.00  9.99
ATOM     49  CB  ILE    10      34.651  19.855  68.673  1.00  9.99
ATOM     50  N   VAL    11      36.423  22.458  67.754  1.00  9.99
ATOM     51  CA  VAL    11      37.823  22.842  67.453  1.00  9.99
ATOM     52  C   VAL    11      38.628  23.092  68.722  1.00  9.99
ATOM     53  O   VAL    11      38.108  23.472  69.780  1.00  9.99
ATOM     54  CB  VAL    11      37.808  24.141  66.635  1.00  9.99
ATOM     55  N   CYS    12      39.954  22.816  68.625  1.00  9.99
ATOM     56  CA  CYS    12      40.862  22.936  69.772  1.00  9.99
ATOM     57  C   CYS    12      41.912  24.014  69.491  1.00  9.99
ATOM     58  O   CYS    12      42.475  23.909  68.407  1.00  9.99
ATOM     59  CB  CYS    12      41.501  21.545  70.049  1.00  9.99
ATOM     60  N   THR    13      41.947  25.062  70.277  1.00  9.99
ATOM     61  CA  THR    13      42.786  26.230  69.898  1.00  9.99
ATOM     62  C   THR    13      43.619  26.755  71.043  1.00  9.99
ATOM     63  O   THR    13      43.212  26.691  72.225  1.00  9.99
ATOM     64  CB  THR    13      41.812  27.349  69.433  1.00  9.99
ATOM     65  N   VAL    14      44.835  27.240  70.714  1.00  9.99
ATOM     66  CA  VAL    14      45.683  27.896  71.700  1.00  9.99
ATOM     67  C   VAL    14      45.328  29.399  71.754  1.00  9.99
ATOM     68  O   VAL    14      44.946  29.987  70.773  1.00  9.99
ATOM     69  CB  VAL    14      47.167  27.815  71.347  1.00  9.99
ATOM     70  N   ARG    15      45.553  30.044  72.904  1.00  9.99
ATOM     71  CA  ARG    15      45.268  31.485  73.019  1.00  9.99
ATOM     72  C   ARG    15      46.115  32.377  72.154  1.00  9.99
ATOM     73  O   ARG    15      45.738  33.433  71.625  1.00  9.99
ATOM     74  CB  ARG    15      45.473  31.864  74.499  1.00  9.99
ATOM     75  N   HIS    16      47.412  32.041  72.073  1.00  9.99
ATOM     76  CA  HIS    16      48.355  32.864  71.340  1.00  9.99
ATOM     77  C   HIS    16      48.861  32.152  70.096  1.00  9.99
ATOM     78  O   HIS    16      48.691  30.938  69.980  1.00  9.99
ATOM     79  CB  HIS    16      49.506  33.309  72.260  1.00  9.99
ATOM     80  N   HIS    17      49.502  32.924  69.230  1.00  9.99
ATOM     81  CA  HIS    17      50.024  32.359  67.996  1.00  9.99
ATOM     82  C   HIS    17      51.412  31.760  68.200  1.00  9.99
ATOM     83  O   HIS    17      52.446  32.409  68.058  1.00  9.99
ATOM     84  CB  HIS    17      50.002  33.343  66.843  1.00  9.99
ATOM     85  N   GLY    18      51.458  30.478  68.515  1.00  9.99
ATOM     86  CA  GLY    18      52.717  29.747  68.672  1.00  9.99
ATOM     87  C   GLY    18      53.020  28.966  67.393  1.00  9.99
ATOM     88  O   GLY    18      52.108  28.877  66.565  1.00  9.99
ATOM     89  N   LEU    19      54.209  28.374  67.307  1.00  9.99
ATOM     90  CA  LEU    19      54.468  27.533  66.109  1.00  9.99
ATOM     91  C   LEU    19      53.602  26.275  66.173  1.00  9.99
ATOM     92  O   LEU    19      53.556  25.736  67.278  1.00  9.99
ATOM     93  CB  LEU    19      55.957  27.251  66.013  1.00  9.99
ATOM     94  N   ALA    20      52.902  25.898  65.099  1.00  9.99
