
#######################################################
#                                                     #
#                        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   24 (  180),  selected   24 , name T0343TS468_1
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS468_1.T0343.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    V      78      T       2           -
LGA    K      79      W       3           -
LGA    L      80      R       4           -
LGA    V      81      E       5           -
LGA    -       -      I       6           -
LGA    -       -      L       7           -
LGA    -       -      R       8           -
LGA    -       -      K       9           -
LGA    -       -      E      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      D      14           -
LGA    -       -      L      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    -       -      I      19           -
LGA    -       -      V      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      Y      24           -
LGA    S      82      I      25           #
LGA    L      83      D      26          2.701
LGA    -       -      C      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      E      30           -
LGA    -       -      P      31           -
LGA    -       -      I      32           -
LGA    D      84      P      33          4.186
LGA    G      85      P      34          2.439
LGA    P      86      T      35           #
LGA    -       -      L      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Y      39           -
LGA    -       -      D      40           -
LGA    -       -      K      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      D      44           -
LGA    -       -      E      45           -
LGA    -       -      W      46           -
LGA    -       -      Y      47           -
LGA    -       -      K      48           -
LGA    -       -      V      49           -
LGA    -       -      E      50           -
LGA    -       -      E      51           -
LGA    -       -      A      52           -
LGA    -       -      P      53           -
LGA    A      87      N      54           #
LGA    -       -      V      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      63           -
LGA    -       -      W      64           -
LGA    -       -      A      65           -
LGA    -       -      I      66           -
LGA    P      88      E      67          1.032
LGA    P      89      V      68          2.989
LGA    K      90      L      69          2.990
LGA    V      91      E      70          1.961
LGA    -       -      R      71           -
LGA    M      92      I      72          0.843
LGA    K      93      R      73          1.436
LGA    R      94      D      74          1.251
LGA    L      95      G      75          0.981
LGA    S      96      E      76          2.543
LGA    L      97      N      77          2.973
LGA    A      98      V      78          2.365
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      V      81           -
LGA    -       -      S      82           -
LGA    -       -      L      83           -
LGA    -       -      D      84           -
LGA    -       -      G      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      P      88           -
LGA    -       -      P      89           -
LGA    -       -      K      90           -
