
#######################################################
#                                                     #
#                        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   95 (   95),  selected   95 , name T0306TS168_3
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS168_3.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      -       -           -
LGA    A       4      L       3          4.174
LGA    V       5      A       4          3.719
LGA    V       6      V       5           -
LGA    T       7      V       6           -
LGA    G       8      T       7           -
LGA    Q       9      G       8           -
LGA    I      10      -       -           -
LGA    V      11      -       -           -
LGA    C      12      Q       9           #
LGA    T      13      I      10          2.985
LGA    V      14      V      11          1.833
LGA    R      15      C      12          4.015
LGA    H      16      T      13          2.176
LGA    H      17      -       -           -
LGA    G      18      -       -           -
LGA    L      19      -       -           -
LGA    A      20      -       -           -
LGA    H      21      -       -           -
LGA    D      22      V      14           #
LGA    K      23      R      15           #
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    L      24      K      23          2.826
LGA    L      25      L      24          2.496
LGA    M      26      L      25          2.001
LGA    V      27      M      26          4.567
LGA    E      28      V      27          2.172
LGA    M      29      E      28          2.700
LGA    I      30      M      29          2.215
LGA    D      31      I      30          2.518
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    P      32      G      34          4.399
LGA    Q      33      N      35          4.109
LGA    G      34      -       -           -
LGA    N      35      -       -           -
LGA    P      36      -       -           -
LGA    D      37      P      36           #
LGA    G      38      D      37          3.666
LGA    Q      39      G      38          3.535
LGA    C      40      Q      39          1.049
LGA    A      41      C      40          1.536
LGA    V      42      A      41          2.159
LGA    A      43      V      42          1.890
LGA    I      44      A      43          2.241
LGA    D      45      I      44          2.355
LGA    N      46      D      45          3.323
LGA    I      47      N      46          2.041
LGA    G      48      I      47          2.791
LGA    A      49      G      48          1.557
LGA    G      50      -       -           -
LGA    T      51      A      49          4.268
LGA    G      52      G      50          3.748
LGA    E      53      -       -           -
LGA    W      54      T      51          2.503
LGA    V      55      G      52          4.663
LGA    L      56      E      53           -
LGA    L      57      W      54           -
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    I      79      -       -           -
LGA    G      80      -       -           -
LGA    I      81      V      55          5.315
LGA    V      82      L      56          5.136
LGA    D      83      L      57          1.635
LGA    E      84      V      58          5.186
LGA    V      85      S      59          5.479
LGA    V      86      G      60          4.162
LGA    S      87      S      61          1.994
LGA    G      88      S      62          2.003
LGA    G      89      A      63           #
LGA    Q      90      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    V      91      D      75           #
LGA    I      92      L      76          1.893
LGA    F      93      C      77           -
LGA    H      94      V      78           -
LGA    K      95      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)   95   95    5.0     41    3.28     9.76     24.833     1.215

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.738162 * X  +   0.631694 * Y  +  -0.236811 * Z  +  38.302013
  Y_new =  -0.246506 * X  +   0.579314 * Y  +   0.776937 * Z  +  24.948170
