
#######################################################
#                                                     #
#                        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  135 (  135),  selected  135 , name T0319TS393_3
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319TS393_3.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      F       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      T       6           -
LGA    -       -      N       7           -
LGA    -       -      F       8           -
LGA    -       -      L       9           -
LGA    -       -      K      10           -
LGA    -       -      C      11           -
LGA    -       -      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    M       1      D      21           #
LGA    K       2      N      22          3.306
LGA    F       3      F      23          3.872
LGA    L       4      P      24          3.509
LGA    T       5      L      25          4.368
LGA    T       6      Q      26           #
LGA    N       7      Y      27          3.180
LGA    F       8      D      28          4.071
LGA    L       9      -       -           -
LGA    K      10      -       -           -
LGA    C      11      -       -           -
LGA    S      12      -       -           -
LGA    V      13      -       -           -
LGA    K      14      -       -           -
LGA    A      15      -       -           -
LGA    C      16      -       -           -
LGA    D      17      -       -           -
LGA    T      18      -       -           -
LGA    S      19      -       -           -
LGA    N      20      -       -           -
LGA    D      21      -       -           -
LGA    N      22      -       -           -
LGA    F      23      -       -           -
LGA    P      24      -       -           -
LGA    L      25      -       -           -
LGA    Q      26      G      29           #
LGA    Y      27      S      30          3.914
LGA    D      28      K      31          1.990
LGA    -       -      C      32           -
LGA    G      29      Q      33          3.838
LGA    S      30      L      34           #
LGA    K      31      V      35           -
LGA    C      32      Q      36           -
LGA    Q      33      D      37           -
LGA    L      34      E      38           -
LGA    V      35      S      39           -
LGA    Q      36      I      40           -
LGA    D      37      E      41           -
LGA    E      38      F      42           -
LGA    S      39      N      43           -
LGA    I      40      P      44           -
LGA    E      41      E      45           -
LGA    F      42      F      46           -
LGA    N      43      L      47           -
LGA    P      44      L      48           -
LGA    E      45      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    -       -      R      53           -
LGA    -       -      V      54           -
LGA    -       -      D      55           -
LGA    F      46      W      56          4.749
LGA    L      47      -       -           -
LGA    L      48      P      57          3.465
LGA    N      49      A      58          3.582
LGA    I      50      V      59          2.120
LGA    V      51      L      60          5.108
LGA    D      52      T      61           #
LGA    R      53      -       -           -
LGA    V      54      -       -           -
LGA    D      55      -       -           -
LGA    W      56      -       -           -
LGA    P      57      V      62          3.398
LGA    A      58      A      63          2.762
LGA    V      59      A      64          4.613
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    L      60      G      67           #
LGA    T      61      N      68          2.308
LGA    V      62      N      69          5.232
