
#######################################################
#                                                     #
#                        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 T0306TS393_3
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS393_3.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    K       2      -       -           -
LGA    L       3      -       -           -
LGA    A       4      M       1          4.200
LGA    V       5      K       2          4.610
LGA    V       6      -       -           -
LGA    T       7      -       -           -
LGA    G       8      -       -           -
LGA    Q       9      -       -           -
LGA    I      10      L       3          3.718
LGA    V      11      A       4          3.528
LGA    C      12      V       5          2.984
LGA    T      13      V       6          4.271
LGA    V      14      T       7           -
LGA    R      15      -       -           -
LGA    H      16      -       -           -
LGA    H      17      -       -           -
LGA    G      18      G       8           #
LGA    L      19      Q       9          4.711
LGA    A      20      I      10          5.171
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    -       -      L      24           -
LGA    H      21      L      25          3.612
LGA    D      22      M      26          3.187
LGA    K      23      V      27          2.807
LGA    L      24      E      28          2.733
LGA    L      25      M      29          2.813
LGA    -       -      I      30           -
LGA    M      26      D      31          4.661
LGA    V      27      P      32           -
LGA    E      28      Q      33           -
LGA    M      29      G      34           -
LGA    I      30      N      35           -
LGA    D      31      P      36           -
LGA    P      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      -       -           -
LGA    N      35      -       -           -
LGA    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      D      37          4.194
LGA    G      48      G      38          3.378
LGA    A      49      -       -           -
LGA    G      50      -       -           -
LGA    T      51      -       -           -
LGA    G      52      Q      39          2.479
LGA    E      53      C      40          4.362
LGA    W      54      A      41          3.521
LGA    V      55      V      42           #
LGA    -       -      A      43           -
LGA    -       -      I      44           -
LGA    -       -      D      45           -
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    -       -      E      53           -
LGA    -       -      W      54           -
LGA    -       -      V      55           -
LGA    -       -      L      56           -
LGA    L      56      L      57          4.114
LGA    L      57      V      58          2.095
LGA    V      58      S      59           -
LGA    S      59      G      60           -
LGA    G      60      S      61           -
LGA    S      61      -       -           -
LGA    S      62      S      62          3.577
LGA    A      63      A      63          2.250
LGA    R      64      R      64          3.947
LGA    Q      65      Q      65          2.208
LGA    A      66      A      66          2.100
LGA    H      67      H      67          1.614
LGA    K      68      K      68          2.391
LGA    S      69      S      69          1.396
LGA    E      70      E      70          3.273
LGA    T      71      T      71          2.203
LGA    -       -      S      72           -
LGA    S      72      P      73          2.868
LGA    P      73      V      74          3.881
LGA    V      74      D      75          2.037
LGA    D      75      L      76          4.625
LGA    L      76      C      77          1.433
LGA    C      77      V      78          1.979
LGA    V      78      I      79          1.723
LGA    I      79      G      80          1.292
LGA    G      80      I      81          3.494
LGA    I      81      V      82          3.775
LGA    V      82      D      83           #
LGA    D      83      E      84          3.704
LGA    E      84      V      85          2.312
LGA    V      85      V      86           #
LGA    V      86      -       -           -
LGA    S      87      S      87          4.770
LGA    G      88      G      88           -
LGA    G      89      G      89           -
