
#######################################################
#                                                     #
#                        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 T0306TS599_2
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS599_2.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      M       1          1.795
LGA    A       4      K       2          1.247
LGA    V       5      L       3          2.880
LGA    V       6      -       -           -
LGA    T       7      -       -           -
LGA    G       8      -       -           -
LGA    Q       9      A       4          4.053
LGA    I      10      V       5          3.161
LGA    V      11      V       6          2.626
LGA    C      12      T       7          4.868
LGA    T      13      G       8          2.006
LGA    V      14      Q       9          1.579
LGA    R      15      I      10          2.639
LGA    H      16      V      11          2.376
LGA    H      17      -       -           -
LGA    G      18      -       -           -
LGA    L      19      -       -           -
LGA    A      20      -       -           -
LGA    H      21      -       -           -
LGA    D      22      C      12          0.567
LGA    K      23      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      L      24          3.937
LGA    L      25      L      25          2.199
LGA    M      26      M      26          1.253
LGA    V      27      V      27          1.272
LGA    E      28      E      28          1.218
LGA    M      29      M      29          1.591
LGA    I      30      I      30          1.799
LGA    D      31      D      31          1.570
LGA    P      32      P      32          1.948
LGA    Q      33      Q      33          1.869
LGA    G      34      G      34          1.729
LGA    N      35      N      35          1.640
LGA    P      36      P      36          1.936
LGA    D      37      D      37          1.108
LGA    G      38      G      38          1.409
LGA    Q      39      Q      39          1.402
LGA    C      40      C      40          0.913
LGA    A      41      A      41          1.696
LGA    V      42      V      42          2.303
LGA    A      43      A      43          3.681
LGA    I      44      I      44           #
LGA    D      45      D      45           -
LGA    N      46      N      46           -
LGA    I      47      I      47           -
LGA    G      48      G      48           -
LGA    A      49      A      49           -
LGA    G      50      G      50           -
LGA    T      51      T      51           -
LGA    G      52      G      52           -
LGA    E      53      E      53           -
LGA    W      54      W      54           -
LGA    V      55      V      55           -
LGA    L      56      L      56           -
LGA    L      57      L      57           -
LGA    V      58      V      58           #
LGA    S      59      S      59          2.033
LGA    G      60      -       -           -
LGA    S      61      -       -           -
LGA    S      62      G      60          2.760
LGA    A      63      -       -           -
LGA    R      64      -       -           -
LGA    Q      65      S      61          2.937
LGA    A      66      -       -           -
LGA    H      67      -       -           -
LGA    K      68      -       -           -
LGA    S      69      -       -           -
LGA    E      70      -       -           -
LGA    T      71      -       -           -
LGA    S      72      S      62          3.089
LGA    P      73      A      63          2.967
LGA    V      74      R      64          3.580
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    D      75      L      76          2.710
LGA    L      76      C      77           #
LGA    C      77      V      78           -
LGA    V      78      I      79           -
LGA    I      79      G      80           -
LGA    G      80      I      81           -
LGA    I      81      V      82           -
LGA    V      82      D      83           -
LGA    D      83      E      84           -
LGA    E      84      V      85           -
LGA    V      85      V      86           -
LGA    V      86      S      87           -
LGA    S      87      G      88           -
LGA    G      88      G      89           -
LGA    G      89      Q      90           -
LGA    Q      90      V      91           -
LGA    V      91      I      92           -
LGA    I      92      F      93           -
