
#######################################################
#                                                     #
#                        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   94 (   94),  selected   94 , name T0283TS383_3-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS383_3-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      S       2           -
LGA    -       -      F       3           -
LGA    -       -      I       4           -
LGA    S       2      E       5          1.814
LGA    F       3      K       6          2.912
LGA    I       4      M       7          1.859
LGA    E       5      I       8          0.699
LGA    K       6      G       9          1.991
LGA    M       7      S      10          1.640
LGA    I       8      L      11          1.639
LGA    G       9      N      12          2.297
LGA    -       -      D      13           -
LGA    S      10      K      14          1.006
LGA    L      11      R      15          2.304
LGA    N      12      E      16          2.701
LGA    D      13      W      17          0.985
LGA    K      14      K      18          2.134
LGA    R      15      A      19          3.316
LGA    E      16      M      20          2.623
LGA    W      17      E      21          1.181
LGA    K      18      A      22          3.809
LGA    A      19      R      23          4.651
LGA    M      20      A      24          1.965
LGA    E      21      K      25          2.625
LGA    A      22      A      26          4.993
LGA    R      23      L      27          3.365
LGA    A      24      P      28          3.434
LGA    K      25      K      29          4.052
LGA    A      26      -       -           -
LGA    L      27      -       -           -
LGA    P      28      E      30           #
LGA    -       -      Y      31           -
LGA    -       -      H      32           -
LGA    K      29      H      33          5.130
LGA    E      30      A      34           -
LGA    Y      31      Y      35           -
LGA    H      32      K      36           -
LGA    H      33      A      37           -
LGA    -       -      I      38           -
LGA    A      34      Q      39           #
LGA    Y      35      K      40          2.486
LGA    K      36      -       -           -
LGA    A      37      -       -           -
LGA    I      38      Y      41          3.354
LGA    Q      39      M      42          3.057
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    K      40      G      46           #
LGA    Y      41      G      47          3.217
LGA    T      44      -       -           -
LGA    S      45      P      48          4.288
LGA    G      46      T      49           #
LGA    G      47      -       -           -
LGA    P      48      -       -           -
LGA    T      49      -       -           -
LGA    D      50      -       -           -
LGA    W      51      -       -           -
LGA    Q      52      -       -           -
LGA    D      53      -       -           -
LGA    T      54      -       -           -
LGA    K      55      -       -           -
LGA    R      56      -       -           -
LGA    I      57      -       -           -
LGA    F      58      -       -           -
LGA    G      59      -       -           -
LGA    G      60      D      50          2.764
LGA    I      61      W      51          1.860
LGA    L      62      Q      52          1.708
LGA    D      63      D      53          1.768
LGA    L      64      T      54          1.808
LGA    F      65      K      55          1.656
LGA    E      66      R      56          1.644
LGA    E      67      I      57          1.415
LGA    G      68      F      58          1.872
LGA    A      69      G      59          2.952
LGA    A      70      G      60          2.575
LGA    E      71      I      61          1.868
LGA    G      72      L      62          2.194
LGA    K      73      D      63          2.623
LGA    K      74      L      64          1.981
LGA    V      75      F      65          1.610
LGA    T      76      E      66          3.102
LGA    D      77      E      67          3.101
LGA    L      78      G      68          1.659
LGA    T      79      A      69          2.998