LGA    -       -      V      91           -
LGA    -       -      M      92           -
LGA    -       -      K      93           -
LGA    -       -      R      94           -
LGA    -       -      L      95           -
LGA    L      99      S      96          2.831
LGA    Q     100      L      97          3.118
LGA    K     101      A      98           -
LGA    -       -      L      99           -
LGA    -       -      Q     100           -
LGA    -       -      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   94    5.0     16    2.47     0.00     13.471     0.623

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.973077 * X  +  -0.230475 * Y  +  -0.001140 * Z  +  35.833210
  Y_new =   0.141464 * X  +   0.593350 * Y  +   0.792416 * Z  +  44.184334
  Z_new =  -0.181956 * X  +  -0.771244 * Y  +   0.609979 * Z  +  19.105263 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.901627    2.239966  [ DEG:   -51.6594    128.3406 ]
  Theta =   0.182975    2.958617  [ DEG:    10.4837    169.5163 ]
  Phi   =   0.144367   -2.997226  [ DEG:     8.2716   -171.7284 ]
 
# 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: T0343TS468_1                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS468_1.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   94   5.0   16   2.47    0.00  13.471
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS468_1
PFRMAT TS
TARGET T0343    
MODEL  1
PARENT n/a
ATOM      1  N   VAL    78      28.915  29.735  -7.455  1.00  0.00
ATOM      2  CA  VAL    78      28.258  31.027  -7.081  1.00  0.00
ATOM      3  C   VAL    78      27.783  31.017  -5.634  1.00  0.00
ATOM      4  O   VAL    78      27.268  30.012  -5.145  1.00  0.00
ATOM      5  CB  VAL    78      27.029  31.310  -7.965  1.00  0.00
ATOM      6  CG1 VAL    78      26.359  32.609  -7.544  1.00  0.00
ATOM      7  CG2 VAL    78      27.439  31.432  -9.424  1.00  0.00
ATOM      8  N   LYS    79      28.712  31.165  -4.681  1.00  0.00
ATOM      9  CA  LYS    79      28.317  31.299  -3.285  1.00  0.00
ATOM     10  C   LYS    79      27.296  32.402  -3.102  1.00  0.00
ATOM     11  O   LYS    79      27.327  33.442  -3.766  1.00  0.00
ATOM     12  CB  LYS    79      29.530  31.630  -2.414  1.00  0.00
ATOM     13  CG  LYS    79      30.580  30.532  -2.368  1.00  0.00
ATOM     14  CD  LYS    79      31.738  30.912  -1.460  1.00  0.00
ATOM     15  CE  LYS    79      32.820  29.845  -1.469  1.00  0.00
ATOM     16  NZ  LYS    79      33.985  30.228  -0.625  1.00  0.00
ATOM     17  N   LEU    80      26.366  32.180  -2.182  1.00  0.00
ATOM     18  CA  LEU    80      25.428  33.186  -1.734  1.00  0.00
ATOM     19  C   LEU    80      25.142  33.000  -0.243  1.00  0.00
ATOM     20  O   LEU    80      24.040  32.647   0.185  1.00  0.00
ATOM     21  CB  LEU    80      24.111  33.074  -2.505  1.00  0.00
ATOM     22  CG  LEU    80      24.182  33.342  -4.010  1.00  0.00
ATOM     23  CD1 LEU    80      22.866  32.983  -4.682  1.00  0.00
ATOM     24  CD2 LEU    80      24.470  34.810  -4.281  1.00  0.00
ATOM     25  N   VAL    81      26.172  33.250   0.555  1.00  0.00
ATOM     26  CA  VAL    81      26.162  32.964   1.978  1.00  0.00
ATOM     27  C   VAL    81      25.287  33.996   2.666  1.00  0.00
ATOM     28  O   VAL    81      25.487  35.208   2.548  1.00  0.00
ATOM     29  CB  VAL    81      27.580  33.029   2.576  1.00  0.00
