
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0283TS168_2-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS168_2-D1.T0283_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    S       2      S       2           #
LGA    F       3      F       3          0.666
LGA    I       4      I       4          0.871
LGA    E       5      E       5          0.811
LGA    K       6      K       6          0.595
LGA    M       7      M       7          0.347
LGA    I       8      I       8          0.295
LGA    G       9      G       9          0.359
LGA    S      10      S      10          0.488
LGA    L      11      L      11          0.512
LGA    N      12      N      12          0.392
LGA    D      13      D      13          0.462
LGA    K      14      K      14          0.291
LGA    R      15      R      15          0.306
LGA    E      16      E      16          0.607
LGA    W      17      W      17          0.410
LGA    K      18      K      18          0.382
LGA    A      19      A      19          0.703
LGA    M      20      M      20          0.618
LGA    E      21      E      21          0.497
LGA    A      22      A      22          0.639
LGA    R      23      R      23          0.826
LGA    A      24      A      24          0.943
LGA    K      25      K      25          1.139
LGA    A      26      A      26          1.466
LGA    L      27      L      27           #
LGA    P      28      P      28           -
LGA    K      29      K      29           -
LGA    E      30      E      30           -
LGA    Y      31      Y      31           -
LGA    H      32      H      32           -
LGA    -       -      H      33           -
LGA    -       -      A      34           -
LGA    -       -      Y      35           -
LGA    -       -      K      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Q      39           -
LGA    -       -      K      40           -
LGA    -       -      Y      41           -
LGA    -       -      M      42           -
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
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    H      33      G      59          4.921
LGA    A      34      G      60          3.721
LGA    Y      35      I      61           -
LGA    K      36      L      62           -
LGA    A      37      -       -           -
LGA    I      38      -       -           -
LGA    Q      39      -       -           -
LGA    K      40      -       -           -
LGA    Y      41      -       -           -
LGA    M      42      -       -           -
LGA    W      43      -       -           -
LGA    T      44      -       -           -
LGA    S      45      -       -           -
LGA    G      46      -       -           -
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      D      63           #
LGA    F      58      L      64          2.633
LGA    G      59      -       -           -
LGA    G      60      F      65          4.957
LGA    I      61      E      66          4.632
LGA    L      62      E      67          2.233
LGA    D      63      G      68          0.639
LGA    L      64      -       -           -
LGA    F      65      -       -           -
LGA    E      66      A      69          1.768
LGA    E      67      A      70           -
LGA    G      68      E      71           -
LGA    A      69      -       -           -
LGA    A      70      -       -           -
LGA    E      71      G      72          3.761
LGA    G      72      K      73          3.054
LGA    K      73      K      74          3.818
LGA    -       -      V      75           -
LGA    -       -      T      76           -
LGA    K      74      D      77          1.160
LGA    V      75      L      78          2.968
LGA    T      76      T      79          4.537
LGA    D      77      G      80          2.364
LGA    -       -      E      81           -
LGA    -       -      D      82           -
LGA    L      78      V      83           #
LGA    T      79      A      84           -
LGA    G      80      -       -           -
LGA    E      81      -       -           -
LGA    D      82      A      85          4.754
LGA    V      83      -       -           -
LGA    A      84      F      86          1.020
LGA    A      85      C      87          3.207
LGA    F      86      D      88          2.558
LGA    C      87      E      89           -
LGA    D      88      L      90           -
LGA    E      89      -       -           -
LGA    L      90      M      91           #