LGA    A      63      -       -           -
LGA    A      64      -       -           -
LGA    E      65      A      70           #
LGA    L      66      L      71           -
LGA    G      67      P      72           -
LGA    N      68      P      73           -
LGA    N      69      T      74           -
LGA    A      70      K      75           -
LGA    L      71      P      76           -
LGA    P      72      S      77           -
LGA    P      73      F      78           -
LGA    T      74      P      79           -
LGA    K      75      S      80           -
LGA    P      76      S      81           -
LGA    S      77      I      82           -
LGA    F      78      Q      83           -
LGA    P      79      E      84           -
LGA    -       -      L      85           -
LGA    S      80      T      86           #
LGA    S      81      D      87          3.610
LGA    I      82      D      88          4.772
LGA    Q      83      D      89          4.701
LGA    E      84      M      90          3.225
LGA    -       -      A      91           -
LGA    L      85      I      92           #
LGA    T      86      -       -           -
LGA    D      87      L      93          3.843
LGA    D      88      N      94          2.056
LGA    D      89      D      95          4.878
LGA    M      90      L      96          3.784
LGA    A      91      H      97          1.246
LGA    I      92      T      98          3.331
LGA    L      93      L      99          3.027
LGA    N      94      L     100          2.517
LGA    D      95      L     101           #
LGA    L      96      Q     102           #
LGA    H      97      T     103          4.928
LGA    T      98      S     104          1.665
LGA    L      99      -       -           -
LGA    L     100      -       -           -
LGA    L     101      I     105          1.612
LGA    Q     102      A     106          4.272
LGA    T     103      E     107          3.682
LGA    S     104      G     108          1.253
LGA    I     105      E     109          3.745
LGA    A     106      M     110           -
LGA    E     107      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    G     108      H     117           #
LGA    E     109      I     118          3.283
LGA    M     110      Y     119          2.733
LGA    K     111      Y     120          3.428
LGA    C     112      I     121          1.482
LGA    R     113      K     122          1.874
LGA    N     114      N     123          2.501
LGA    C     115      G     124          2.204
LGA    G     116      I     125           #
LGA    H     117      P     126           #
LGA    I     118      -       -           -
LGA    Y     119      -       -           -
LGA    Y     120      N     127           #
LGA    I     121      L     128          4.923
LGA    K     122      L     129          3.871
LGA    N     123      L     130          3.332
LGA    G     124      P     131          3.855
LGA    I     125      P     132          4.471
LGA    P     126      H     133           -
LGA    N     127      L     134           -
LGA    L     128      V     135           -
LGA    L     129      -       -           -
LGA    L     130      -       -           -
LGA    P     131      -       -           -
LGA    P     132      -       -           -
LGA    H     133      -       -           -
LGA    L     134      -       -           -
LGA    V     135      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  135  135    5.0     50    3.55    10.00     20.379     1.368

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.037053 * X  +  -0.708268 * Y  +   0.704971 * Z  +  19.191217
  Y_new =   0.985118 * X  +  -0.144373 * Y  +  -0.093271 * Z  +   2.093885