LGA    G      80      A      70          4.156
LGA    E      81      E      71          3.755
LGA    D      82      G      72          5.095
LGA    V      83      K      73           -
LGA    A      84      K      74           -
LGA    A      85      V      75           -
LGA    F      86      T      76           -
LGA    C      87      D      77           -
LGA    D      88      L      78           -
LGA    E      89      T      79           -
LGA    L      90      G      80           -
LGA    M      91      E      81           -
LGA    K      92      D      82           -
LGA    D      93      V      83           -
LGA    T      94      A      84           -
LGA    K      95      A      85           -
LGA    T      96      F      86           -
LGA    W      97      C      87           -
LGA    -       -      D      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    -       -      M      91           -
LGA    -       -      K      92           -
LGA    -       -      D      93           -
LGA    -       -      T      94           -
LGA    -       -      K      95           -
LGA    -       -      T      96           -
LGA    -       -      W      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   94   97    5.0     53    2.81     9.43     39.040     1.821

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.920103 * X  +  -0.297920 * Y  +   0.254272 * Z  +  73.644394
  Y_new =  -0.348460 * X  +   0.326202 * Y  +  -0.878731 * Z  +  29.325720
  Z_new =   0.178847 * X  +  -0.897127 * Y  +  -0.403952 * Z  +  23.696880 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.993877    1.147715  [ DEG:  -114.2408     65.7592 ]
  Theta =  -0.179815   -2.961778  [ DEG:   -10.3026   -169.6974 ]
  Phi   =  -2.779566    0.362027  [ DEG:  -159.2574     20.7426 ]
 
# 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: T0283TS383_3-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS383_3-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   94   97   5.0   53   2.81    9.43  39.040
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS383_3-D1
PFRMAT TS
TARGET T0283
MODEL 3
PARENT 2fjcA
ATOM      1  CA  SER     2      24.226   7.325  16.421  1.00  0.00
ATOM      2  CA  PHE     3      24.452  11.079  15.673  1.00  0.00
ATOM      3  CA  ILE     4      28.191  11.007  14.861  1.00  0.00
ATOM      4  CA  GLU     5      27.141   8.515  12.232  1.00  0.00
ATOM      5  CA  LYS     6      24.039  10.255  10.910  1.00  0.00
ATOM      6  CA  MET     7      25.911  13.511  10.237  1.00  0.00
ATOM      7  CA  ILE     8      28.564  11.682   8.169  1.00  0.00
ATOM      8  CA  GLY     9      25.713  10.139   6.178  1.00  0.00
ATOM      9  CA  SER    10      26.810  15.415   4.364  1.00  0.00
ATOM     10  CA  LEU    11      27.348  12.539   1.947  1.00  0.00
ATOM     11  CA  ASN    12      23.855  13.199   0.638  1.00  0.00
ATOM     12  CA  ASP    13      24.462  16.951   0.626  1.00  0.00
ATOM     13  CA  LYS    14      27.710  16.668  -1.321  1.00  0.00
ATOM     14  CA  ARG    15      25.840  14.450  -3.777  1.00  0.00
ATOM     15  CA  GLU    16      23.235  17.150  -4.429  1.00  0.00
ATOM     16  CA  TRP    17      26.115  19.648  -4.428  1.00  0.00
ATOM     17  CA  LYS    18      27.709  17.810  -7.318  1.00  0.00
ATOM     18  CA  ALA    19      24.600  17.072  -9.408  1.00  0.00
ATOM     19  CA  MET    20      23.291  20.637  -9.206  1.00  0.00
ATOM     20  CA  GLU    21      26.704  22.102 -10.047  1.00  0.00
ATOM     21  CA  ALA    22      26.827  19.809 -13.088  1.00  0.00
ATOM     22  CA  ARG    23      23.329  20.806 -14.140  1.00  0.00
ATOM     23  CA  ALA    24      24.534  24.384 -13.997  1.00  0.00
ATOM     24  CA  LYS    25      27.423  23.424 -16.285  1.00  0.00
ATOM     25  CA  ALA    26      25.012  21.760 -18.717  1.00  0.00
ATOM     26  CA  LEU    27      22.940  24.947 -18.824  1.00  0.00
ATOM     27  CA  PRO    28      29.685  26.733 -11.214  1.00  0.00
ATOM     28  CA  LYS    29      30.857  28.712  -8.182  1.00  0.00
ATOM     29  CA  GLU    30      33.938  26.791  -7.070  1.00  0.00
ATOM     30  CA  TYR    31      35.633  28.430  -4.087  1.00  0.00
ATOM     31  CA  HIS    32      34.791  29.012  -0.441  1.00  0.00