ATOM     30  CG1 VAL    81      27.534  32.803   4.080  1.00  0.00
ATOM     31  CG2 VAL    81      28.467  31.959   1.957  1.00  0.00
ATOM     32  N   SER    82      24.300  33.516   3.397  1.00  0.00
ATOM     33  CA  SER    82      23.448  34.409   4.178  1.00  0.00
ATOM     34  C   SER    82      23.640  34.045   5.658  1.00  0.00
ATOM     35  O   SER    82      24.134  32.963   5.985  1.00  0.00
ATOM     36  CB  SER    82      21.981  34.235   3.780  1.00  0.00
ATOM     37  OG  SER    82      21.784  34.547   2.412  1.00  0.00
ATOM     38  N   LEU    83      23.260  34.920   6.569  1.00  0.00
ATOM     39  CA  LEU    83      23.275  34.673   8.001  1.00  0.00
ATOM     40  C   LEU    83      22.440  33.443   8.337  1.00  0.00
ATOM     41  O   LEU    83      21.359  33.216   7.786  1.00  0.00
ATOM     42  CB  LEU    83      22.699  35.872   8.757  1.00  0.00
ATOM     43  CG  LEU    83      23.518  37.163   8.707  1.00  0.00
ATOM     44  CD1 LEU    83      22.770  38.301   9.382  1.00  0.00
ATOM     45  CD2 LEU    83      24.851  36.982   9.417  1.00  0.00
ATOM     46  N   ASP    84      22.944  32.629   9.256  1.00  0.00
ATOM     47  CA  ASP    84      22.218  31.469   9.717  1.00  0.00
ATOM     48  C   ASP    84      20.890  31.881  10.369  1.00  0.00
ATOM     49  O   ASP    84      20.822  32.795  11.195  1.00  0.00
ATOM     50  CB  ASP    84      23.042  30.697  10.751  1.00  0.00
ATOM     51  CG  ASP    84      24.204  29.949  10.129  1.00  0.00
ATOM     52  OD1 ASP    84      24.260  29.868   8.884  1.00  0.00
ATOM     53  OD2 ASP    84      25.058  29.443  10.887  1.00  0.00
ATOM     54  N   GLY    85      19.814  31.192   9.987  1.00  0.00
ATOM     55  CA  GLY    85      18.534  31.343  10.654  1.00  0.00
ATOM     56  C   GLY    85      18.532  30.639  12.005  1.00  0.00
ATOM     57  O   GLY    85      18.905  29.469  12.122  1.00  0.00
ATOM     58  N   PRO    86      18.108  31.342  13.057  1.00  0.00
ATOM     59  CA  PRO    86      17.999  30.689  14.368  1.00  0.00
ATOM     60  C   PRO    86      16.993  29.535  14.333  1.00  0.00
ATOM     61  O   PRO    86      15.914  29.629  13.741  1.00  0.00
ATOM     62  CB  PRO    86      17.532  31.808  15.301  1.00  0.00
ATOM     63  CG  PRO    86      17.997  33.063  14.641  1.00  0.00
ATOM     64  CD  PRO    86      17.843  32.838  13.163  1.00  0.00
ATOM     65  N   ALA    87      17.346  28.441  14.967  1.00  0.00
ATOM     66  CA  ALA    87      16.520  27.267  15.201  1.00  0.00
ATOM     67  C   ALA    87      16.473  26.964  16.676  1.00  0.00
ATOM     68  O   ALA    87      17.497  26.809  17.347  1.00  0.00
ATOM     69  CB  ALA    87      17.092  26.063  14.468  1.00  0.00
ATOM     70  N   PRO    88      15.255  26.873  17.210  1.00  0.00
ATOM     71  CA  PRO    88      15.100  26.590  18.633  1.00  0.00
ATOM     72  C   PRO    88      15.884  25.339  19.019  1.00  0.00
ATOM     73  O   PRO    88      15.642  24.231  18.532  1.00  0.00
ATOM     74  CB  PRO    88      13.594  26.387  18.808  1.00  0.00
ATOM     75  CG  PRO    88      12.978  27.215  17.729  1.00  0.00
ATOM     76  CD  PRO    88      13.869  27.063  16.528  1.00  0.00
ATOM     77  N   PRO    89      16.843  25.523  19.915  1.00  0.00
ATOM     78  CA  PRO    89      17.712  24.427  20.335  1.00  0.00
ATOM     79  C   PRO    89      16.961  23.238  20.883  1.00  0.00