  Z_new =   0.167840 * X  +   0.691023 * Y  +   0.703076 * Z  +   7.437327 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.776753   -2.364840  [ DEG:    44.5046   -135.4954 ]
  Theta =  -0.168638   -2.972955  [ DEG:    -9.6622   -170.3378 ]
  Phi   =   1.608391   -1.533202  [ DEG:    92.1540    -87.8460 ]
 
# 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: T0319TS393_3                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319TS393_3.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  135  135   5.0   50   3.55   10.00  20.379
REMARK  ---------------------------------------------------------- 
MOLECULE T0319TS393_3
PFRMAT TS
TARGET T0319
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1       3.717   0.358  12.196  1.00 25.00           C
ATOM      2  CA  LYS     2       7.017   0.070  10.418  1.00 25.00           C
ATOM      3  CA  PHE     3      10.530  -0.678  11.747  1.00 25.00           C
ATOM      4  CA  LEU     4      12.524   1.836   9.729  1.00 25.00           C
ATOM      5  CA  THR     5      13.893   4.974   8.091  1.00 25.00           C
ATOM      6  CA  THR     6      15.870   7.476   6.081  1.00 25.00           C
ATOM      7  CA  ASN     7      13.122   7.789   3.486  1.00 25.00           C
ATOM      8  CA  PHE     8      13.002  10.461   0.709  1.00 25.00           C
ATOM      9  CA  LEU     9      16.623  11.005  -0.424  1.00 25.00           C
ATOM     10  CA  LYS    10      17.439  14.683  -0.501  1.00 25.00           C
ATOM     11  CA  CYS    11      14.205  15.272   1.433  1.00 25.00           C
ATOM     12  CA  SER    12      12.351  15.369  -1.878  1.00 25.00           C
ATOM     13  CA  VAL    13      11.822  19.061  -1.025  1.00 25.00           C
ATOM     14  CA  LYS    14       8.847  20.426   0.787  1.00 25.00           C
ATOM     15  CA  ALA    15       7.462  17.014   1.521  1.00 25.00           C
ATOM     16  CA  CYS    16       8.561  13.408   1.881  1.00 25.00           C
ATOM     17  CA  ASP    17       5.152  12.716   0.347  1.00 25.00           C
ATOM     18  CA  THR    18       6.614  14.342  -2.779  1.00 25.00           C
ATOM     19  CA  SER    19       8.801  11.410  -3.761  1.00 25.00           C
ATOM     20  CA  ASN    20       5.867   9.529  -5.283  1.00 25.00           C
ATOM     21  CA  ASP    21       6.407   6.920  -2.616  1.00 25.00           C
ATOM     22  CA  ASN    22       5.058   7.463   0.881  1.00 25.00           C
ATOM     23  CA  PHE    23       8.126   6.284   2.738  1.00 25.00           C
ATOM     24  CA  PRO    24       9.198   5.717   6.381  1.00 25.00           C
ATOM     25  CA  LEU    25       9.400   9.570   6.335  1.00 25.00           C
ATOM     26  CA  GLN    26      12.327  12.036   5.976  1.00 25.00           C
ATOM     27  CA  TYR    27      16.133  12.237   5.573  1.00 25.00           C
ATOM     28  CA  ASP    28      18.548  15.094   5.009  1.00 25.00           C
ATOM     29  CA  GLY    29      21.594  16.240   6.990  1.00 25.00           C
ATOM     30  CA  SER    30      23.697  13.323   5.679  1.00 25.00           C
ATOM     31  CA  LYS    31      21.129  10.615   4.974  1.00 25.00           C
ATOM     32  CA  CYS    32      19.429   8.129   2.590  1.00 25.00           C
ATOM     33  CA  GLN    33      16.750   5.804   1.178  1.00 25.00           C
ATOM     34  CA  LEU    34      14.800   3.102   3.009  1.00 25.00           C
ATOM     35  CA  VAL    35      11.724   1.650   4.603  1.00 25.00           C
ATOM     36  CA  GLN    36      10.832  -0.004   1.339  1.00 25.00           C
ATOM     37  CA  ASP    37       8.867  -3.172   0.573  1.00 25.00           C
ATOM     38  CA  GLU    38       7.939  -5.651  -2.161  1.00 25.00           C
ATOM     39  CA  SER    39       8.370  -8.015  -5.047  1.00 25.00           C
ATOM     40  CA  ILE    40      12.144  -7.420  -4.604  1.00 25.00           C