LGA    Q      90      Q      90           -
LGA    V      91      -       -           -
LGA    I      92      -       -           -
LGA    F      93      -       -           -
LGA    H      94      V      91           #
LGA    K      95      I      92          3.807
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     45    3.36    28.89     25.491     1.301

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.155859 * X  +  -0.822814 * Y  +  -0.546521 * Z  +  42.551952
  Y_new =   0.850033 * X  +  -0.393549 * Y  +   0.350091 * Z  +  31.949238
  Z_new =  -0.503143 * X  +  -0.409996 * Y  +   0.760757 * Z  +  63.512032 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.494306    2.647287  [ DEG:   -28.3216    151.6784 ]
  Theta =   0.527232    2.614361  [ DEG:    30.2081    149.7919 ]
  Phi   =   1.752139   -1.389454  [ DEG:   100.3902    -79.6098 ]
 
# 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: T0306TS393_3                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS393_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   45   3.36   28.89  25.491
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS393_3
PFRMAT TS
TARGET T0306
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      36.811  46.076  70.172  1.00 25.00           C
ATOM      2  CA  LYS     2      36.563  42.274  70.227  1.00 25.00           C
ATOM      3  CA  LEU     3      39.371  40.585  68.410  1.00 25.00           C
ATOM      4  CA  ALA     4      40.930  37.977  66.153  1.00 25.00           C
ATOM      5  CA  VAL     5      44.523  38.774  67.217  1.00 25.00           C
ATOM      6  CA  VAL     6      48.114  37.791  66.356  1.00 25.00           C
ATOM      7  CA  THR     7      51.200  38.923  64.329  1.00 25.00           C
ATOM      8  CA  GLY     8      49.996  36.557  61.594  1.00 25.00           C
ATOM      9  CA  GLN     9      48.806  33.073  60.627  1.00 25.00           C
ATOM     10  CA  ILE    10      47.941  29.948  62.576  1.00 25.00           C
ATOM     11  CA  VAL    11      46.778  27.130  64.876  1.00 25.00           C
ATOM     12  CA  CYS    12      44.388  24.408  65.988  1.00 25.00           C
ATOM     13  CA  THR    13      40.670  25.061  66.583  1.00 25.00           C
ATOM     14  CA  VAL    14      40.170  22.063  64.217  1.00 25.00           C
ATOM     15  CA  ARG    15      40.722  18.977  62.001  1.00 25.00           C
ATOM     16  CA  HIS    16      38.789  16.818  64.481  1.00 25.00           C
ATOM     17  CA  HIS    17      40.546  14.019  66.441  1.00 25.00           C
ATOM     18  CA  GLY    18      40.858  11.874  69.567  1.00 25.00           C
ATOM     19  CA  LEU    19      40.682  15.199  71.421  1.00 25.00           C
ATOM     20  CA  ALA    20      37.242  15.880  70.021  1.00 25.00           C
ATOM     21  CA  HIS    21      37.401  19.360  71.444  1.00 25.00           C
ATOM     22  CA  ASP    22      40.889  20.727  70.869  1.00 25.00           C
ATOM     23  CA  LYS    23      43.231  23.682  70.867  1.00 25.00           C
ATOM     24  CA  LEU    24      45.463  26.792  70.516  1.00 25.00           C
ATOM     25  CA  LEU    25      46.702  30.174  69.191  1.00 25.00           C
ATOM     26  CA  MET    26      47.156  32.725  66.406  1.00 25.00           C
ATOM     27  CA  VAL    27      44.623  34.650  64.270  1.00 25.00           C
ATOM     28  CA  GLU    28      44.211  37.903  62.327  1.00 25.00           C
ATOM     29  CA  MET    29      43.634  39.448  58.931  1.00 25.00           C
ATOM     30  CA  ILE    30      46.786  38.701  56.842  1.00 25.00           C
ATOM     31  CA  ASP    31      47.395  40.953  53.846  1.00 25.00           C
ATOM     32  CA  PRO    32      48.877  44.380  53.096  1.00 25.00           C
ATOM     33  CA  GLN    33      46.659  47.518  53.400  1.00 25.00           C
ATOM     34  CA  GLY    34      43.735  47.680  50.962  1.00 25.00           C
ATOM     35  CA  ASN    35      46.183  45.922  48.670  1.00 25.00           C
ATOM     36  CA  PRO    36      48.726  43.306  47.643  1.00 25.00           C
ATOM     37  CA  ASP    37      49.351  39.573  47.415  1.00 25.00           C
ATOM     38  CA  GLY    38      46.012  38.726  48.975  1.00 25.00           C
ATOM     39  CA  GLN    39      46.634  35.883  51.439  1.00 25.00           C
ATOM     40  CA  CYS    40      44.237  34.450  53.981  1.00 25.00           C