ATOM     95  CA  ALA    20      52.051  24.699  65.148  1.00  9.99
ATOM     96  C   ALA    20      52.881  23.489  65.593  1.00  9.99
ATOM     97  O   ALA    20      54.082  23.348  65.328  1.00  9.99
ATOM     98  CB  ALA    20      51.320  24.478  63.816  1.00  9.99
ATOM     99  N   HIS    21      52.291  22.630  66.417  1.00  9.99
ATOM    100  CA  HIS    21      52.856  21.374  66.884  1.00  9.99
ATOM    101  C   HIS    21      52.061  20.186  66.347  1.00  9.99
ATOM    102  O   HIS    21      52.018  19.108  66.961  1.00  9.99
ATOM    103  CB  HIS    21      52.909  21.298  68.428  1.00  9.99
ATOM    104  N   ASP    22      51.405  20.356  65.201  1.00  9.99
ATOM    105  CA  ASP    22      50.571  19.285  64.656  1.00  9.99
ATOM    106  C   ASP    22      51.384  18.202  63.944  1.00  9.99
ATOM    107  O   ASP    22      52.513  18.449  63.535  1.00  9.99
ATOM    108  CB  ASP    22      49.546  19.905  63.697  1.00  9.99
ATOM    109  N   LYS    23      50.779  17.042  63.778  1.00  9.99
ATOM    110  CA  LYS    23      51.379  15.927  63.036  1.00  9.99
ATOM    111  C   LYS    23      50.288  14.941  62.652  1.00  9.99
ATOM    112  O   LYS    23      49.199  14.926  63.290  1.00  9.99
ATOM    113  CB  LYS    23      52.556  15.302  63.761  1.00  9.99
ATOM    114  N   LEU    24      50.539  14.141  61.629  1.00  9.99
ATOM    115  CA  LEU    24      49.568  13.163  61.119  1.00  9.99
ATOM    116  C   LEU    24      49.089  12.176  62.207  1.00  9.99
ATOM    117  O   LEU    24      49.954  11.652  62.897  1.00  9.99
ATOM    118  CB  LEU    24      50.186  12.306  59.986  1.00  9.99
ATOM    119  N   LEU    25      47.634  12.993  64.987  1.00  9.99
ATOM    120  CA  LEU    25      47.518  13.632  66.290  1.00  9.99
ATOM    121  C   LEU    25      46.417  14.697  66.277  1.00  9.99
ATOM    122  O   LEU    25      45.952  15.127  65.175  1.00  9.99
ATOM    123  CB  LEU    25      48.852  14.237  66.754  1.00  9.99
ATOM    124  N   MET    26      45.994  15.139  67.456  1.00  9.99
ATOM    125  CA  MET    26      44.901  16.136  67.527  1.00  9.99
ATOM    126  C   MET    26      45.223  17.427  66.779  1.00  9.99
ATOM    127  O   MET    26      46.374  17.910  66.911  1.00  9.99
ATOM    128  CB  MET    26      44.612  16.501  69.006  1.00  9.99
ATOM    129  N   VAL    27      44.267  17.913  65.983  1.00  9.99
ATOM    130  CA  VAL    27      44.520  19.215  65.331  1.00  9.99
ATOM    131  C   VAL    27      44.331  20.316  66.371  1.00  9.99
ATOM    132  O   VAL    27      43.243  20.530  66.928  1.00  9.99
ATOM    133  CB  VAL    27      43.552  19.449  64.157  1.00  9.99
ATOM    134  N   GLU    28      45.419  21.061  66.625  1.00  9.99
ATOM    135  CA  GLU    28      45.380  22.200  67.544  1.00  9.99
ATOM    136  C   GLU    28      45.726  23.470  66.747  1.00  9.99
ATOM    137  O   GLU    28      46.846  23.560  66.259  1.00  9.99
ATOM    138  CB  GLU    28      46.353  22.082  68.719  1.00  9.99
ATOM    139  N   MET    29      44.813  24.428  66.700  1.00  9.99
ATOM    140  CA  MET    29      45.110  25.667  65.952  1.00  9.99
