
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS168_1-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           -
LGA    I       4      I       4           -
LGA    E       5      -       -           -
LGA    K       6      -       -           -
LGA    M       7      -       -           -
LGA    I       8      -       -           -
LGA    G       9      -       -           -
LGA    S      10      -       -           -
LGA    L      11      E       5           #
LGA    N      12      K       6           -
LGA    D      13      M       7           -
LGA    K      14      I       8           -
LGA    R      15      G       9           #
LGA    E      16      S      10           -
LGA    W      17      L      11           -
LGA    -       -      N      12           -
LGA    K      18      D      13          4.544
LGA    A      19      K      14           #
LGA    M      20      R      15           -
LGA    E      21      -       -           -
LGA    A      22      -       -           -
LGA    R      23      E      16           #
LGA    A      24      -       -           -
LGA    K      25      -       -           -
LGA    A      26      -       -           -
LGA    L      27      -       -           -
LGA    P      28      W      17           #
LGA    K      29      K      18          3.425
LGA    E      30      A      19           #
LGA    Y      31      -       -           -
LGA    H      32      M      20          5.215
LGA    H      33      E      21          2.746
LGA    A      34      A      22           -
LGA    Y      35      R      23           #
LGA    K      36      A      24          1.902
LGA    A      37      K      25           -
LGA    I      38      A      26           -
LGA    Q      39      L      27          5.332
LGA    K      40      P      28           -
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      K      29          4.837
LGA    W      51      E      30          3.862
LGA    -       -      Y      31           -
LGA    -       -      H      32           -
LGA    Q      52      H      33          1.567
LGA    D      53      A      34          1.818
LGA    T      54      Y      35          1.606
LGA    K      55      K      36          1.440
LGA    R      56      A      37          1.487
LGA    I      57      I      38          1.370
LGA    F      58      Q      39          1.494
LGA    G      59      K      40          2.111
LGA    G      60      Y      41          2.171
LGA    I      61      M      42          1.948
LGA    L      62      W      43          2.414
LGA    D      63      -       -           -
LGA    L      64      T      44          0.997
LGA    F      65      -       -           -
LGA    E      66      -       -           -
LGA    E      67      S      45          4.803
LGA    G      68      -       -           -
LGA    A      69      -       -           -
LGA    A      70      -       -           -
LGA    E      71      -       -           -
LGA    G      72      -       -           -
LGA    K      73      -       -           -
LGA    K      74      -       -           -
LGA    V      75      -       -           -
LGA    T      76      G      46          4.068
LGA    D      77      G      47           -
LGA    L      78      P      48           -
LGA    T      79      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           -
LGA    -       -      I      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      L      64           -
LGA    -       -      F      65           -
LGA    -       -      E      66           -
LGA    -       -      E      67           -
LGA    -       -      G      68           -
LGA    -       -      A      69           -
LGA    -       -      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    -       -      K      73           -
LGA    -       -      K      74           -
LGA    -       -      V      75           -
LGA    -       -      T      76           -
LGA    -       -      D      77           -
LGA    -       -      L      78           -
LGA    -       -      T      79           -
LGA    G      80      G      80           #
LGA    E      81      E      81          4.830
LGA    D      82      D      82          2.266
LGA    V      83      V      83          0.950
LGA    A      84      A      84          1.073
LGA    A      85      A      85          1.742
LGA    F      86      F      86          1.271
LGA    C      87      C      87          0.535
LGA    D      88      D      88          0.970
