
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0374AL509_1
# Molecule2: number of CA atoms  160 ( 2486),  selected  160 , name T0374.pdb
# PARAMETERS: T0374AL509_1.T0374.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    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      L       3           -
LGA    -       -      S       4           -
LGA    -       -      H       5           -
LGA    D      58      R       6          2.390
LGA    G      59      P       7          3.060
LGA    Q      60      A       8          2.402
LGA    V      61      E       9          5.038
LGA    -       -      T      10           -
LGA    -       -      G      11           -
LGA    -       -      D      12           -
LGA    -       -      L      13           -
LGA    -       -      E      14           -
LGA    -       -      T      15           -
LGA    -       -      V      16           -
LGA    -       -      A      17           -
LGA    -       -      G      18           -
LGA    -       -      F      19           -
LGA    -       -      P      20           -
LGA    -       -      Q      21           -
LGA    -       -      D      22           -
LGA    -       -      R      23           -
LGA    -       -      D      24           -
LGA    -       -      E      25           -
LGA    -       -      L      26           -
LGA    -       -      F      27           -
LGA    -       -      Y      28           -
LGA    -       -      C      29           -
LGA    -       -      Y      30           -
LGA    -       -      P      31           -
LGA    -       -      K      32           -
LGA    -       -      A      33           -
LGA    -       -      I      34           -
LGA    -       -      W      35           -
LGA    -       -      P      36           -
LGA    -       -      F      37           -
LGA    -       -      S      38           -
LGA    -       -      V      39           -
LGA    -       -      A      40           -
LGA    -       -      Q      41           -
LGA    -       -      L      42           -
LGA    -       -      A      43           -
LGA    -       -      A      44           -
LGA    -       -      A      45           -
LGA    -       -      I      46           -
LGA    -       -      A      47           -
LGA    -       -      E      48           -
LGA    -       -      R      49           -
LGA    -       -      R      50           -
LGA    -       -      G      51           -
LGA    -       -      S      52           -
LGA    -       -      T      53           -
LGA    -       -      V      54           -
LGA    -       -      A      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    -       -      D      58           -
LGA    -       -      G      59           -
LGA    -       -      Q      60           -
LGA    -       -      V      61           -
LGA    -       -      L      62           -
LGA    -       -      G      63           -
LGA    L      62      F      64          2.993
LGA    G      63      A      65          2.229
LGA    F      64      N      66          2.544
LGA    E     106      F      67           -
LGA    -       -      Y      68           -
LGA    -       -      Q      69           -
LGA    -       -      W      70           -
LGA    -       -      Q      71           -
LGA    -       -      H      72           -
LGA    -       -      G      73           -
LGA    -       -      D      74           -
LGA    -       -      F      75           -
LGA    K     109      C      76          2.785
LGA    A     110      A      77          1.933
LGA    -       -      L      78           -
LGA    -       -      G      79           -
LGA    -       -      N      80           -
LGA    -       -      M      81           -
LGA    -       -      M      82           -
LGA    -       -      V      83           -
LGA    -       -      A      84           -
LGA    -       -      P      85           -
LGA    -       -      A      86           -
LGA    -       -      A      87           -
LGA    -       -      R      88           -
LGA    -       -      G      89           -
LGA    -       -      L      90           -
LGA    -       -      G      91           -
LGA    -       -      V      92           -
LGA    -       -      A      93           -
LGA    -       -      R      94           -
LGA    -       -      Y      95           -
LGA    -       -      L      96           -
LGA    -       -      I      97           -
LGA    -       -      G      98           -
LGA    -       -      V      99           -
LGA    -       -      M     100           -
LGA    -       -      E     101           -
LGA    -       -      N     102           -
LGA    -       -      L     103           -
