
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0378TS393_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS393_1-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    L       2      -       -           -
LGA    S       3      -       -           -
LGA    A       4      L       2           #
LGA    -       -      S       3           -
LGA    N       5      A       4          2.448
LGA    Q       6      N       5          1.651
LGA    I       7      Q       6          3.158
LGA    -       -      I       7           -
LGA    K       8      K       8          2.313
LGA    F       9      F       9          3.728
LGA    L      10      L      10          3.135
LGA    R      11      R      11          2.295
LGA    S      12      S      12          4.172
LGA    L      13      -       -           -
LGA    R      14      L      13          4.095
LGA    E      15      R      14           #
LGA    R      16      E      15          4.214
LGA    K      17      R      16          4.807
LGA    Y      18      K      17          2.772
LGA    R      19      Y      18          3.894
LGA    -       -      R      19           -
LGA    L      20      L      20          4.432
LGA    R      21      R      21          3.536
LGA    E      22      E      22          1.869
LGA    Q      23      Q      23          1.182
LGA    A      24      A      24          1.501
LGA    F      25      F      25          0.813
LGA    A      26      A      26          1.461
LGA    V      27      V      27          2.335
LGA    E      28      E      28          3.988
LGA    G      29      G      29          2.640
LGA    P      30      P      30          2.022
LGA    K      31      K      31          2.286
LGA    L      32      L      32          1.384
LGA    V      33      V      33          1.723
LGA    G      34      G      34          2.088
LGA    E      35      E      35          1.588
LGA    M      36      M      36          1.321
LGA    L      37      L      37          2.442
LGA    P      38      P      38          2.998
LGA    F      39      F      39          2.341
LGA    Y      40      Y      40          2.337
LGA    R      41      R      41          1.118
LGA    C      42      C      42          1.593
LGA    R      43      R      43          1.124
LGA    M      44      M      44          1.887
LGA    L      45      L      45          3.091
LGA    V      46      V      46          2.085
LGA    G      47      G      47           #
LGA    T      48      T      48          3.595
LGA    A      49      A      49          1.758
LGA    A      50      -       -           -
LGA    M      51      A      50          3.386
LGA    L      52      M      51          2.656
LGA    R      53      L      52          2.097
LGA    A      54      R      53          1.652
LGA    V      55      A      54          1.113
LGA    S      56      V      55          1.615
LGA    T      57      S      56          2.098
LGA    P      58      -       -           -
LGA    H      59      T      57          4.637
LGA    D      60      P      58          4.295
LGA    A      61      H      59          2.040
LGA    E      62      D      60          3.099
LGA    V      63      A      61          2.774
LGA    V      64      E      62          3.148
LGA    E      65      V      63          2.674
LGA    L      66      V      64           #
LGA    P      67      E      65           #
LGA    E      68      L      66          5.092
LGA    S      69      P      67          5.111
LGA    F      70      E      68           #
LGA    -       -      S      69           -
LGA    D      71      F      70          4.892
LGA    F      72      D      71          5.100
LGA    K      73      F      72          1.233
LGA    R      74      K      73          1.124
LGA    I      75      R      74          3.323
LGA    -       -      I      75           -
LGA    S      76      S      76          1.046
LGA    -       -      T      77           -
LGA    T      77      Q      78          2.273
LGA    Q      78      T      79          3.985
LGA    T      79      T      80          2.481
LGA    T      80      P      81           #
LGA    P      81      Q      82          0.753