ATOM     41  CA  GLU    41      13.778  -6.322  -7.889  1.00 25.00           C
ATOM     42  CA  PHE    42      16.094  -3.610  -6.445  1.00 25.00           C
ATOM     43  CA  ASN    43      18.207  -6.498  -5.243  1.00 25.00           C
ATOM     44  CA  PRO    44      20.905  -6.439  -2.485  1.00 25.00           C
ATOM     45  CA  GLU    45      18.681  -8.985  -0.685  1.00 25.00           C
ATOM     46  CA  PHE    46      20.655  -8.456   2.554  1.00 25.00           C
ATOM     47  CA  LEU    47      20.264  -4.663   2.203  1.00 25.00           C
ATOM     48  CA  LEU    48      16.495  -5.077   1.659  1.00 25.00           C
ATOM     49  CA  ASN    49      16.266  -7.296   4.772  1.00 25.00           C
ATOM     50  CA  ILE    50      18.184  -4.680   6.809  1.00 25.00           C
ATOM     51  CA  VAL    51      15.817  -1.938   5.562  1.00 25.00           C
ATOM     52  CA  ASP    52      12.792  -4.075   6.533  1.00 25.00           C
ATOM     53  CA  ARG    53      14.127  -4.510  10.102  1.00 25.00           C
ATOM     54  CA  VAL    54      16.742  -1.912  10.777  1.00 25.00           C
ATOM     55  CA  ASP    55      20.549  -1.658  10.293  1.00 25.00           C
ATOM     56  CA  TRP    56      19.892   1.709   8.650  1.00 25.00           C
ATOM     57  CA  PRO    57      20.765  -0.460   5.616  1.00 25.00           C
ATOM     58  CA  ALA    58      19.840   2.417   3.264  1.00 25.00           C
ATOM     59  CA  VAL    59      22.039   4.812   5.288  1.00 25.00           C
ATOM     60  CA  LEU    60      24.948   2.328   5.111  1.00 25.00           C
ATOM     61  CA  THR    61      24.489   2.022   1.321  1.00 25.00           C
ATOM     62  CA  VAL    62      24.487   5.837   0.988  1.00 25.00           C
ATOM     63  CA  ALA    63      27.698   6.044   3.066  1.00 25.00           C
ATOM     64  CA  ALA    64      29.333   3.381   0.851  1.00 25.00           C
ATOM     65  CA  GLU    65      28.304   5.324  -2.285  1.00 25.00           C
ATOM     66  CA  LEU    66      29.776   8.537  -0.807  1.00 25.00           C
ATOM     67  CA  GLY    67      33.072   8.353  -2.699  1.00 25.00           C
ATOM     68  CA  ASN    68      34.582   9.998  -5.707  1.00 25.00           C
ATOM     69  CA  ASN    69      34.799   7.045  -8.065  1.00 25.00           C
ATOM     70  CA  ALA    70      34.649   3.420  -9.296  1.00 25.00           C
ATOM     71  CA  LEU    71      36.966   2.730  -6.336  1.00 25.00           C
ATOM     72  CA  PRO    72      40.592   1.960  -5.253  1.00 25.00           C
ATOM     73  CA  PRO    73      41.910  -0.546  -7.804  1.00 25.00           C
ATOM     74  CA  THR    74      41.324  -4.083  -6.526  1.00 25.00           C
ATOM     75  CA  LYS    75      44.786  -3.624  -5.071  1.00 25.00           C
ATOM     76  CA  PRO    76      45.153  -5.072  -1.557  1.00 25.00           C
ATOM     77  CA  SER    77      43.855  -8.474  -0.508  1.00 25.00           C
ATOM     78  CA  PHE    78      40.113  -9.226  -0.667  1.00 25.00           C
ATOM     79  CA  PRO    79      39.322 -12.788   0.568  1.00 25.00           C
ATOM     80  CA  SER    80      40.130 -12.327   4.293  1.00 25.00           C
ATOM     81  CA  SER    81      41.178 -10.108   7.212  1.00 25.00           C
ATOM     82  CA  ILE    82      41.956  -7.916  10.271  1.00 25.00           C
ATOM     83  CA  GLN    83      40.036 -10.367  12.457  1.00 25.00           C
ATOM     84  CA  GLU    84      37.904 -10.385  15.616  1.00 25.00           C
ATOM     85  CA  LEU    85      34.456 -10.261  14.083  1.00 25.00           C
ATOM     86  CA  THR    86      30.791  -9.518  14.508  1.00 25.00           C
ATOM     87  CA  ASP    87      32.075  -6.480  16.455  1.00 25.00           C