  Z_new =   0.627974 * X  +  -0.515130 * Y  +   0.583344 * Z  +  70.941437 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.723379    2.418213  [ DEG:   -41.4466    138.5534 ]
  Theta =  -0.678947   -2.462646  [ DEG:   -38.9008   -141.0992 ]
  Phi   =  -0.322301    2.819292  [ DEG:   -18.4665    161.5335 ]
 
# 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: T0306TS168_3                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS168_3.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   95   95   5.0   41   3.28    9.76  24.833
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS168_3
PFRMAT TS
TARGET T0306
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      51.746  20.499  64.506  1.00 25.00           C
ATOM      2  CA  LYS     2      48.748  22.637  65.608  1.00 25.00           C
ATOM      3  CA  LEU     3      45.412  24.545  65.927  1.00 25.00           C
ATOM      4  CA  ALA     4      43.982  28.044  65.294  1.00 25.00           C
ATOM      5  CA  VAL     5      41.803  30.155  67.530  1.00 25.00           C
ATOM      6  CA  VAL     6      39.293  31.669  69.970  1.00 25.00           C
ATOM      7  CA  THR     7      38.752  35.145  71.398  1.00 25.00           C
ATOM      8  CA  GLY     8      34.997  34.651  71.946  1.00 25.00           C
ATOM      9  CA  GLN     9      36.044  31.913  74.269  1.00 25.00           C
ATOM     10  CA  ILE    10      34.263  28.815  75.420  1.00 25.00           C
ATOM     11  CA  VAL    11      32.114  26.241  73.661  1.00 25.00           C
ATOM     12  CA  CYS    12      34.180  23.086  74.145  1.00 25.00           C
ATOM     13  CA  THR    13      31.533  20.895  72.487  1.00 25.00           C
ATOM     14  CA  VAL    14      31.149  17.834  70.290  1.00 25.00           C
ATOM     15  CA  ARG    15      28.936  14.758  70.597  1.00 25.00           C
ATOM     16  CA  HIS    16      25.701  16.084  69.189  1.00 25.00           C
ATOM     17  CA  HIS    17      24.715  12.447  68.810  1.00 25.00           C
ATOM     18  CA  GLY    18      24.744  10.268  65.727  1.00 25.00           C
ATOM     19  CA  LEU    19      27.661  12.494  64.600  1.00 25.00           C
ATOM     20  CA  ALA    20      26.381  14.172  61.369  1.00 25.00           C
ATOM     21  CA  HIS    21      24.355  16.520  63.639  1.00 25.00           C
ATOM     22  CA  ASP    22      24.988  19.715  65.661  1.00 25.00           C
ATOM     23  CA  LYS    23      28.317  20.744  67.131  1.00 25.00           C
ATOM     24  CA  LEU    24      31.990  21.383  66.343  1.00 25.00           C
ATOM     25  CA  LEU    25      34.096  23.359  68.856  1.00 25.00           C
ATOM     26  CA  MET    26      37.870  23.174  69.245  1.00 25.00           C
ATOM     27  CA  VAL    27      40.939  25.204  68.144  1.00 25.00           C
ATOM     28  CA  GLU    28      43.375  25.314  71.081  1.00 25.00           C
ATOM     29  CA  MET    29      45.752  26.332  73.868  1.00 25.00           C
ATOM     30  CA  ILE    30      46.347  29.597  72.109  1.00 25.00           C
ATOM     31  CA  ASP    31      50.093  29.982  72.221  1.00 25.00           C
ATOM     32  CA  PRO    32      53.627  30.839  73.344  1.00 25.00           C
ATOM     33  CA  GLN    33      57.031  29.353  74.173  1.00 25.00           C
ATOM     34  CA  GLY    34      56.638  29.161  77.903  1.00 25.00           C
ATOM     35  CA  ASN    35      55.906  32.931  77.693  1.00 25.00           C
ATOM     36  CA  PRO    36      53.629  35.391  75.840  1.00 25.00           C
ATOM     37  CA  ASP    37      50.710  37.254  77.516  1.00 25.00           C
ATOM     38  CA  GLY    38      49.369  33.902  78.620  1.00 25.00           C
ATOM     39  CA  GLN    39      46.552  34.552  76.062  1.00 25.00           C
ATOM     40  CA  CYS    40      43.823  31.870  75.796  1.00 25.00           C
ATOM     41  CA  ALA    41      41.706  29.346  74.011  1.00 25.00           C
ATOM     42  CA  VAL    42      38.926  27.241  72.385  1.00 25.00           C
ATOM     43  CA  ALA    43      35.670  28.051  70.595  1.00 25.00           C
