
#######################################################
#                                                     #
#                        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  103 (  103),  selected  103 , name T0314TS599_2-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314TS599_2-D1.T0314_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    M       1      S       2          1.561
LGA    S       2      I       3          3.042
LGA    I       3      T       4          2.474
LGA    T       4      S       5          2.724
LGA    S       5      T       6          3.499
LGA    T       6      D       7          2.470
LGA    D       7      I       8          2.202
LGA    I       8      -       -           -
LGA    C       9      C       9          2.583
LGA    Q      10      Q      10          2.100
LGA    A      11      A      11          2.253
LGA    A      12      A      12          2.102
LGA    D      13      D      13          1.275
LGA    A      14      A      14          2.285
LGA    L      15      L      15          1.603
LGA    K      16      K      16          2.890
LGA    G      17      -       -           -
LGA    F      18      G      17          5.017
LGA    V      19      F      18          5.161
LGA    G      20      V      19           #
LGA    F      21      G      20           -
LGA    N      22      F      21           -
LGA    R      23      N      22           -
LGA    K      24      R      23           -
LGA    T      25      K      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    -       -      R      27           -
LGA    G      26      Y      28           #
LGA    R      27      I      29          0.533
LGA    Y      28      V      30          1.433
LGA    I      29      R      31          4.115
LGA    V      30      F      32          4.193
LGA    R      31      S      33           -
LGA    F      32      -       -           -
LGA    S      33      -       -           -
LGA    E      34      -       -           -
LGA    D      35      -       -           -
LGA    S      36      -       -           -
LGA    F      37      -       -           -
LGA    G      38      E      34           #
LGA    M      39      D      35           -
LGA    -       -      S      36           -
LGA    -       -      F      37           -
LGA    -       -      G      38           -
LGA    -       -      M      39           -
LGA    -       -      D      40           -
LGA    -       -      V      41           -
LGA    D      40      A      42          4.685
LGA    V      41      D      43          4.212
LGA    A      42      D      44          5.093
LGA    D      43      S      45           #
LGA    D      44      -       -           -
LGA    S      45      -       -           -
LGA    I      46      -       -           -
LGA    T      47      I      46           #
LGA    P      48      -       -           -
LGA    T      49      -       -           -
LGA    S      50      -       -           -
LGA    E      51      -       -           -
LGA    F      52      -       -           -
LGA    V      53      T      47          2.752
LGA    W      54      P      48           #
LGA    S      55      T      49           -
LGA    S      56      S      50           -
LGA    V      57      E      51           -
LGA    R      58      F      52           -
LGA    D      59      V      53           -
LGA    D      60      W      54           -
LGA    V      61      S      55           -
LGA    M      62      S      56           -
LGA    R      63      V      57           -
LGA    L      64      R      58           -
LGA    G      65      D      59           -
LGA    R      66      D      60           -
LGA    E      67      V      61           -
LGA    Q      68      M      62           -
LGA    L      69      R      63           -
LGA    Q      70      L      64           -
LGA    I      71      G      65           -
LGA    L      72      R      66           -
LGA    -       -      E      67           -
LGA    L      73      Q      68          3.629
LGA    E      74      L      69          1.020
LGA    Q      75      Q      70          3.290
LGA    -       -      I      71           -
LGA    -       -      L      72           -
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    N      76      Q      75           #
LGA    I      77      N      76           -
LGA    N      78      I      77           -
LGA    E      79      N      78          4.589
LGA    -       -      E      79           -
LGA    -       -      R      80           -
LGA    -       -      L      81           -
LGA    -       -      N      82           -
LGA    R      80      I      83          2.488
LGA    L      81      G      84          1.862
LGA    N      82      E      85          1.985
LGA    I      83      P      86          2.563
LGA    -       -      L      87           -
LGA    -       -      L      88           -
LGA    G      84      V      89          2.589
LGA    -       -      Y      90           -
LGA    E      85      L      91           #
LGA    P      86      R      92          3.261
LGA    L      87      R      93           #