ATOM     88  CA  ASP    88      32.960  -4.719  13.171  1.00 25.00           C
ATOM     89  CA  ASP    89      29.462  -5.463  11.801  1.00 25.00           C
ATOM     90  CA  MET    90      27.884  -4.060  14.996  1.00 25.00           C
ATOM     91  CA  ALA    91      30.022  -0.898  14.692  1.00 25.00           C
ATOM     92  CA  ILE    92      28.949  -0.493  11.038  1.00 25.00           C
ATOM     93  CA  LEU    93      25.276  -0.892  12.047  1.00 25.00           C
ATOM     94  CA  ASN    94      25.717   1.748  14.787  1.00 25.00           C
ATOM     95  CA  ASP    95      27.329   4.134  12.262  1.00 25.00           C
ATOM     96  CA  LEU    96      24.421   3.571   9.835  1.00 25.00           C
ATOM     97  CA  HIS    97      21.911   4.285  12.638  1.00 25.00           C
ATOM     98  CA  THR    98      23.784   7.505  13.528  1.00 25.00           C
ATOM     99  CA  LEU    99      23.736   8.579   9.851  1.00 25.00           C
ATOM    100  CA  LEU   100      19.972   7.891   9.675  1.00 25.00           C
ATOM    101  CA  LEU   101      19.420   9.962  12.848  1.00 25.00           C
ATOM    102  CA  GLN   102      21.467  12.836  11.359  1.00 25.00           C
ATOM    103  CA  THR   103      18.093  13.874   9.980  1.00 25.00           C
ATOM    104  CA  SER   104      14.623  12.530  10.589  1.00 25.00           C
ATOM    105  CA  ILE   105      11.721  14.526  12.128  1.00 25.00           C
ATOM    106  CA  ALA   106      11.537  14.873  15.947  1.00 25.00           C
ATOM    107  CA  GLU   107       8.009  13.635  16.644  1.00 25.00           C
ATOM    108  CA  GLY   108       6.999  10.205  15.263  1.00 25.00           C
ATOM    109  CA  GLU   109       7.171  11.878  11.843  1.00 25.00           C
ATOM    110  CA  MET   110      10.287   9.778  11.474  1.00 25.00           C
ATOM    111  CA  LYS   111      12.222   9.487  14.795  1.00 25.00           C
ATOM    112  CA  CYS   112      15.301  11.470  15.798  1.00 25.00           C
ATOM    113  CA  ARG   113      16.664  14.364  17.863  1.00 25.00           C
ATOM    114  CA  ASN   114      20.439  15.017  18.293  1.00 25.00           C
ATOM    115  CA  CYS   115      20.798  11.224  18.217  1.00 25.00           C
ATOM    116  CA  GLY   116      20.078   8.030  20.118  1.00 25.00           C
ATOM    117  CA  HIS   117      19.132   6.433  16.814  1.00 25.00           C
ATOM    118  CA  ILE   118      16.998   6.724  13.695  1.00 25.00           C
ATOM    119  CA  TYR   119      13.414   5.702  13.055  1.00 25.00           C
ATOM    120  CA  TYR   120       9.628   5.278  12.879  1.00 25.00           C
ATOM    121  CA  ILE   121      10.224   3.052  15.872  1.00 25.00           C
ATOM    122  CA  LYS   122      10.192   1.705  19.480  1.00 25.00           C
ATOM    123  CA  ASN   123      10.189  -0.623  22.471  1.00 25.00           C
ATOM    124  CA  GLY   124       9.543  -1.758  26.084  1.00 25.00           C
ATOM    125  CA  ILE   125       9.843  -4.359  28.900  1.00 25.00           C
ATOM    126  CA  PRO   126       6.238  -5.382  28.479  1.00 25.00           C
ATOM    127  CA  ASN   127       5.154  -8.276  26.213  1.00 25.00           C
ATOM    128  CA  LEU   128       8.167 -10.534  26.415  1.00 25.00           C
ATOM    129  CA  LEU   129       6.799 -13.908  25.377  1.00 25.00           C
ATOM    130  CA  LEU   130       6.293 -14.734  21.681  1.00 25.00           C
ATOM    131  CA  PRO   131       5.252 -17.258  18.988  1.00 25.00           C
ATOM    132  CA  PRO   132       8.390 -19.453  19.049  1.00 25.00           C
ATOM    133  CA  HIS   133      11.447 -21.528  19.971  1.00 25.00           C
ATOM    134  CA  LEU   134      13.107 -20.828  23.339  1.00 25.00           C
ATOM    135  CA  VAL   135      16.075 -19.545  21.407  1.00 25.00           C
TER
END