LGA    F      93      H      94           -
LGA    H      94      K      95           -
LGA    K      95      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   95   95    5.0     39    2.41    58.97     29.399     1.555

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.158522 * X  +  -0.688723 * Y  +   0.707483 * Z  +  33.566048
  Y_new =  -0.754130 * X  +   0.378049 * Y  +   0.536999 * Z  +  30.456217
  Z_new =  -0.637306 * X  +  -0.618660 * Y  +  -0.459457 * Z  +  69.940277 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.209586    0.932006  [ DEG:  -126.6000     53.4000 ]
  Theta =   0.690997    2.450596  [ DEG:    39.5912    140.4088 ]
  Phi   =  -1.363607    1.777986  [ DEG:   -78.1289    101.8711 ]
 
# 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: T0306TS599_2                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS599_2.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   39   2.41   58.97  29.399
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS599_2
PFRMAT TS                                                                       
TARGET T0306                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      38.624  28.891  62.737  1.00  0.00              
ATOM      2  CA  LYS     2      38.793  32.489  62.818  1.00  0.00              
ATOM      3  CA  LEU     3      41.763  35.102  61.339  1.00  0.00              
ATOM      4  CA  ALA     4      44.015  35.886  64.818  1.00  0.00              
ATOM      5  CA  VAL     5      43.272  32.179  65.538  1.00  0.00              
ATOM      6  CA  VAL     6      44.975  31.320  62.277  1.00  0.00              
ATOM      7  CA  THR     7      48.112  33.368  62.481  1.00  0.00              
ATOM      8  CA  GLY     8      49.245  32.500  65.927  1.00  0.00              
ATOM      9  CA  GLN     9      48.906  28.808  65.896  1.00  0.00              
ATOM     10  CA  ILE    10      45.569  27.459  66.356  1.00  0.00              
ATOM     11  CA  VAL    11      45.151  24.265  68.041  1.00  0.00              
ATOM     12  CA  CYS    12      41.802  22.612  67.755  1.00  0.00              
ATOM     13  CA  THR    13      40.523  20.096  70.290  1.00  0.00              
ATOM     14  CA  VAL    14      37.498  18.078  69.430  1.00  0.00              
ATOM     15  CA  ARG    15      35.262  16.709  72.075  1.00  0.00              
ATOM     16  CA  HIS    16      32.102  15.108  70.834  1.00  0.00              
ATOM     17  CA  HIS    17      32.002  12.077  73.097  1.00  0.00              
ATOM     18  CA  GLY    18      32.000  14.347  76.107  1.00  0.00              
ATOM     19  CA  LEU    19      28.853  16.211  75.274  1.00  0.00              
ATOM     20  CA  ALA    20      26.562  13.204  74.599  1.00  0.00              
ATOM     21  CA  HIS    21      25.548  13.981  70.979  1.00  0.00              
ATOM     22  CA  ASP    22      26.565  17.597  71.214  1.00  0.00              
ATOM     23  CA  LYS    23      29.421  18.838  69.215  1.00  0.00              
ATOM     24  CA  LEU    24      32.143  20.518  71.369  1.00  0.00              
ATOM     25  CA  LEU    25      35.015  22.311  69.796  1.00  0.00              
ATOM     26  CA  MET    26      37.777  23.663  71.921  1.00  0.00              
ATOM     27  CA  VAL    27      40.124  26.168  70.430  1.00  0.00              
ATOM     28  CA  GLU    28      43.433  26.769  71.909  1.00  0.00              
ATOM     29  CA  MET    29      45.400  29.635  70.797  1.00  0.00              
ATOM     30  CA  ILE    30      49.046  29.397  70.804  1.00  0.00              
ATOM     31  CA  ASP    31      51.066  32.379  69.805  1.00  0.00              
ATOM     32  CA  PRO    32      53.716  32.247  67.166  1.00  0.00              
ATOM     33  CA  GLN    33      56.530  31.044  69.329  1.00  0.00              
ATOM     34  CA  GLY    34      54.468  28.178  70.865  1.00  0.00              
ATOM     35  CA  ASN    35      53.963  29.990  74.158  1.00  0.00              
ATOM     36  CA  PRO    36      50.629  29.860  75.896  1.00  0.00              
ATOM     37  CA  ASP    37      49.086  33.362  75.598  1.00  0.00              
ATOM     38  CA  GLY    38      46.033  32.946  77.787  1.00  0.00              
ATOM     39  CA  GLN    39      43.387  32.908  75.089  1.00  0.00              
ATOM     40  CA  CYS    40      41.189  29.868  74.968  1.00  0.00              
ATOM     41  CA  ALA    41      38.295  29.773  72.626  1.00  0.00              