LGA    -       -      A     104           -
LGA    -       -      R     105           -
LGA    -       -      E     106           -
LGA    -       -      Q     107           -
LGA    -       -      Y     108           -
LGA    -       -      K     109           -
LGA    -       -      A     110           -
LGA    -       -      R     111           -
LGA    -       -      L     112           -
LGA    -       -      M     113           -
LGA    -       -      K     114           -
LGA    -       -      I     115           -
LGA    I     115      S     116          3.015
LGA    S     116      C     117          3.953
LGA    C     117      F     118          2.184
LGA    -       -      N     119           -
LGA    F     118      A     120          0.889
LGA    N     119      N     121          4.674
LGA    A     120      A     122          4.698
LGA    N     121      -       -           -
LGA    A     122      -       -           -
LGA    A     123      A     123          2.691
LGA    G     124      G     124          1.023
LGA    L     125      L     125          1.829
LGA    L     126      L     126          1.981
LGA    L     127      L     127          1.685
LGA    Y     128      Y     128          1.497
LGA    T     129      T     129          0.637
LGA    Q     130      Q     130          1.862
LGA    L     131      L     131          3.156
LGA    G     132      G     132          2.948
LGA    -       -      Y     133           -
LGA    Y     133      Q     134          2.192
LGA    K     156      P     135          3.417
LGA    P     157      R     136          4.692
LGA    L     158      A     137           -
LGA    -       -      I     138           -
LGA    -       -      A     139           -
LGA    -       -      E     140           -
LGA    -       -      R     141           -
LGA    -       -      H     142           -
LGA    -       -      D     143           -
LGA    -       -      P     144           -
LGA    -       -      D     145           -
LGA    -       -      G     146           -
LGA    -       -      R     147           -
LGA    -       -      R     148           -
LGA    -       -      V     149           -
LGA    -       -      A     150           -
LGA    -       -      L     151           -
LGA    -       -      I     152           -
LGA    -       -      Q     153           -
LGA    -       -      M     154           -
LGA    -       -      D     155           -
LGA    -       -      K     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      E     159           -
LGA    -       -      P     160           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32  160    5.0     28    2.89    46.43     11.057     0.936

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.004735 * X  +   0.574500 * Y  +   0.818491 * Z  + -62.991756
  Y_new =   0.377946 * X  +  -0.756761 * Y  +   0.533357 * Z  +  27.470987
  Z_new =   0.925816 * X  +   0.311871 * Y  +  -0.213547 * Z  + -13.355418 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.171199   -0.970393  [ DEG:   124.4006    -55.5994 ]
  Theta =  -1.183187   -1.958405  [ DEG:   -67.7916   -112.2084 ]
  Phi   =   1.583323   -1.558269  [ DEG:    90.7177    -89.2823 ]
 
# 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: T0374AL509_1                                  
REMARK     2: T0374.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0374AL509_1.T0374.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32  160   5.0   28   2.89   46.43  11.057
REMARK  ---------------------------------------------------------- 
MOLECULE T0374AL509_1
REMARK Aligment from pdb entry: 1tiq_A
ATOM      1  N   ASP    58      10.147  26.644  10.871  1.00  0.00              
ATOM      2  CA  ASP    58       9.308  27.751  10.432  1.00  0.00              
ATOM      3  C   ASP    58       8.015  27.251   9.788  1.00  0.00              
ATOM      4  O   ASP    58       7.546  27.817   8.804  1.00  0.00              
ATOM      5  N   GLY    59       7.453  26.187  10.361  1.00  0.00              
ATOM      6  CA  GLY    59       6.206  25.582   9.887  1.00  0.00              
ATOM      7  C   GLY    59       6.352  24.793   8.589  1.00  0.00              
ATOM      8  O   GLY    59       5.365  24.301   8.044  1.00  0.00              
ATOM      9  N   GLN    60       7.581  24.672   8.097  1.00  0.00              
ATOM     10  CA  GLN    60       7.844  23.932   6.864  1.00  0.00              
ATOM     11  C   GLN    60       8.480  22.572   7.145  1.00  0.00              
ATOM     12  O   GLN    60       9.420  22.476   7.929  1.00  0.00              
ATOM     13  N   VAL    61       7.958  21.526   6.507  1.00  0.00              