ATOM     80  O   PRO    89      17.344  22.087  20.662  1.00  0.00
ATOM     81  CB  PRO    89      18.593  25.049  21.421  1.00  0.00
ATOM     82  CG  PRO    89      18.655  26.497  21.068  1.00  0.00
ATOM     83  CD  PRO    89      17.290  26.861  20.558  1.00  0.00
ATOM     84  N   LYS    90      15.861  23.474  21.620  1.00  0.00
ATOM     85  CA  LYS    90      15.076  22.348  22.111  1.00  0.00
ATOM     86  C   LYS    90      14.264  21.693  21.013  1.00  0.00
ATOM     87  O   LYS    90      13.085  21.382  21.199  1.00  0.00
ATOM     88  CB  LYS    90      14.099  22.807  23.195  1.00  0.00
ATOM     89  CG  LYS    90      14.769  23.269  24.480  1.00  0.00
ATOM     90  CD  LYS    90      13.741  23.690  25.517  1.00  0.00
ATOM     91  CE  LYS    90      14.411  24.174  26.793  1.00  0.00
ATOM     92  NZ  LYS    90      13.417  24.612  27.811  1.00  0.00
ATOM     93  N   VAL    91      14.893  21.490  19.747  1.00  0.00
ATOM     94  CA  VAL    91      14.069  20.823  18.752  1.00  0.00
ATOM     95  C   VAL    91      14.757  19.529  18.363  1.00  0.00
ATOM     96  O   VAL    91      14.124  18.477  18.302  1.00  0.00
ATOM     97  CB  VAL    91      13.883  21.695  17.496  1.00  0.00
ATOM     98  CG1 VAL    91      13.086  20.945  16.440  1.00  0.00
ATOM     99  CG2 VAL    91      13.137  22.975  17.843  1.00  0.00
ATOM    100  N   MET    92      16.060  19.606  18.121  1.00  0.00
ATOM    101  CA  MET    92      16.834  18.432  17.749  1.00  0.00
ATOM    102  C   MET    92      16.756  17.380  18.843  1.00  0.00
ATOM    103  O   MET    92      16.462  16.220  18.585  1.00  0.00
ATOM    104  CB  MET    92      18.303  18.805  17.537  1.00  0.00
ATOM    105  CG  MET    92      18.554  19.660  16.306  1.00  0.00
ATOM    106  SD  MET    92      20.273  20.186  16.163  1.00  0.00
ATOM    107  CE  MET    92      21.077  18.625  15.815  1.00  0.00
ATOM    108  N   LYS    93      17.014  17.795  20.073  1.00  0.00
ATOM    109  CA  LYS    93      16.971  16.877  21.201  1.00  0.00
ATOM    110  C   LYS    93      15.598  16.211  21.335  1.00  0.00
ATOM    111  O   LYS    93      15.503  15.039  21.715  1.00  0.00
ATOM    112  CB  LYS    93      17.260  17.618  22.507  1.00  0.00
ATOM    113  CG  LYS    93      18.701  18.082  22.652  1.00  0.00
ATOM    114  CD  LYS    93      18.916  18.815  23.966  1.00  0.00
ATOM    115  CE  LYS    93      20.356  19.282  24.108  1.00  0.00
ATOM    116  NZ  LYS    93      20.574  20.030  25.377  1.00  0.00
ATOM    117  N   ARG    94      14.541  16.952  21.014  1.00  0.00
ATOM    118  CA  ARG    94      13.187  16.415  21.096  1.00  0.00
ATOM    119  C   ARG    94      12.933  15.421  19.954  1.00  0.00
ATOM    120  O   ARG    94      12.239  14.417  20.132  1.00  0.00
ATOM    121  CB  ARG    94      12.157  17.541  20.995  1.00  0.00
ATOM    122  CG  ARG    94      12.096  18.439  22.221  1.00  0.00
ATOM    123  CD  ARG    94      11.111  19.579  22.022  1.00  0.00
ATOM    124  NE  ARG    94      11.045  20.455  23.190  1.00  0.00
ATOM    125  CZ  ARG    94      10.322  21.568  23.249  1.00  0.00
ATOM    126  NH1 ARG    94      10.323  22.302  24.352  1.00  0.00
ATOM    127  NH2 ARG    94       9.600  21.946  22.201  1.00  0.00
ATOM    128  N   LEU    95      13.497  15.698  18.781  1.00  0.00
ATOM    129  CA  LEU    95      13.325  14.798  17.644  1.00  0.00
ATOM    130  C   LEU    95      14.100  13.510  17.888  1.00  0.00