LGA    M      91      K      92           -
LGA    K      92      D      93           -
LGA    -       -      T      94           -
LGA    -       -      K      95           -
LGA    -       -      T      96           -
LGA    D      93      W      97           #
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)   97   97    5.0     43    2.29    60.47     34.040     1.800

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.229823 * X  +  -0.915907 * Y  +  -0.329084 * Z  +  20.341280
  Y_new =  -0.391997 * X  +  -0.396610 * Y  +   0.830084 * Z  +  24.483137
  Z_new =  -0.890797 * X  +  -0.061772 * Y  +  -0.450182 * Z  +   0.790108 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.005228    0.136365  [ DEG:  -172.1869      7.8131 ]
  Theta =   1.099097    2.042495  [ DEG:    62.9736    117.0264 ]
  Phi   =  -1.040520    2.101073  [ DEG:   -59.6174    120.3826 ]
 
# 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: T0283TS168_2-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS168_2-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   97   5.0   43   2.29   60.47  34.040
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS168_2-D1
PFRMAT TS
TARGET T0283
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      29.905  14.742  20.423  1.00 25.00           C
ATOM      2  CA  SER     2      32.166  12.173  18.806  1.00 25.00           C
ATOM      3  CA  PHE     3      30.665   8.905  19.991  1.00 25.00           C
ATOM      4  CA  ILE     4      29.612   6.247  17.441  1.00 25.00           C
ATOM      5  CA  GLU     5      26.091   7.747  17.296  1.00 25.00           C
ATOM      6  CA  LYS     6      27.572  11.235  16.743  1.00 25.00           C
ATOM      7  CA  MET     7      29.784   9.876  13.928  1.00 25.00           C
ATOM      8  CA  ILE     8      26.739   8.211  12.307  1.00 25.00           C
ATOM      9  CA  GLY     9      24.790  11.501  12.533  1.00 25.00           C
ATOM     10  CA  SER    10      27.717  13.375  10.923  1.00 25.00           C
ATOM     11  CA  LEU    11      27.855  10.787   8.103  1.00 25.00           C
ATOM     12  CA  ASN    12      24.086  11.164   7.540  1.00 25.00           C
ATOM     13  CA  ASP    13      24.463  14.972   7.403  1.00 25.00           C
ATOM     14  CA  LYS    14      27.306  14.625   4.861  1.00 25.00           C
ATOM     15  CA  ARG    15      25.147  12.288   2.729  1.00 25.00           C
ATOM     16  CA  GLU    16      22.259  14.799   2.858  1.00 25.00           C
ATOM     17  CA  TRP    17      24.626  17.615   1.794  1.00 25.00           C
ATOM     18  CA  LYS    18      25.898  15.478  -1.119  1.00 25.00           C
ATOM     19  CA  ALA    19      22.294  14.756  -2.195  1.00 25.00           C
ATOM     20  CA  MET    20      21.479  18.495  -2.062  1.00 25.00           C
ATOM     21  CA  GLU    21      24.572  19.270  -4.184  1.00 25.00           C
ATOM     22  CA  ALA    22      23.518  16.614  -6.733  1.00 25.00           C
ATOM     23  CA  ARG    23      19.996  18.113  -6.879  1.00 25.00           C
ATOM     24  CA  ALA    24      21.479  21.601  -7.431  1.00 25.00           C
ATOM     25  CA  LYS    25      23.691  20.242 -10.247  1.00 25.00           C
ATOM     26  CA  ALA    26      20.646  18.577 -11.868  1.00 25.00           C
ATOM     27  CA  LEU    27      17.303  17.352 -10.531  1.00 25.00           C
ATOM     28  CA  PRO    28      15.387  15.845  -7.658  1.00 25.00           C
ATOM     29  CA  LYS    29      15.040  14.303  -4.216  1.00 25.00           C
ATOM     30  CA  GLU    30      17.185  17.307  -3.195  1.00 25.00           C
ATOM     31  CA  TYR    31      14.329  19.688  -4.111  1.00 25.00           C
ATOM     32  CA  HIS    32      11.885  17.593  -2.036  1.00 25.00           C
ATOM     33  CA  HIS    33      14.299  17.676   0.936  1.00 25.00           C
ATOM     34  CA  ALA    34      14.613  21.479   0.606  1.00 25.00           C
ATOM     35  CA  TYR    35      10.799  21.812   0.526  1.00 25.00           C
ATOM     36  CA  LYS    36      10.518  19.630   3.661  1.00 25.00           C
ATOM     37  CA  ALA    37      13.139  21.791   5.430  1.00 25.00           C
ATOM     38  CA  ILE    38      11.219  24.959   4.458  1.00 25.00           C
ATOM     39  CA  GLN    39       7.973  23.434   5.804  1.00 25.00           C
ATOM     40  CA  LYS    40       9.729  22.532   9.086  1.00 25.00           C
ATOM     41  CA  TYR    41      11.073  26.107   9.377  1.00 25.00           C