ATOM    141  C   MET    29      45.797  26.677  66.841  1.00  9.99
ATOM    142  O   MET    29      45.502  26.904  68.042  1.00  9.99
ATOM    143  CB  MET    29      43.798  26.248  65.382  1.00  9.99
ATOM    144  N   ILE    30      46.786  27.393  66.261  1.00  9.99
ATOM    145  CA  ILE    30      47.462  28.457  67.003  1.00  9.99
ATOM    146  C   ILE    30      47.686  29.715  66.138  1.00  9.99
ATOM    147  O   ILE    30      46.971  30.710  66.251  1.00  9.99
ATOM    148  CB  ILE    30      48.756  27.986  67.642  1.00  9.99
ATOM    149  N   ASP    31      48.603  29.594  65.199  1.00  9.99
ATOM    150  CA  ASP    31      48.995  30.652  64.293  1.00  9.99
ATOM    151  C   ASP    31      47.951  30.953  63.225  1.00  9.99
ATOM    152  O   ASP    31      47.740  32.138  62.933  1.00  9.99
ATOM    153  CB  ASP    31      50.334  30.310  63.608  1.00  9.99
ATOM    154  N   PRO    32      47.228  29.960  62.736  1.00  9.99
ATOM    155  CA  PRO    32      46.252  30.209  61.669  1.00  9.99
ATOM    156  C   PRO    32      44.811  29.945  62.065  1.00  9.99
ATOM    157  O   PRO    32      44.424  28.805  62.349  1.00  9.99
ATOM    158  CB  PRO    32      46.675  29.359  60.457  1.00  9.99
ATOM    159  N   GLN    33      44.014  31.001  62.124  1.00  9.99
ATOM    160  CA  GLN    33      42.589  30.901  62.487  1.00  9.99
ATOM    161  C   GLN    33      41.681  31.093  61.292  1.00  9.99
ATOM    162  O   GLN    33      40.444  31.233  61.366  1.00  9.99
ATOM    163  CB  GLN    33      42.341  31.973  63.557  1.00  9.99
ATOM    164  N   GLY    34      42.223  30.970  60.059  1.00  9.99
ATOM    165  CA  GLY    34      41.468  31.186  58.842  1.00  9.99
ATOM    166  C   GLY    34      40.290  30.271  58.561  1.00  9.99
ATOM    167  O   GLY    34      39.352  30.721  57.896  1.00  9.99
ATOM    168  N   ASN    35      40.237  29.048  59.113  1.00  9.99
ATOM    169  CA  ASN    35      39.057  28.197  58.925  1.00  9.99
ATOM    170  C   ASN    35      37.776  28.839  59.471  1.00  9.99
ATOM    171  O   ASN    35      36.660  28.423  59.086  1.00  9.99
ATOM    172  CB  ASN    35      39.290  26.856  59.674  1.00  9.99
ATOM    173  N   PRO    36      37.860  29.846  60.366  1.00  9.99
ATOM    174  CA  PRO    36      36.678  30.468  60.918  1.00  9.99
ATOM    175  C   PRO    36      36.077  31.600  60.073  1.00  9.99
ATOM    176  O   PRO    36      35.051  32.161  60.434  1.00  9.99
ATOM    177  CB  PRO    36      36.931  30.970  62.359  1.00  9.99
ATOM    178  N   ASP    37      36.677  31.917  58.927  1.00  9.99
ATOM    179  CA  ASP    37      36.103  32.988  58.064  1.00  9.99
ATOM    180  C   ASP    37      34.674  32.658  57.683  1.00  9.99
ATOM    181  O   ASP    37      34.418  31.520  57.279  1.00  9.99
ATOM    182  CB  ASP    37      36.994  33.181  56.835  1.00  9.99
ATOM    183  N   GLY    38      33.755  33.605  57.839  1.00  9.99
ATOM    184  CA  GLY    38      32.346  33.488  57.583  1.00  9.99
ATOM    185  C   GLY    38      31.607  32.379  58.363  1.00  9.99
ATOM    186  O   GLY    38      30.572  31.897  57.875  1.00  9.99
TER
END