ATOM     32  CA  HIS    33      35.123  32.745  -1.059  1.00  0.00
ATOM     33  CA  ALA    34      32.298  32.600  -3.598  1.00  0.00
ATOM     34  CA  TYR    35      30.212  30.283  -1.442  1.00  0.00
ATOM     35  CA  LYS    36      30.471  32.588   1.572  1.00  0.00
ATOM     36  CA  ALA    37      29.438  35.446  -0.709  1.00  0.00
ATOM     37  CA  ILE    38      26.421  33.621  -2.180  1.00  0.00
ATOM     38  CA  GLN    39      25.232  31.415   0.660  1.00  0.00
ATOM     39  CA  LYS    40      22.188  32.238   2.739  1.00  0.00
ATOM     40  CA  TYR    41      23.293  29.690   5.318  1.00  0.00
ATOM     41  CA  THR    44      23.980  30.553   7.574  1.00  0.00
ATOM     42  CA  SER    45      25.249  30.870   8.356  1.00  0.00
ATOM     43  CA  GLY    46      28.327  28.860   9.292  1.00  0.00
ATOM     44  CA  GLY    47      28.486  27.209  12.707  1.00  0.00
ATOM     45  CA  PRO    48      30.995  29.165  14.784  1.00  0.00
ATOM     46  CA  THR    49      30.675  27.186  17.969  1.00  0.00
ATOM     47  CA  ASP    50      32.151  23.784  18.713  1.00  0.00
ATOM     48  CA  TRP    51      30.935  21.476  21.475  1.00  0.00
ATOM     49  CA  GLN    52      27.204  21.369  20.898  1.00  0.00
ATOM     50  CA  ASP    53      24.238  19.461  22.239  1.00  0.00
ATOM     51  CA  THR    54      22.700  16.755  20.069  1.00  0.00
ATOM     52  CA  LYS    55      19.184  18.223  20.090  1.00  0.00
ATOM     53  CA  ARG    56      20.674  21.652  19.446  1.00  0.00
ATOM     54  CA  ILE    57      22.651  20.378  16.431  1.00  0.00
ATOM     55  CA  PHE    58      19.733  18.435  14.958  1.00  0.00
ATOM     56  CA  GLY    59      17.387  21.414  15.391  1.00  0.00
ATOM     57  CA  GLY    60      19.854  23.522  13.430  1.00  0.00
ATOM     58  CA  ILE    61      20.252  21.078  10.558  1.00  0.00
ATOM     59  CA  LEU    62      16.462  20.714  10.434  1.00  0.00
ATOM     60  CA  ASP    63      16.263  24.491  10.130  1.00  0.00
ATOM     61  CA  LEU    64      18.840  24.579   7.330  1.00  0.00
ATOM     62  CA  PHE    65      17.127  21.675   5.561  1.00  0.00
ATOM     63  CA  GLU    66      13.846  23.603   5.702  1.00  0.00
ATOM     64  CA  GLU    67      15.558  26.728   4.385  1.00  0.00
ATOM     65  CA  GLY    68      17.008  24.684   1.515  1.00  0.00
ATOM     66  CA  ALA    69      13.615  23.110   0.916  1.00  0.00
ATOM     67  CA  ALA    70      11.839  26.434   0.371  1.00  0.00
ATOM     68  CA  GLU    71      14.744  27.654  -1.759  1.00  0.00
ATOM     69  CA  GLY    72      14.720  24.495  -3.881  1.00  0.00
ATOM     70  CA  LYS    73      10.943  24.649  -4.280  1.00  0.00
ATOM     71  CA  LYS    74      11.254  28.079  -5.886  1.00  0.00
ATOM     72  CA  VAL    75      13.662  26.607  -8.413  1.00  0.00
ATOM     73  CA  THR    76      11.340  23.640  -8.994  1.00  0.00
ATOM     74  CA  ASP    77       8.543  26.081  -9.789  1.00  0.00
ATOM     75  CA  LEU    78      10.732  28.096 -12.151  1.00  0.00
ATOM     76  CA  THR    79      11.930  24.989 -13.975  1.00  0.00
ATOM     77  CA  GLY    80       8.405  23.594 -14.154  1.00  0.00
ATOM     78  CA  GLU    81       6.899  26.766 -15.597  1.00  0.00
ATOM     79  CA  ASP    82      13.135  22.783 -17.889  1.00  0.00
ATOM     80  CA  VAL    83      16.267  20.647 -13.759  1.00  0.00
ATOM     81  CA  ALA    84      12.762  20.070 -12.437  1.00  0.00
ATOM     82  CA  ALA    85      13.463  16.383 -11.909  1.00  0.00
ATOM     83  CA  PHE    86      16.850  17.022 -10.362  1.00  0.00
ATOM     84  CA  CYS    87      15.536  19.487  -7.797  1.00  0.00
ATOM     85  CA  ASP    88      12.436  17.419  -7.080  1.00  0.00
ATOM     86  CA  GLU    89      14.585  14.360  -6.321  1.00  0.00
ATOM     87  CA  LEU    90      16.558  16.443  -3.831  1.00  0.00
ATOM     88  CA  MET    91      13.338  17.902  -2.472  1.00  0.00
ATOM     89  CA  LYS    92      12.135  14.349  -1.822  1.00  0.00
ATOM     90  CA  ASP    93      15.147  13.373   0.274  1.00  0.00
ATOM     91  CA  THR    94      14.978  16.703   2.132  1.00  0.00
ATOM     92  CA  LYS    95      11.332  16.138   2.941  1.00  0.00
ATOM     93  CA  THR    96      12.031  12.740   4.409  1.00  0.00
ATOM     94  CA  TRP    97      14.970  14.031   6.483  1.00  0.00
TER
END