LGA    Q      82      P      83          3.570
LGA    P      83      L      84           #
LGA    L      84      M      85           #
LGA    M      85      A      86           #
LGA    A      86      V      87           #
LGA    V      87      F      88           #
LGA    F      88      D      89          3.592
LGA    D      89      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     70    2.91    51.43     47.695     2.328

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.946747 * X  +  -0.283310 * Y  +   0.152991 * Z  +  17.707125
  Y_new =  -0.122736 * X  +  -0.121731 * Y  +  -0.984945 * Z  +  11.534190
  Z_new =   0.297668 * X  +  -0.951271 * Y  +   0.080476 * Z  +  42.888729 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.486399    1.655194  [ DEG:   -85.1644     94.8356 ]
  Theta =  -0.302249   -2.839344  [ DEG:   -17.3176   -162.6824 ]
  Phi   =  -3.012672    0.128921  [ DEG:  -172.6134      7.3866 ]
 
# 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: T0378TS393_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS393_1-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89   89   5.0   70   2.91   51.43  47.695
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS393_1-D1
PFRMAT TS
TARGET T0378
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      10.485  39.778  63.643  1.00 25.00           C
ATOM      2  CA  LEU     2       7.878  37.043  63.054  1.00 25.00           C
ATOM      3  CA  SER     3       5.642  36.251  60.025  1.00 25.00           C
ATOM      4  CA  ALA     4       4.496  38.083  56.929  1.00 25.00           C
ATOM      5  CA  ASN     5       8.041  37.662  55.461  1.00 25.00           C
ATOM      6  CA  GLN     6       7.996  33.832  55.451  1.00 25.00           C
ATOM      7  CA  ILE     7       7.866  33.820  51.623  1.00 25.00           C
ATOM      8  CA  LYS     8      10.827  36.245  51.490  1.00 25.00           C
ATOM      9  CA  PHE     9      12.800  34.005  53.891  1.00 25.00           C
ATOM     10  CA  LEU    10      12.023  30.949  51.717  1.00 25.00           C
ATOM     11  CA  ARG    11      13.192  32.841  48.597  1.00 25.00           C
ATOM     12  CA  SER    12      16.432  33.831  50.382  1.00 25.00           C
ATOM     13  CA  LEU    13      17.010  30.187  51.408  1.00 25.00           C
ATOM     14  CA  ARG    14      16.440  29.054  47.794  1.00 25.00           C
ATOM     15  CA  GLU    15      18.931  31.683  46.551  1.00 25.00           C
ATOM     16  CA  ARG    16      21.507  30.494  49.123  1.00 25.00           C
ATOM     17  CA  LYS    17      23.727  27.926  50.910  1.00 25.00           C
ATOM     18  CA  TYR    18      21.761  28.500  54.048  1.00 25.00           C
ATOM     19  CA  ARG    19      22.097  25.031  55.676  1.00 25.00           C
ATOM     20  CA  LEU    20      21.465  24.639  59.406  1.00 25.00           C
ATOM     21  CA  ARG    21      18.725  23.325  61.695  1.00 25.00           C
ATOM     22  CA  GLU    22      15.550  23.086  59.722  1.00 25.00           C
ATOM     23  CA  GLN    23      16.431  20.890  56.767  1.00 25.00           C
ATOM     24  CA  ALA    24      14.000  21.925  53.992  1.00 25.00           C
ATOM     25  CA  PHE    25      13.426  20.811  50.381  1.00 25.00           C
ATOM     26  CA  ALA    26      10.916  20.744  47.449  1.00 25.00           C
ATOM     27  CA  VAL    27       7.374  21.433  46.218  1.00 25.00           C
ATOM     28  CA  GLU    28       4.028  19.655  45.866  1.00 25.00           C
ATOM     29  CA  GLY    29       1.840  18.851  42.886  1.00 25.00           C
ATOM     30  CA  PRO    30       0.673  15.627  41.206  1.00 25.00           C
ATOM     31  CA  LYS    31       2.266  12.157  40.911  1.00 25.00           C
ATOM     32  CA  LEU    32       5.155  13.264  43.169  1.00 25.00           C
ATOM     33  CA  VAL    33       2.659  14.614  45.741  1.00 25.00           C
ATOM     34  CA  GLY    34       0.737  11.302  45.651  1.00 25.00           C
ATOM     35  CA  GLU    35       4.001   9.367  46.171  1.00 25.00           C
ATOM     36  CA  MET    36       4.890  11.615  49.143  1.00 25.00           C