ATOM     14  CA  VAL    61       8.483  20.175   6.693  1.00  0.00              
ATOM     15  C   VAL    61       9.930  20.094   6.213  1.00  0.00              
ATOM     16  O   VAL    61      10.231  20.366   5.047  1.00  0.00              
ATOM     17  N   LEU    62      10.825  19.702   7.116  1.00  0.00              
ATOM     18  CA  LEU    62      12.245  19.620   6.797  1.00  0.00              
ATOM     19  C   LEU    62      12.825  18.208   6.743  1.00  0.00              
ATOM     20  O   LEU    62      13.914  18.010   6.212  1.00  0.00              
ATOM     21  N   GLY    63      12.116  17.228   7.292  1.00  0.00              
ATOM     22  CA  GLY    63      12.630  15.871   7.266  1.00  0.00              
ATOM     23  C   GLY    63      11.878  14.958   8.207  1.00  0.00              
ATOM     24  O   GLY    63      10.878  15.355   8.795  1.00  0.00              
ATOM     25  N   PHE    64      12.338  13.722   8.347  1.00  0.00              
ATOM     26  CA  PHE    64      11.660  12.798   9.243  1.00  0.00              
ATOM     27  C   PHE    64      12.593  11.709   9.737  1.00  0.00              
ATOM     28  O   PHE    64      13.703  11.538   9.231  1.00  0.00              
ATOM     29  N   GLU   106      15.986   0.820  16.949  1.00  0.00              
ATOM     30  CA  GLU   106      16.660   1.067  15.686  1.00  0.00              
ATOM     31  C   GLU   106      16.215   2.377  15.040  1.00  0.00              
ATOM     32  O   GLU   106      15.034   2.724  15.079  1.00  0.00              
ATOM     33  N   LYS   109      15.917  12.739  19.375  1.00  0.00              
ATOM     34  CA  LYS   109      14.540  12.374  19.657  1.00  0.00              
ATOM     35  C   LYS   109      14.502  10.848  19.692  1.00  0.00              
ATOM     36  O   LYS   109      13.823  10.259  20.533  1.00  0.00              
ATOM     37  N   ALA   110      15.232  10.210  18.776  1.00  0.00              
ATOM     38  CA  ALA   110      15.282   8.743  18.740  1.00  0.00              
ATOM     39  C   ALA   110      15.923   8.234  20.027  1.00  0.00              
ATOM     40  O   ALA   110      15.519   7.205  20.564  1.00  0.00              
ATOM     41  N   ILE   115      21.841   1.360  14.165  1.00  0.00              
ATOM     42  CA  ILE   115      21.380   1.659  12.821  1.00  0.00              
ATOM     43  C   ILE   115      22.316   1.024  11.809  1.00  0.00              
ATOM     44  O   ILE   115      23.442   0.639  12.130  1.00  0.00              
ATOM     45  N   SER   116      21.826   0.915  10.584  1.00  0.00              
ATOM     46  CA  SER   116      22.624   0.368   9.514  1.00  0.00              
ATOM     47  C   SER   116      22.858   1.521   8.553  1.00  0.00              
ATOM     48  O   SER   116      21.935   2.304   8.302  1.00  0.00              
ATOM     49  N   CYS   117      24.081   1.658   8.042  1.00  0.00              
ATOM     50  CA  CYS   117      24.387   2.731   7.091  1.00  0.00              
ATOM     51  C   CYS   117      25.363   2.303   6.002  1.00  0.00              
ATOM     52  O   CYS   117      26.415   1.731   6.276  1.00  0.00              
ATOM     53  N   PHE   118      24.982   2.568   4.756  1.00  0.00              
ATOM     54  CA  PHE   118      25.804   2.230   3.593  1.00  0.00              
ATOM     55  C   PHE   118      27.204   2.816   3.765  1.00  0.00              
ATOM     56  O   PHE   118      27.361   4.015   4.002  1.00  0.00              
ATOM     57  N   ASN   119      28.221   1.969   3.646  1.00  0.00              
ATOM     58  CA  ASN   119      29.601   2.412   3.828  1.00  0.00              
ATOM     59  C   ASN   119      30.003   3.616   2.966  1.00  0.00              
ATOM     60  O   ASN   119      30.871   4.388   3.364  1.00  0.00              
ATOM     61  N   ALA   120      29.367   3.782   1.805  1.00  0.00              
ATOM     62  CA  ALA   120      29.677   4.900   0.907  1.00  0.00              
ATOM     63  C   ALA   120      29.078   6.230   1.376  1.00  0.00              
ATOM     64  O   ALA   120      29.463   7.294   0.894  1.00  0.00              
ATOM     65  N   ASN   121      28.126   6.172   2.298  1.00  0.00              
ATOM     66  CA  ASN   121      27.498   7.391   2.792  1.00  0.00              
ATOM     67  C   ASN   121      28.387   8.027   3.868  1.00  0.00              
ATOM     68  O   ASN   121      28.085   7.977   5.062  1.00  0.00              
ATOM     69  N   ALA   122      29.490   8.625   3.425  1.00  0.00              
ATOM     70  CA  ALA   122      30.446   9.260   4.324  1.00  0.00              