LGA    E      89      E      89          1.202
LGA    L      90      L      90          0.789
LGA    M      91      M      91          0.971
LGA    K      92      K      92          2.169
LGA    D      93      D      93           #
LGA    T      94      T      94          4.086
LGA    K      95      K      95           #
LGA    T      96      T      96           -
LGA    W      97      W      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     35    2.80    45.71     25.844     1.207

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.794369 * X  +  -0.545443 * Y  +  -0.267340 * Z  +  17.853390
  Y_new =  -0.048630 * X  +  -0.381594 * Y  +   0.923050 * Z  +  25.958046
  Z_new =  -0.605486 * X  +   0.746243 * Y  +   0.276601 * Z  +   4.847558 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.215837   -1.925756  [ DEG:    69.6623   -110.3377 ]
  Theta =   0.650377    2.491216  [ DEG:    37.2638    142.7362 ]
  Phi   =  -3.080451    0.061142  [ DEG:  -176.4968      3.5032 ]
 
# 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_1-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS168_1-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   35   2.80   45.71  25.844
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS168_1-D1
PFRMAT TS
TARGET T0283
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1       5.854   3.220  19.226  1.00 25.00           C
ATOM      2  CA  SER     2       4.815   5.732  16.531  1.00 25.00           C
ATOM      3  CA  PHE     3       3.168   3.722  13.694  1.00 25.00           C
ATOM      4  CA  ILE     4       5.769   2.548  11.140  1.00 25.00           C
ATOM      5  CA  GLU     5       4.918   5.516   8.873  1.00 25.00           C
ATOM      6  CA  LYS     6       5.289   7.915  11.834  1.00 25.00           C
ATOM      7  CA  MET     7       8.687   6.371  12.693  1.00 25.00           C
ATOM      8  CA  ILE     8       9.813   6.764   9.054  1.00 25.00           C
ATOM      9  CA  GLY     9       8.700  10.428   9.080  1.00 25.00           C
ATOM     10  CA  SER    10      10.636  11.019  12.330  1.00 25.00           C
ATOM     11  CA  LEU    11      13.752   9.406  10.796  1.00 25.00           C
ATOM     12  CA  ASN    12      13.409  11.632   7.698  1.00 25.00           C
ATOM     13  CA  ASP    13      13.089  14.729   9.929  1.00 25.00           C
ATOM     14  CA  LYS    14      16.219  13.683  11.873  1.00 25.00           C
ATOM     15  CA  ARG    15      18.129  13.206   8.587  1.00 25.00           C
ATOM     16  CA  GLU    16      17.011  16.673   7.405  1.00 25.00           C
ATOM     17  CA  TRP    17      18.165  18.203  10.721  1.00 25.00           C
ATOM     18  CA  LYS    18      21.558  16.461  10.372  1.00 25.00           C
ATOM     19  CA  ALA    19      21.901  17.793   6.797  1.00 25.00           C
ATOM     20  CA  MET    20      21.066  21.329   8.009  1.00 25.00           C
ATOM     21  CA  GLU    21      23.688  21.025  10.783  1.00 25.00           C
ATOM     22  CA  ALA    22      26.290  19.851   8.229  1.00 25.00           C
ATOM     23  CA  ARG    23      25.439  22.819   5.962  1.00 25.00           C
ATOM     24  CA  ALA    24      25.810  25.219   8.923  1.00 25.00           C
ATOM     25  CA  LYS    25      29.207  23.674   9.782  1.00 25.00           C
ATOM     26  CA  ALA    26      30.333  24.068   6.143  1.00 25.00           C
ATOM     27  CA  LEU    27      29.518  22.093   3.029  1.00 25.00           C
ATOM     28  CA  PRO    28      30.661  20.839  -0.437  1.00 25.00           C
ATOM     29  CA  LYS    29      28.229  17.912  -0.915  1.00 25.00           C
ATOM     30  CA  GLU    30      25.376  19.367   1.185  1.00 25.00           C
ATOM     31  CA  TYR    31      25.937  22.811  -0.394  1.00 25.00           C
ATOM     32  CA  HIS    32      25.867  21.246  -3.888  1.00 25.00           C
ATOM     33  CA  HIS    33      22.603  19.433  -3.038  1.00 25.00           C
ATOM     34  CA  ALA    34      21.078  22.714  -1.782  1.00 25.00           C
ATOM     35  CA  TYR    35      22.145  24.474  -5.012  1.00 25.00           C
ATOM     36  CA  LYS    36      20.570  21.669  -7.089  1.00 25.00           C
ATOM     37  CA  ALA    37      17.324  21.970  -5.081  1.00 25.00           C
ATOM     38  CA  ILE    38      17.297  25.758  -5.644  1.00 25.00           C
ATOM     39  CA  GLN    39      17.826  25.228  -9.399  1.00 25.00           C
ATOM     40  CA  LYS    40      14.941  22.710  -9.476  1.00 25.00           C