ATOM     37  CA  LEU    37       1.418  11.033  50.652  1.00 25.00           C
ATOM     38  CA  PRO    38       1.837   7.251  50.219  1.00 25.00           C
ATOM     39  CA  PHE    39       4.309   7.997  52.992  1.00 25.00           C
ATOM     40  CA  TYR    40       6.069  10.855  54.817  1.00 25.00           C
ATOM     41  CA  ARG    41       5.586  14.381  56.289  1.00 25.00           C
ATOM     42  CA  CYS    42       6.248  18.110  55.659  1.00 25.00           C
ATOM     43  CA  ARG    43       5.925  21.834  56.420  1.00 25.00           C
ATOM     44  CA  MET    44       4.522  22.572  52.920  1.00 25.00           C
ATOM     45  CA  LEU    45       3.439  24.915  50.126  1.00 25.00           C
ATOM     46  CA  VAL    46       1.088  27.875  49.638  1.00 25.00           C
ATOM     47  CA  GLY    47      -2.160  29.700  49.026  1.00 25.00           C
ATOM     48  CA  THR    48      -5.253  28.920  47.031  1.00 25.00           C
ATOM     49  CA  ALA    49      -7.983  26.995  45.239  1.00 25.00           C
ATOM     50  CA  ALA    50     -10.645  25.054  47.192  1.00 25.00           C
ATOM     51  CA  MET    51     -10.841  22.454  44.388  1.00 25.00           C
ATOM     52  CA  LEU    52      -7.028  22.102  44.414  1.00 25.00           C
ATOM     53  CA  ARG    53      -7.073  21.629  48.214  1.00 25.00           C
ATOM     54  CA  ALA    54      -9.787  18.950  47.873  1.00 25.00           C
ATOM     55  CA  VAL    55      -7.717  17.157  45.197  1.00 25.00           C
ATOM     56  CA  SER    56      -4.638  17.263  47.472  1.00 25.00           C
ATOM     57  CA  THR    57      -6.696  15.823  50.363  1.00 25.00           C
ATOM     58  CA  PRO    58      -9.484  13.599  51.589  1.00 25.00           C
ATOM     59  CA  HIS    59      -8.280  14.814  55.031  1.00 25.00           C
ATOM     60  CA  ASP    60      -4.608  13.767  54.641  1.00 25.00           C
ATOM     61  CA  ALA    61      -2.630  15.708  57.247  1.00 25.00           C
ATOM     62  CA  GLU    62       0.588  17.103  58.790  1.00 25.00           C
ATOM     63  CA  VAL    63       1.142  19.460  55.848  1.00 25.00           C
ATOM     64  CA  VAL    64      -0.222  22.836  54.849  1.00 25.00           C
ATOM     65  CA  GLU    65      -1.786  24.167  51.588  1.00 25.00           C
ATOM     66  CA  LEU    66      -2.406  24.467  47.854  1.00 25.00           C
ATOM     67  CA  PRO    67      -0.732  26.150  44.877  1.00 25.00           C
ATOM     68  CA  GLU    68      -2.186  28.733  42.413  1.00 25.00           C
ATOM     69  CA  SER    69      -0.804  31.876  44.066  1.00 25.00           C
ATOM     70  CA  PHE    70       0.577  33.980  41.180  1.00 25.00           C
ATOM     71  CA  ASP    71       3.709  34.786  43.234  1.00 25.00           C
ATOM     72  CA  PHE    72       4.185  31.067  44.014  1.00 25.00           C
ATOM     73  CA  LYS    73       3.833  30.217  40.296  1.00 25.00           C
ATOM     74  CA  ARG    74       6.424  32.896  39.414  1.00 25.00           C
ATOM     75  CA  ILE    75       8.820  31.480  42.044  1.00 25.00           C
ATOM     76  CA  SER    76       8.676  27.719  41.630  1.00 25.00           C
ATOM     77  CA  THR    77       9.737  27.951  37.999  1.00 25.00           C
ATOM     78  CA  GLN    78       7.024  28.526  35.413  1.00 25.00           C
ATOM     79  CA  THR    79       4.822  25.974  33.700  1.00 25.00           C
ATOM     80  CA  THR    80       1.542  24.205  34.506  1.00 25.00           C
ATOM     81  CA  PRO    81       2.292  23.955  38.199  1.00 25.00           C
ATOM     82  CA  GLN    82       3.550  24.021  41.839  1.00 25.00           C
ATOM     83  CA  PRO    83       5.889  21.120  41.152  1.00 25.00           C
ATOM     84  CA  LEU    84       7.278  17.761  42.399  1.00 25.00           C
ATOM     85  CA  MET    85       8.262  16.441  45.873  1.00 25.00           C
ATOM     86  CA  ALA    86       9.090  17.096  49.493  1.00 25.00           C
ATOM     87  CA  VAL    87      11.980  14.717  50.314  1.00 25.00           C
ATOM     88  CA  PHE    88      12.990  15.854  53.765  1.00 25.00           C
ATOM     89  CA  ASP    89      15.103  12.741  54.198  1.00 25.00           C
TER
END