ATOM     42  CA  MET    42       7.559  27.503   8.772  1.00 25.00           C
ATOM     43  CA  TRP    43       6.144  25.181  11.468  1.00 25.00           C
ATOM     44  CA  THR    44       8.859  26.327  13.915  1.00 25.00           C
ATOM     45  CA  SER    45       9.892  29.812  12.896  1.00 25.00           C
ATOM     46  CA  GLY    46       8.260  32.673  10.924  1.00 25.00           C
ATOM     47  CA  GLY    47       4.937  31.756   9.189  1.00 25.00           C
ATOM     48  CA  PRO    48       5.305  34.405   6.430  1.00 25.00           C
ATOM     49  CA  THR    49       3.216  32.109   4.181  1.00 25.00           C
ATOM     50  CA  ASP    50       3.264  28.392   4.879  1.00 25.00           C
ATOM     51  CA  TRP    51       3.780  25.085   3.058  1.00 25.00           C
ATOM     52  CA  GLN    52       2.631  27.493   0.310  1.00 25.00           C
ATOM     53  CA  ASP    53       5.850  29.529   0.716  1.00 25.00           C
ATOM     54  CA  THR    54       7.936  26.327   0.464  1.00 25.00           C
ATOM     55  CA  LYS    55       6.048  25.317  -2.711  1.00 25.00           C
ATOM     56  CA  ARG    56       6.674  28.783  -4.215  1.00 25.00           C
ATOM     57  CA  ILE    57      10.399  28.503  -3.374  1.00 25.00           C
ATOM     58  CA  PHE    58      10.536  25.048  -5.020  1.00 25.00           C
ATOM     59  CA  GLY    59       8.818  26.441  -8.146  1.00 25.00           C
ATOM     60  CA  GLY    60      11.334  29.326  -8.272  1.00 25.00           C
ATOM     61  CA  ILE    61      14.233  26.844  -7.960  1.00 25.00           C
ATOM     62  CA  LEU    62      12.766  24.735 -10.799  1.00 25.00           C
ATOM     63  CA  ASP    63      12.432  27.863 -12.984  1.00 25.00           C
ATOM     64  CA  LEU    64      16.070  28.799 -12.242  1.00 25.00           C
ATOM     65  CA  PHE    65      17.196  25.259 -13.173  1.00 25.00           C
ATOM     66  CA  GLU    66      15.222  25.465 -16.448  1.00 25.00           C
ATOM     67  CA  GLU    67      16.837  28.847 -17.236  1.00 25.00           C
ATOM     68  CA  GLY    68      20.306  27.380 -16.545  1.00 25.00           C
ATOM     69  CA  ALA    69      19.542  24.421 -18.854  1.00 25.00           C
ATOM     70  CA  ALA    70      18.394  26.830 -21.602  1.00 25.00           C
ATOM     71  CA  GLU    71      15.515  29.349 -21.477  1.00 25.00           C
ATOM     72  CA  GLY    72      13.156  31.550 -19.471  1.00 25.00           C
ATOM     73  CA  LYS    73      12.091  32.238 -15.847  1.00 25.00           C
ATOM     74  CA  LYS    74      13.162  35.092 -13.547  1.00 25.00           C
ATOM     75  CA  VAL    75      15.030  34.040 -10.408  1.00 25.00           C
ATOM     76  CA  THR    76      18.251  35.539  -8.978  1.00 25.00           C
ATOM     77  CA  ASP    77      16.505  38.917  -8.520  1.00 25.00           C
ATOM     78  CA  LEU    78      13.588  37.195  -6.732  1.00 25.00           C
ATOM     79  CA  THR    79      11.013  34.836  -5.349  1.00 25.00           C
ATOM     80  CA  GLY    80       9.295  37.579  -3.423  1.00 25.00           C
ATOM     81  CA  GLU    81      11.915  40.240  -2.574  1.00 25.00           C
ATOM     82  CA  ASP    82      11.992  39.040   1.061  1.00 25.00           C
ATOM     83  CA  VAL    83      12.451  35.425  -0.116  1.00 25.00           C
ATOM     84  CA  ALA    84      15.320  36.509  -2.409  1.00 25.00           C
ATOM     85  CA  ALA    85      16.971  38.376   0.499  1.00 25.00           C
ATOM     86  CA  PHE    86      16.634  35.272   2.715  1.00 25.00           C
ATOM     87  CA  CYS    87      18.206  33.112  -0.029  1.00 25.00           C
ATOM     88  CA  ASP    88      21.102  35.595  -0.359  1.00 25.00           C
ATOM     89  CA  GLU    89      21.630  35.522   3.434  1.00 25.00           C
ATOM     90  CA  LEU    90      21.656  31.692   3.380  1.00 25.00           C
ATOM     91  CA  MET    91      24.225  31.724   0.540  1.00 25.00           C
ATOM     92  CA  LYS    92      26.412  34.171   2.513  1.00 25.00           C
ATOM     93  CA  ASP    93      26.189  31.918   5.602  1.00 25.00           C
ATOM     94  CA  THR    94      27.185  28.882   3.490  1.00 25.00           C
ATOM     95  CA  LYS    95      30.168  30.819   2.068  1.00 25.00           C
ATOM     96  CA  THR    96      31.242  31.811   5.608  1.00 25.00           C
ATOM     97  CA  TRP    97      30.992  28.159   6.734  1.00 25.00           C
TER
END