LGA    L      88      Q      94          4.855
LGA    V      89      -       -           -
LGA    Y      90      D      95          1.715
LGA    L      91      L      96          0.965
LGA    R      92      P      97          2.992
LGA    R      93      E      98          3.404
LGA    Q      94      -       -           -
LGA    D      95      -       -           -
LGA    L      96      I      99          1.849
LGA    P      97      T     100          1.566
LGA    E      98      A     101          3.061
LGA    I      99      -       -           -
LGA    T     100      -       -           -
LGA    A     101      Q     102          3.201
LGA    Q     102      R     103           #
LGA    R     103      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  103  103    5.0     44    3.04    22.73     25.952     1.403

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.583388 * X  +   0.592828 * Y  +  -0.555169 * Z  +  15.758740
  Y_new =  -0.300633 * X  +   0.792610 * Y  +   0.530461 * Z  +   7.066865
  Z_new =   0.754505 * X  +  -0.142563 * Y  +   0.640623 * Z  + -15.271624 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.218969    2.922623  [ DEG:   -12.5460    167.4540 ]
  Theta =  -0.854900   -2.286693  [ DEG:   -48.9822   -131.0179 ]
  Phi   =  -0.475830    2.665762  [ DEG:   -27.2631    152.7369 ]
 
# 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: T0314TS599_2-D1                               
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314TS599_2-D1.T0314_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  103  103   5.0   44   3.04   22.73  25.952
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS599_2-D1
PFRMAT TS                                                                       
TARGET T0314                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -1.485   4.137  -1.577  1.00  0.00              
ATOM      2  CA  SER     2       2.411   5.707  -1.577  1.00  0.00              
ATOM      3  CA  ILE     3       3.080   8.133  -4.240  1.00  0.00              
ATOM      4  CA  THR     4       2.857  12.005  -4.612  1.00  0.00              
ATOM      5  CA  SER     5       4.563  13.658  -7.509  1.00  0.00              
ATOM      6  CA  THR     6       7.295  15.116  -5.354  1.00  0.00              
ATOM      7  CA  ASP     7       8.287  11.633  -4.087  1.00  0.00              
ATOM      8  CA  ILE     8       8.524   9.980  -7.460  1.00  0.00              
ATOM      9  CA  CYS     9      10.572  12.810  -8.907  1.00  0.00              
ATOM     10  CA  GLN    10      12.997  12.762  -5.934  1.00  0.00              
ATOM     11  CA  ALA    11      13.558   9.049  -5.934  1.00  0.00              
ATOM     12  CA  ALA    12      14.043   8.819  -9.655  1.00  0.00              
ATOM     13  CA  ASP    13      16.538  11.641  -9.659  1.00  0.00              
ATOM     14  CA  ALA    14      18.604  10.170  -6.853  1.00  0.00              
ATOM     15  CA  LEU    15      18.784   6.700  -8.454  1.00  0.00              
ATOM     16  CA  LYS    16      19.803   8.153 -11.766  1.00  0.00              
ATOM     17  CA  GLY    17      22.563  10.297 -10.346  1.00  0.00              
ATOM     18  CA  PHE    18      24.064   7.466  -8.411  1.00  0.00              
ATOM     19  CA  VAL    19      24.247   4.717 -10.965  1.00  0.00              
ATOM     20  CA  GLY    20      21.376   2.647 -12.134  1.00  0.00              
ATOM     21  CA  PHE    21      21.799  -1.135 -12.639  1.00  0.00              
ATOM     22  CA  ASN    22      19.282  -3.025 -14.531  1.00  0.00              
ATOM     23  CA  ARG    23      19.343  -6.614 -13.537  1.00  0.00              
ATOM     24  CA  LYS    24      16.843  -8.034 -16.036  1.00  0.00              
ATOM     25  CA  THR    25      18.220  -6.535 -19.209  1.00  0.00              
ATOM     26  CA  GLY    26      21.952  -6.491 -18.209  1.00  0.00              
ATOM     27  CA  ARG    27      22.218  -2.815 -18.706  1.00  0.00              
ATOM     28  CA  TYR    28      24.458  -0.651 -16.491  1.00  0.00              
ATOM     29  CA  ILE    29      23.739   3.008 -16.403  1.00  0.00              
ATOM     30  CA  VAL    30      26.440   5.443 -15.446  1.00  0.00              
ATOM     31  CA  ARG    31      25.616   9.073 -15.063  1.00  0.00              
ATOM     32  CA  PHE    32      28.259  11.765 -15.689  1.00  0.00              
ATOM     33  CA  SER    33      27.499  15.298 -14.715  1.00  0.00              
ATOM     34  CA  GLU    34      28.590  17.888 -17.227  1.00  0.00              
ATOM     35  CA  ASP    35      32.065  18.630 -15.804  1.00  0.00              
ATOM     36  CA  SER    36      33.344  15.019 -16.141  1.00  0.00              
ATOM     37  CA  PHE    37      31.972  14.234 -19.528  1.00  0.00              
ATOM     38  CA  GLY    38      31.249  10.688 -20.578  1.00  0.00              
ATOM     39  CA  MET    39      28.879  10.454 -23.566  1.00  0.00              
ATOM     40  CA  ASP    40      27.292   7.177 -24.577  1.00  0.00              
ATOM     41  CA  VAL    41      24.364   7.678 -26.905  1.00  0.00              