ATOM    131  O   LEU    95      13.618  12.416  17.590  1.00  0.00
ATOM    132  CB  LEU    95      13.842  15.450  16.360  1.00  0.00
ATOM    133  CG  LEU    95      13.035  16.637  15.831  1.00  0.00
ATOM    134  CD1 LEU    95      13.752  17.298  14.664  1.00  0.00
ATOM    135  CD2 LEU    95      11.663  16.185  15.352  1.00  0.00
ATOM    136  N   SER    96      15.297  13.643  18.446  1.00  0.00
ATOM    137  CA  SER    96      16.131  12.485  18.739  1.00  0.00
ATOM    138  C   SER    96      15.426  11.565  19.729  1.00  0.00
ATOM    139  O   SER    96      15.461  10.349  19.601  1.00  0.00
ATOM    140  CB  SER    96      17.465  12.925  19.346  1.00  0.00
ATOM    141  OG  SER    96      18.236  13.656  18.409  1.00  0.00
ATOM    142  N   LEU    97      14.780  12.160  20.718  1.00  0.00
ATOM    143  CA  LEU    97      14.088  11.388  21.732  1.00  0.00
ATOM    144  C   LEU    97      12.904  10.633  21.141  1.00  0.00
ATOM    145  O   LEU    97      12.684   9.464  21.451  1.00  0.00
ATOM    146  CB  LEU    97      13.560  12.306  22.837  1.00  0.00
ATOM    147  CG  LEU    97      14.613  12.964  23.733  1.00  0.00
ATOM    148  CD1 LEU    97      13.967  13.980  24.662  1.00  0.00
ATOM    149  CD2 LEU    97      15.320  11.921  24.585  1.00  0.00
ATOM    150  N   ALA    98      12.134  11.313  20.300  1.00  0.00
ATOM    151  CA  ALA    98      10.976  10.704  19.657  1.00  0.00
ATOM    152  C   ALA    98      11.489   9.616  18.722  1.00  0.00
ATOM    153  O   ALA    98      10.833   8.605  18.475  1.00  0.00
ATOM    154  CB  ALA    98      10.200  11.746  18.866  1.00  0.00
ATOM    155  N   LEU    99      12.698   9.834  18.227  1.00  0.00
ATOM    156  CA  LEU    99      13.345   8.910  17.314  1.00  0.00
ATOM    157  C   LEU    99      13.651   7.589  18.009  1.00  0.00
ATOM    158  O   LEU    99      13.355   6.523  17.485  1.00  0.00
ATOM    159  CB  LEU    99      14.661   9.497  16.800  1.00  0.00
ATOM    160  CG  LEU    99      15.463   8.622  15.835  1.00  0.00
ATOM    161  CD1 LEU    99      14.659   8.332  14.577  1.00  0.00
ATOM    162  CD2 LEU    99      16.753   9.316  15.426  1.00  0.00
ATOM    163  N   GLN   100      14.233   7.664  19.200  1.00  0.00
ATOM    164  CA  GLN   100      14.587   6.467  19.948  1.00  0.00
ATOM    165  C   GLN   100      13.397   5.619  20.381  1.00  0.00
ATOM    166  O   GLN   100      13.571   4.513  20.887  1.00  0.00
ATOM    167  CB  GLN   100      15.341   6.837  21.227  1.00  0.00
ATOM    168  CG  GLN   100      16.742   7.376  20.989  1.00  0.00
ATOM    169  CD  GLN   100      17.434   7.785  22.273  1.00  0.00
ATOM    170  OE1 GLN   100      16.850   7.718  23.354  1.00  0.00
ATOM    171  NE2 GLN   100      18.686   8.214  22.157  1.00  0.00
ATOM    172  N   LYS   101      12.186   6.125  20.202  1.00  0.00
ATOM    173  CA  LYS   101      11.030   5.321  20.567  1.00  0.00
ATOM    174  C   LYS   101      10.829   4.233  19.500  1.00  0.00
ATOM    175  O   LYS   101      10.125   3.248  19.729  1.00  0.00
ATOM    176  CB  LYS   101       9.775   6.192  20.644  1.00  0.00
ATOM    177  CG  LYS   101       9.813   7.239  21.746  1.00  0.00
ATOM    178  CD  LYS   101       8.492   7.984  21.846  1.00  0.00
ATOM    179  CE  LYS   101       8.532   9.035  22.943  1.00  0.00
ATOM    180  NZ  LYS   101       7.252   9.792  23.034  1.00  0.00
TER
END