ATOM     42  CA  VAL    42      35.404  27.453  73.270  1.00  0.00              
ATOM     43  CA  ALA    43      33.186  26.465  70.504  1.00  0.00              
ATOM     44  CA  ILE    44      29.909  24.814  71.305  1.00  0.00              
ATOM     45  CA  ASP    45      27.778  23.352  68.634  1.00  0.00              
ATOM     46  CA  ASN    46      24.127  23.002  69.433  1.00  0.00              
ATOM     47  CA  ILE    47      23.488  19.348  68.891  1.00  0.00              
ATOM     48  CA  GLY    48      21.838  18.380  72.197  1.00  0.00              
ATOM     49  CA  ALA    49      22.783  21.235  74.461  1.00  0.00              
ATOM     50  CA  GLY    50      20.037  22.751  76.351  1.00  0.00              
ATOM     51  CA  THR    51      18.679  26.241  76.786  1.00  0.00              
ATOM     52  CA  GLY    52      20.658  27.671  79.671  1.00  0.00              
ATOM     53  CA  GLU    53      23.938  26.197  78.570  1.00  0.00              
ATOM     54  CA  TRP    54      26.840  28.503  78.042  1.00  0.00              
ATOM     55  CA  VAL    55      28.887  28.100  74.845  1.00  0.00              
ATOM     56  CA  LEU    56      31.650  30.532  73.958  1.00  0.00              
ATOM     57  CA  LEU    57      32.410  31.109  70.218  1.00  0.00              
ATOM     58  CA  VAL    58      35.557  32.729  69.303  1.00  0.00              
ATOM     59  CA  SER    59      36.145  33.792  65.747  1.00  0.00              
ATOM     60  CA  GLY    60      38.221  36.928  65.032  1.00  0.00              
ATOM     61  CA  SER    61      35.566  39.117  63.515  1.00  0.00              
ATOM     62  CA  SER    62      33.141  40.615  65.963  1.00  0.00              
ATOM     63  CA  ALA    63      33.342  44.146  64.755  1.00  0.00              
ATOM     64  CA  ARG    64      32.907  43.322  61.019  1.00  0.00              
ATOM     65  CA  GLN    65      29.922  41.141  61.745  1.00  0.00              
ATOM     66  CA  ALA    66      27.732  43.216  63.959  1.00  0.00              
ATOM     67  CA  HIS    67      27.849  46.643  62.398  1.00  0.00              
ATOM     68  CA  LYS    68      27.637  45.983  58.807  1.00  0.00              
ATOM     69  CA  SER    69      25.038  43.241  58.518  1.00  0.00              
ATOM     70  CA  GLU    70      27.113  40.873  56.288  1.00  0.00              
ATOM     71  CA  THR    71      26.563  37.458  57.724  1.00  0.00              
ATOM     72  CA  SER    72      30.099  36.347  58.745  1.00  0.00              
ATOM     73  CA  PRO    73      30.467  32.802  60.001  1.00  0.00              
ATOM     74  CA  VAL    74      30.938  32.674  63.741  1.00  0.00              
ATOM     75  CA  ASP    75      32.633  29.661  65.191  1.00  0.00              
ATOM     76  CA  LEU    76      31.211  29.875  68.856  1.00  0.00              
ATOM     77  CA  CYS    77      27.521  28.894  69.656  1.00  0.00              
ATOM     78  CA  VAL    78      25.953  30.710  72.537  1.00  0.00              
ATOM     79  CA  ILE    79      23.242  29.209  74.441  1.00  0.00              
ATOM     80  CA  GLY    80      21.439  31.330  76.946  1.00  0.00              
ATOM     81  CA  ILE    81      23.578  34.371  77.899  1.00  0.00              
ATOM     82  CA  VAL    82      24.469  35.295  74.325  1.00  0.00              
ATOM     83  CA  ASP    83      20.898  35.195  73.133  1.00  0.00              
ATOM     84  CA  GLU    84      19.831  37.350  76.012  1.00  0.00              
ATOM     85  CA  VAL    85      22.170  40.086  75.410  1.00  0.00              
ATOM     86  CA  VAL    86      22.864  40.632  71.882  1.00  0.00              
ATOM     87  CA  SER    87      24.063  43.905  70.801  1.00  0.00              
ATOM     88  CA  GLY    88      24.879  44.248  67.248  1.00  0.00              
ATOM     89  CA  GLY    89      26.609  40.807  67.289  1.00  0.00              
ATOM     90  CA  GLN    90      28.489  41.707  70.304  1.00  0.00              
ATOM     91  CA  VAL    91      27.749  39.349  72.865  1.00  0.00              
ATOM     92  CA  ILE    92      27.364  40.403  76.340  1.00  0.00              
ATOM     93  CA  PHE    93      27.737  37.923  78.919  1.00  0.00              
ATOM     94  CA  HIS    94      28.170  33.893  80.186  1.00  0.00              
ATOM     95  CA  LYS    95      30.187  30.176  80.283  1.00  0.00              
TER                                                                             
END