ATOM     42  CA  ALA    42      22.212   4.624 -26.589  1.00  0.00              
ATOM     43  CA  ASP    43      19.462   2.923 -28.321  1.00  0.00              
ATOM     44  CA  ASP    44      16.996   5.758 -28.802  1.00  0.00              
ATOM     45  CA  SER    45      17.940   7.760 -25.781  1.00  0.00              
ATOM     46  CA  ILE    46      19.623  10.873 -27.070  1.00  0.00              
ATOM     47  CA  THR    47      21.765  12.150 -24.271  1.00  0.00              
ATOM     48  CA  PRO    48      21.948  15.893 -23.566  1.00  0.00              
ATOM     49  CA  THR    49      25.556  16.878 -23.229  1.00  0.00              
ATOM     50  CA  SER    50      25.224  18.614 -19.858  1.00  0.00              
ATOM     51  CA  GLU    51      24.090  15.223 -18.607  1.00  0.00              
ATOM     52  CA  PHE    52      26.164  12.472 -20.090  1.00  0.00              
ATOM     53  CA  VAL    53      25.022   8.988 -19.956  1.00  0.00              
ATOM     54  CA  TRP    54      27.566   6.254 -20.053  1.00  0.00              
ATOM     55  CA  SER    55      26.472   2.858 -20.767  1.00  0.00              
ATOM     56  CA  SER    56      28.784  -0.103 -19.925  1.00  0.00              
ATOM     57  CA  VAL    57      26.856  -3.276 -20.349  1.00  0.00              
ATOM     58  CA  ARG    58      29.117  -5.681 -22.101  1.00  0.00              
ATOM     59  CA  ASP    59      28.935  -8.738 -19.919  1.00  0.00              
ATOM     60  CA  ASP    60      25.135  -8.917 -19.341  1.00  0.00              
ATOM     61  CA  VAL    61      23.928  -8.021 -22.856  1.00  0.00              
ATOM     62  CA  MET    62      21.547  -5.296 -23.819  1.00  0.00              
ATOM     63  CA  ARG    63      19.594  -5.322 -27.133  1.00  0.00              
ATOM     64  CA  LEU    64      18.335  -1.791 -27.342  1.00  0.00              
ATOM     65  CA  GLY    65      15.112  -0.963 -29.220  1.00  0.00              
ATOM     66  CA  ARG    66      13.273   2.176 -28.060  1.00  0.00              
ATOM     67  CA  GLU    67      10.218   0.391 -26.692  1.00  0.00              
ATOM     68  CA  GLN    68      12.540  -1.980 -24.775  1.00  0.00              
ATOM     69  CA  LEU    69      14.701   0.728 -23.207  1.00  0.00              
ATOM     70  CA  GLN    70      11.556   2.514 -22.067  1.00  0.00              
ATOM     71  CA  ILE    71      10.297  -0.818 -20.626  1.00  0.00              
ATOM     72  CA  LEU    72      13.563  -1.543 -18.834  1.00  0.00              
ATOM     73  CA  LEU    73      13.563   1.972 -17.261  1.00  0.00              
ATOM     74  CA  GLU    74       9.927   2.409 -16.115  1.00  0.00              
ATOM     75  CA  GLN    75       9.831  -0.964 -14.341  1.00  0.00              
ATOM     76  CA  ASN    76      13.231  -0.366 -12.737  1.00  0.00              
ATOM     77  CA  ILE    77      12.665   3.088 -11.261  1.00  0.00              
ATOM     78  CA  ASN    78       9.373   2.009  -9.664  1.00  0.00              
ATOM     79  CA  GLU    79      10.995  -1.055  -8.153  1.00  0.00              
ATOM     80  CA  ARG    80      14.171   0.614  -6.821  1.00  0.00              
ATOM     81  CA  LEU    81      12.001   3.189  -5.038  1.00  0.00              
ATOM     82  CA  ASN    82       8.699   1.699  -3.790  1.00  0.00              
ATOM     83  CA  ILE    83       6.000   4.049  -4.892  1.00  0.00              
ATOM     84  CA  GLY    84       2.676   2.342  -4.453  1.00  0.00              
ATOM     85  CA  GLU    85       0.549   4.152  -6.970  1.00  0.00              
ATOM     86  CA  PRO    86       0.920   4.544 -10.695  1.00  0.00              
ATOM     87  CA  LEU    87       3.143   7.544 -11.480  1.00  0.00              
ATOM     88  CA  LEU    88       1.001   9.350 -14.075  1.00  0.00              
ATOM     89  CA  VAL    89      -2.183   8.965 -12.007  1.00  0.00              
ATOM     90  CA  TYR    90      -0.837   9.900  -8.555  1.00  0.00              
ATOM     91  CA  LEU    91       0.757  13.001 -10.141  1.00  0.00              
ATOM     92  CA  ARG    92      -2.014  14.276 -12.416  1.00  0.00              
ATOM     93  CA  ARG    93      -0.938  13.950 -16.063  1.00  0.00              
ATOM     94  CA  GLN    94      -0.548  17.713 -16.645  1.00  0.00              
ATOM     95  CA  ASP    95       1.554  18.197 -13.508  1.00  0.00              
ATOM     96  CA  LEU    96       4.361  15.707 -14.223  1.00  0.00              
ATOM     97  CA  PRO    97       6.294  17.954 -16.641  1.00  0.00              
ATOM     98  CA  GLU    98       6.016  20.697 -14.021  1.00  0.00              
ATOM     99  CA  ILE    99       7.314  18.552 -11.111  1.00  0.00              
ATOM    100  CA  THR   100      10.270  17.441 -13.254  1.00  0.00              
ATOM    101  CA  ALA   101      10.987  21.016 -14.272  1.00  0.00              
ATOM    102  CA  GLN   102      10.935  22.481 -10.742  1.00  0.00              
ATOM    103  CA  ARG   103      13.494  20.067  -9.418  1.00  0.00              
TER                                                                             
END