ATOM     71  C   ALA   122      29.855  10.386   5.154  1.00  0.00              
ATOM     72  O   ALA   122      30.225  10.549   6.313  1.00  0.00              
ATOM     73  N   ALA   123      28.952  11.166   4.567  1.00  0.00              
ATOM     74  CA  ALA   123      28.328  12.266   5.298  1.00  0.00              
ATOM     75  C   ALA   123      27.551  11.726   6.495  1.00  0.00              
ATOM     76  O   ALA   123      27.681  12.232   7.613  1.00  0.00              
ATOM     77  N   GLY   124      26.746  10.692   6.276  1.00  0.00              
ATOM     78  CA  GLY   124      25.960  10.141   7.383  1.00  0.00              
ATOM     79  C   GLY   124      26.826   9.472   8.449  1.00  0.00              
ATOM     80  O   GLY   124      26.535   9.576   9.643  1.00  0.00              
ATOM     81  N   LEU   125      27.876   8.780   8.021  1.00  0.00              
ATOM     82  CA  LEU   125      28.773   8.110   8.960  1.00  0.00              
ATOM     83  C   LEU   125      29.429   9.136   9.877  1.00  0.00              
ATOM     84  O   LEU   125      29.468   8.959  11.098  1.00  0.00              
ATOM     85  N   LEU   126      29.912  10.224   9.289  1.00  0.00              
ATOM     86  CA  LEU   126      30.559  11.290  10.048  1.00  0.00              
ATOM     87  C   LEU   126      29.582  11.913  11.046  1.00  0.00              
ATOM     88  O   LEU   126      29.959  12.234  12.170  1.00  0.00              
ATOM     89  N   LEU   127      28.336  12.093  10.618  1.00  0.00              
ATOM     90  CA  LEU   127      27.293  12.652  11.478  1.00  0.00              
ATOM     91  C   LEU   127      27.067  11.719  12.671  1.00  0.00              
ATOM     92  O   LEU   127      27.122  12.151  13.826  1.00  0.00              
ATOM     93  N   TYR   128      26.838  10.439  12.394  1.00  0.00              
ATOM     94  CA  TYR   128      26.606   9.467  13.466  1.00  0.00              
ATOM     95  C   TYR   128      27.764   9.403  14.470  1.00  0.00              
ATOM     96  O   TYR   128      27.538   9.333  15.681  1.00  0.00              
ATOM     97  N   THR   129      29.000   9.409  13.976  1.00  0.00              
ATOM     98  CA  THR   129      30.161   9.356  14.867  1.00  0.00              
ATOM     99  C   THR   129      30.196  10.588  15.765  1.00  0.00              
ATOM    100  O   THR   129      30.559  10.507  16.941  1.00  0.00              
ATOM    101  N   GLN   130      29.817  11.731  15.209  1.00  0.00              
ATOM    102  CA  GLN   130      29.789  12.964  15.985  1.00  0.00              
ATOM    103  C   GLN   130      28.721  12.808  17.071  1.00  0.00              
ATOM    104  O   GLN   130      28.885  13.298  18.191  1.00  0.00              
ATOM    105  N   LEU   131      27.635  12.110  16.745  1.00  0.00              
ATOM    106  CA  LEU   131      26.565  11.905  17.708  1.00  0.00              
ATOM    107  C   LEU   131      26.856  10.790  18.726  1.00  0.00              
ATOM    108  O   LEU   131      25.991  10.442  19.527  1.00  0.00              
ATOM    109  N   GLY   132      28.059  10.228  18.689  1.00  0.00              
ATOM    110  CA  GLY   132      28.417   9.203  19.655  1.00  0.00              
ATOM    111  C   GLY   132      28.280   7.746  19.255  1.00  0.00              
ATOM    112  O   GLY   132      28.533   6.849  20.067  1.00  0.00              
ATOM    113  N   TYR   133      27.883   7.496  18.015  1.00  0.00              
ATOM    114  CA  TYR   133      27.737   6.123  17.536  1.00  0.00              
ATOM    115  C   TYR   133      29.084   5.575  17.071  1.00  0.00              
ATOM    116  O   TYR   133      29.934   6.331  16.607  1.00  0.00              
ATOM    117  N   LYS   156      25.294   2.526  20.017  1.00  0.00              
ATOM    118  CA  LYS   156      25.677   3.227  21.223  1.00  0.00              
ATOM    119  C   LYS   156      24.892   2.629  22.378  1.00  0.00              
ATOM    120  O   LYS   156      23.695   2.352  22.262  1.00  0.00              
ATOM    121  N   PRO   157      25.584   2.417  23.491  1.00  0.00              
ATOM    122  CA  PRO   157      24.958   1.863  24.676  1.00  0.00              
ATOM    123  C   PRO   157      24.378   3.005  25.491  1.00  0.00              
ATOM    124  O   PRO   157      25.015   4.040  25.663  1.00  0.00              
ATOM    125  N   LEU   158      23.158   2.818  25.977  1.00  0.00              
ATOM    126  CA  LEU   158      22.486   3.845  26.762  1.00  0.00              
ATOM    127  C   LEU   158      22.482   3.489  28.250  1.00  0.00              
ATOM    128  O   LEU   158      23.480   3.005  28.786  1.00  0.00              
END