ATOM     44  CA  ILE    44      37.237  28.032  67.128  1.00 25.00           C
ATOM     45  CA  ASP    45      33.752  27.444  65.882  1.00 25.00           C
ATOM     46  CA  ASN    46      32.305  25.323  63.100  1.00 25.00           C
ATOM     47  CA  ILE    47      34.105  23.869  60.048  1.00 25.00           C
ATOM     48  CA  GLY    48      37.757  23.992  58.929  1.00 25.00           C
ATOM     49  CA  ALA    49      38.417  20.258  59.656  1.00 25.00           C
ATOM     50  CA  GLY    50      40.813  20.523  56.703  1.00 25.00           C
ATOM     51  CA  THR    51      44.173  20.829  58.463  1.00 25.00           C
ATOM     52  CA  GLY    52      43.507  17.567  60.259  1.00 25.00           C
ATOM     53  CA  GLU    53      40.704  16.972  62.781  1.00 25.00           C
ATOM     54  CA  TRP    54      41.599  17.343  66.445  1.00 25.00           C
ATOM     55  CA  VAL    55      42.943  20.629  67.859  1.00 25.00           C
ATOM     56  CA  LEU    56      40.897  19.556  70.941  1.00 25.00           C
ATOM     57  CA  LEU    57      39.959  22.093  73.665  1.00 25.00           C
ATOM     58  CA  VAL    58      40.106  24.462  76.650  1.00 25.00           C
ATOM     59  CA  SER    59      38.768  27.828  77.931  1.00 25.00           C
ATOM     60  CA  GLY    60      36.452  30.249  79.732  1.00 25.00           C
ATOM     61  CA  SER    61      33.000  29.519  81.171  1.00 25.00           C
ATOM     62  CA  SER    62      33.975  25.872  81.211  1.00 25.00           C
ATOM     63  CA  ALA    63      36.743  23.380  80.317  1.00 25.00           C
ATOM     64  CA  ARG    64      38.792  24.534  83.341  1.00 25.00           C
ATOM     65  CA  GLN    65      35.734  24.105  85.606  1.00 25.00           C
ATOM     66  CA  ALA    66      35.169  20.580  84.218  1.00 25.00           C
ATOM     67  CA  HIS    67      38.663  19.234  83.839  1.00 25.00           C
ATOM     68  CA  LYS    68      39.613  20.618  87.237  1.00 25.00           C
ATOM     69  CA  SER    69      41.240  17.311  88.041  1.00 25.00           C
ATOM     70  CA  GLU    70      44.807  16.653  86.772  1.00 25.00           C
ATOM     71  CA  THR    71      43.119  13.761  84.897  1.00 25.00           C
ATOM     72  CA  SER    72      45.262  14.630  81.876  1.00 25.00           C
ATOM     73  CA  PRO    73      42.523  13.044  79.716  1.00 25.00           C
ATOM     74  CA  VAL    74      41.469  16.624  78.949  1.00 25.00           C
ATOM     75  CA  ASP    75      37.776  15.839  78.931  1.00 25.00           C
ATOM     76  CA  LEU    76      37.403  18.933  76.664  1.00 25.00           C
ATOM     77  CA  CYS    77      36.329  18.667  73.031  1.00 25.00           C
ATOM     78  CA  VAL    78      36.022  18.523  69.239  1.00 25.00           C
ATOM     79  CA  ILE    79      37.131  19.495  65.677  1.00 25.00           C
ATOM     80  CA  GLY    80      36.671  23.043  64.366  1.00 25.00           C
ATOM     81  CA  ILE    81      40.305  23.464  63.389  1.00 25.00           C
ATOM     82  CA  VAL    82      39.529  27.168  63.190  1.00 25.00           C
ATOM     83  CA  ASP    83      38.764  30.878  63.022  1.00 25.00           C
ATOM     84  CA  GLU    84      35.865  29.781  60.855  1.00 25.00           C
ATOM     85  CA  VAL    85      33.070  31.443  62.847  1.00 25.00           C
ATOM     86  CA  VAL    86      31.019  34.368  64.072  1.00 25.00           C
ATOM     87  CA  SER    87      30.525  37.157  61.460  1.00 25.00           C
ATOM     88  CA  GLY    88      34.014  38.532  60.910  1.00 25.00           C
ATOM     89  CA  GLY    89      37.638  39.652  61.523  1.00 25.00           C
ATOM     90  CA  GLN    90      37.231  37.629  64.768  1.00 25.00           C
ATOM     91  CA  VAL    91      35.899  34.283  65.884  1.00 25.00           C
ATOM     92  CA  ILE    92      33.491  32.081  67.893  1.00 25.00           C
ATOM     93  CA  PHE    93      31.020  30.201  70.034  1.00 25.00           C
ATOM     94  CA  HIS    94      27.908  32.044  71.155  1.00 25.00           C
ATOM     95  CA  LYS    95      26.024  33.697  74.002  1.00 25.00           C
TER
END