ATOM     41  CA  ALA    41      44.746  34.037  57.777  1.00 25.00           C
ATOM     42  CA  VAL    42      43.506  31.179  59.936  1.00 25.00           C
ATOM     43  CA  ALA    43      42.749  29.946  63.496  1.00 25.00           C
ATOM     44  CA  ILE    44      41.827  29.726  67.222  1.00 25.00           C
ATOM     45  CA  ASP    45      42.669  33.124  68.625  1.00 25.00           C
ATOM     46  CA  ASN    46      42.633  35.959  71.203  1.00 25.00           C
ATOM     47  CA  ILE    47      46.212  34.884  71.708  1.00 25.00           C
ATOM     48  CA  GLY    48      46.007  33.639  75.278  1.00 25.00           C
ATOM     49  CA  ALA    49      46.911  30.128  74.076  1.00 25.00           C
ATOM     50  CA  GLY    50      47.749  28.851  77.595  1.00 25.00           C
ATOM     51  CA  THR    51      43.940  28.591  77.896  1.00 25.00           C
ATOM     52  CA  GLY    52      42.596  32.064  78.686  1.00 25.00           C
ATOM     53  CA  GLU    53      40.993  33.416  75.493  1.00 25.00           C
ATOM     54  CA  TRP    54      40.089  30.918  72.691  1.00 25.00           C
ATOM     55  CA  VAL    55      38.200  32.356  69.699  1.00 25.00           C
ATOM     56  CA  LEU    56      37.732  33.364  66.042  1.00 25.00           C
ATOM     57  CA  LEU    57      39.820  33.654  62.875  1.00 25.00           C
ATOM     58  CA  VAL    58      40.266  35.481  59.569  1.00 25.00           C
ATOM     59  CA  SER    59      39.846  33.071  56.694  1.00 25.00           C
ATOM     60  CA  GLY    60      36.733  31.360  55.462  1.00 25.00           C
ATOM     61  CA  SER    61      34.329  34.370  55.466  1.00 25.00           C
ATOM     62  CA  SER    62      35.425  36.265  58.525  1.00 25.00           C
ATOM     63  CA  ALA    63      34.609  33.911  61.434  1.00 25.00           C
ATOM     64  CA  ARG    64      31.506  35.992  62.279  1.00 25.00           C
ATOM     65  CA  GLN    65      30.389  35.856  58.618  1.00 25.00           C
ATOM     66  CA  ALA    66      30.868  32.057  58.586  1.00 25.00           C
ATOM     67  CA  HIS    67      29.573  28.732  57.281  1.00 25.00           C
ATOM     68  CA  LYS    68      27.746  29.956  54.160  1.00 25.00           C
ATOM     69  CA  SER    69      26.446  32.745  56.279  1.00 25.00           C
ATOM     70  CA  GLU    70      22.896  32.200  57.454  1.00 25.00           C
ATOM     71  CA  THR    71      23.480  32.185  61.191  1.00 25.00           C
ATOM     72  CA  SER    72      25.461  33.107  64.342  1.00 25.00           C
ATOM     73  CA  PRO    73      28.210  34.843  66.295  1.00 25.00           C
ATOM     74  CA  VAL    74      30.142  31.641  66.987  1.00 25.00           C
ATOM     75  CA  ASP    75      30.915  28.807  64.658  1.00 25.00           C
ATOM     76  CA  LEU    76      34.633  29.167  64.263  1.00 25.00           C
ATOM     77  CA  CYS    77      38.311  28.518  63.555  1.00 25.00           C
ATOM     78  CA  VAL    78      38.545  29.073  59.802  1.00 25.00           C
ATOM     79  CA  ILE    79      41.295  26.897  58.300  1.00 25.00           C
ATOM     80  CA  GLY    80      42.746  25.265  61.346  1.00 25.00           C
ATOM     81  CA  ILE    81      46.296  23.993  60.926  1.00 25.00           C
ATOM     82  CA  VAL    82      46.795  27.040  58.641  1.00 25.00           C
ATOM     83  CA  ASP    83      50.560  26.910  59.421  1.00 25.00           C
ATOM     84  CA  GLU    84      53.024  29.633  60.410  1.00 25.00           C
ATOM     85  CA  VAL    85      52.452  32.097  63.246  1.00 25.00           C
ATOM     86  CA  VAL    86      55.707  33.778  64.153  1.00 25.00           C
ATOM     87  CA  SER    87      59.493  33.988  64.315  1.00 25.00           C
ATOM     88  CA  GLY    88      58.735  36.582  66.991  1.00 25.00           C
ATOM     89  CA  GLY    89      56.336  39.130  68.446  1.00 25.00           C
ATOM     90  CA  GLN    90      52.896  37.788  69.319  1.00 25.00           C
ATOM     91  CA  VAL    91      51.749  34.266  68.276  1.00 25.00           C
ATOM     92  CA  ILE    92      52.076  30.488  67.979  1.00 25.00           C
ATOM     93  CA  PHE    93      51.942  27.459  65.666  1.00 25.00           C
ATOM     94  CA  HIS    94      52.844  23.973  64.501  1.00 25.00           C
ATOM     95  CA  LYS    95      56.293  24.566  63.166  1.00 25.00           C
TER
END