ATOM     41  CA  TYR    41      12.686  25.202  -7.636  1.00 25.00           C
ATOM     42  CA  MET    42      13.627  27.941 -10.142  1.00 25.00           C
ATOM     43  CA  TRP    43      12.827  25.585 -13.054  1.00 25.00           C
ATOM     44  CA  THR    44       9.436  24.751 -11.480  1.00 25.00           C
ATOM     45  CA  SER    45       8.766  28.438 -11.408  1.00 25.00           C
ATOM     46  CA  GLY    46      11.040  30.426 -13.790  1.00 25.00           C
ATOM     47  CA  GLY    47      14.338  32.306 -14.011  1.00 25.00           C
ATOM     48  CA  PRO    48      18.013  31.888 -14.899  1.00 25.00           C
ATOM     49  CA  THR    49      20.342  32.945 -12.162  1.00 25.00           C
ATOM     50  CA  ASP    50      22.252  29.830 -13.149  1.00 25.00           C
ATOM     51  CA  TRP    51      24.617  27.087 -11.901  1.00 25.00           C
ATOM     52  CA  GLN    52      27.306  29.734 -11.244  1.00 25.00           C
ATOM     53  CA  ASP    53      24.768  31.874  -9.337  1.00 25.00           C
ATOM     54  CA  THR    54      23.743  28.837  -7.241  1.00 25.00           C
ATOM     55  CA  LYS    55      27.421  28.104  -6.462  1.00 25.00           C
ATOM     56  CA  ARG    56      27.951  31.749  -5.413  1.00 25.00           C
ATOM     57  CA  ILE    57      24.873  31.569  -3.142  1.00 25.00           C
ATOM     58  CA  PHE    58      26.194  28.340  -1.564  1.00 25.00           C
ATOM     59  CA  GLY    59      29.597  29.994  -0.969  1.00 25.00           C
ATOM     60  CA  GLY    60      27.875  33.002   0.662  1.00 25.00           C
ATOM     61  CA  ILE    61      25.854  30.655   2.914  1.00 25.00           C
ATOM     62  CA  LEU    62      29.060  28.816   3.916  1.00 25.00           C
ATOM     63  CA  ASP    63      30.750  32.154   4.730  1.00 25.00           C
ATOM     64  CA  LEU    64      27.740  33.188   6.860  1.00 25.00           C
ATOM     65  CA  PHE    65      27.878  29.844   8.721  1.00 25.00           C
ATOM     66  CA  GLU    66      31.623  30.324   9.359  1.00 25.00           C
ATOM     67  CA  GLU    67      30.968  33.854  10.691  1.00 25.00           C
ATOM     68  CA  GLY    68      28.233  32.501  13.005  1.00 25.00           C
ATOM     69  CA  ALA    69      30.621  29.793  14.284  1.00 25.00           C
ATOM     70  CA  ALA    70      33.310  32.441  14.940  1.00 25.00           C
ATOM     71  CA  GLU    71      33.510  36.224  14.440  1.00 25.00           C
ATOM     72  CA  GLY    72      31.858  38.647  11.928  1.00 25.00           C
ATOM     73  CA  LYS    73      30.597  38.346   8.344  1.00 25.00           C
ATOM     74  CA  LYS    74      29.075  39.739   5.144  1.00 25.00           C
ATOM     75  CA  VAL    75      26.525  38.061   2.910  1.00 25.00           C
ATOM     76  CA  THR    76      24.080  39.216   5.623  1.00 25.00           C
ATOM     77  CA  ASP    77      23.872  42.677   3.996  1.00 25.00           C
ATOM     78  CA  LEU    78      23.185  41.063   0.592  1.00 25.00           C
ATOM     79  CA  THR    79      23.261  40.651  -3.204  1.00 25.00           C
ATOM     80  CA  GLY    80      21.728  40.426  -6.662  1.00 25.00           C
ATOM     81  CA  GLU    81      18.953  42.521  -5.057  1.00 25.00           C
ATOM     82  CA  ASP    82      16.339  39.945  -6.152  1.00 25.00           C
ATOM     83  CA  VAL    83      18.462  37.124  -4.668  1.00 25.00           C
ATOM     84  CA  ALA    84      18.778  39.060  -1.378  1.00 25.00           C
ATOM     85  CA  ALA    85      14.986  39.589  -1.296  1.00 25.00           C
ATOM     86  CA  PHE    86      14.427  35.850  -1.906  1.00 25.00           C
ATOM     87  CA  CYS    87      16.853  34.999   0.934  1.00 25.00           C
ATOM     88  CA  ASP    88      15.009  37.414   3.265  1.00 25.00           C
ATOM     89  CA  GLU    89      11.663  35.805   2.326  1.00 25.00           C
ATOM     90  CA  LEU    90      13.109  32.330   3.030  1.00 25.00           C
ATOM     91  CA  MET    91      14.393  33.525   6.433  1.00 25.00           C
ATOM     92  CA  LYS    92      10.942  34.966   7.258  1.00 25.00           C
ATOM     93  CA  ASP    93       9.296  31.650   6.276  1.00 25.00           C
ATOM     94  CA  THR    94      11.758  29.741   8.502  1.00 25.00           C
ATOM     95  CA  LYS    95      10.989  32.100  11.419  1.00 25.00           C
ATOM     96  CA  THR    96       7.234  31.570  10.889  1.00 25.00           C
ATOM     97  CA  TRP    97       7.748  27.775  10.865  1.00 25.00           C
TER
END
