
#######################################################
#                                                     #
#                        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   39 (  157),  selected   39 , name T0372AL380_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL380_1-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    K      79      K      74          2.357
LGA    L      80      A      75          3.449
LGA    I      81      V      76          3.279
LGA    E      82      L      77          2.097
LGA    D      83      R      78          1.103
LGA    A      84      K      79          2.591
LGA    D      85      L      80          4.187
LGA    K      86      I      81          3.573
LGA    E      87      E      82          1.748
LGA    -       -      D      83           -
LGA    K      88      A      84          3.101
LGA    H      89      D      85          2.531
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    N      90      H      89          0.956
LGA    F      91      N      90          2.836
LGA    C      92      F      91          2.593
LGA    M      93      C      92          3.508
LGA    L      94      M      93          1.203
LGA    G      95      L      94          2.218
LGA    V      96      G      95          3.184
LGA    -       -      V      96           -
LGA    C      97      C      97          1.784
LGA    S      98      S      98          1.595
LGA    N      99      N      99          0.709
LGA    M     100      M     100          1.155
LGA    R     101      R     101          0.493
LGA    A     102      A     102          2.176
LGA    D     103      D     103          2.040
LGA    L     104      L     104          1.677
LGA    E     105      E     105          3.598
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    A     106      E     110          3.262
LGA    I     107      R     111          3.750
LGA    L     108      F     112          1.929
LGA    P     109      I     113          4.926
LGA    E     110      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    R     111      L     295          2.450
LGA    F     112      K     296          1.785
LGA    I     113      D     297          2.062
LGA    F     114      H     298          2.545
LGA    T     115      -       -           -
LGA    E     116      -       -           -
LGA    D     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39  126    5.0     35    2.62    31.43     19.013     1.289

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.296146 * X  +   0.809481 * Y  +  -0.506990 * Z  +  25.483423
  Y_new =  -0.382904 * X  +   0.586896 * Y  +   0.713399 * Z  +   9.014977
  Z_new =   0.875033 * X  +  -0.017142 * Y  +   0.483760 * Z  + -43.932156 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.035420    3.106173  [ DEG:    -2.0294    177.9706 ]
  Theta =  -1.065503   -2.076089  [ DEG:   -61.0489   -118.9511 ]
  Phi   =  -0.912473    2.229120  [ DEG:   -52.2809    127.7191 ]
 
# 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: T0372AL380_1-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL380_1-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39  126   5.0   35   2.62   31.43  19.013
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL380_1-D1
REMARK Aligment from pdb entry: 2f5tX
ATOM      1  N   LYS    79      31.238  62.996  -3.041  1.00  0.00              
ATOM      2  CA  LYS    79      31.528  63.162  -4.468  1.00  0.00              
ATOM      3  C   LYS    79      32.768  62.369  -4.883  1.00  0.00              
ATOM      4  O   LYS    79      32.794  61.781  -5.975  1.00  0.00              
ATOM      5  N   LEU    80      33.793  62.354  -4.041  1.00  0.00              
ATOM      6  CA  LEU    80      34.974  61.524  -4.374  1.00  0.00              
ATOM      7  C   LEU    80      34.658  60.038  -4.391  1.00  0.00              
ATOM      8  O   LEU    80      35.138  59.292  -5.229  1.00  0.00              
ATOM      9  N   ILE    81      33.848  59.622  -3.434  1.00  0.00              
ATOM     10  CA  ILE    81      33.388  58.240  -3.384  1.00  0.00              
ATOM     11  C   ILE    81      32.661  57.890  -4.685  1.00  0.00              
ATOM     12  O   ILE    81      32.946  56.867  -5.322  1.00  0.00              
ATOM     13  N   GLU    82      31.731  58.750  -5.100  1.00  0.00              
ATOM     14  CA  GLU    82      30.997  58.516  -6.353  1.00  0.00              
ATOM     15  C   GLU    82      31.909  58.474  -7.580  1.00  0.00              
ATOM     16  O   GLU    82      31.758  57.594  -8.460  1.00  0.00              
ATOM     17  N   ASP    83      32.877  59.392  -7.601  1.00  0.00              
ATOM     18  CA  ASP    83      33.825  59.468  -8.735  1.00  0.00              
ATOM     19  C   ASP    83      34.685  58.214  -8.791  1.00  0.00              
ATOM     20  O   ASP    83      34.948  57.682  -9.878  1.00  0.00              
ATOM     21  N   ALA    84      35.040  57.688  -7.621  1.00  0.00              
ATOM     22  CA  ALA    84      35.800  56.437  -7.574  1.00  0.00              
ATOM     23  C   ALA    84      34.978  55.244  -8.116  1.00  0.00              
ATOM     24  O   ALA    84      35.465  54.481  -8.972  1.00  0.00              
ATOM     25  N   ASP    85      33.728  55.098  -7.656  1.00  0.00              
ATOM     26  CA  ASP    85      32.861  54.023  -8.120  1.00  0.00              
ATOM     27  C   ASP    85      32.670  54.121  -9.642  1.00  0.00              
ATOM     28  O   ASP    85      32.651  53.105 -10.341  1.00  0.00              
ATOM     29  N   LYS    86      32.535  55.343 -10.157  1.00  0.00              
ATOM     30  CA  LYS    86      32.296  55.547 -11.571  1.00  0.00              
ATOM     31  C   LYS    86      33.440  55.013 -12.464  1.00  0.00              
ATOM     32  O   LYS    86      33.197  54.593 -13.609  1.00  0.00              
ATOM     33  N   GLU    87      34.654  54.995 -11.928  1.00  0.00              
ATOM     34  CA  GLU    87      35.805  54.502 -12.646  1.00  0.00              
ATOM     35  C   GLU    87      35.933  52.961 -12.627  1.00  0.00              
ATOM     36  O   GLU    87      36.833  52.408 -13.282  1.00  0.00              
ATOM     37  N   LYS    88      35.121  52.271 -11.804  1.00  0.00              
ATOM     38  CA  LYS    88      35.323  50.833 -11.599  1.00  0.00              
ATOM     39  C   LYS    88      35.037  50.041 -12.872  1.00  0.00              
ATOM     40  O   LYS    88      34.069  50.331 -13.606  1.00  0.00              
ATOM     41  N   HIS    89      35.857  49.023 -13.096  1.00  0.00              
ATOM     42  CA  HIS    89      35.681  48.089 -14.231  1.00  0.00              
ATOM     43  C   HIS    89      35.330  46.674 -13.792  1.00  0.00              
ATOM     44  O   HIS    89      34.720  45.948 -14.573  1.00  0.00              
ATOM     45  N   ASN    90      35.743  46.271 -12.578  1.00  0.00              
ATOM     46  CA  ASN    90      35.553  44.875 -12.129  1.00  0.00              
ATOM     47  C   ASN    90      34.687  44.783 -10.889  1.00  0.00              
ATOM     48  O   ASN    90      33.617  44.174 -10.945  1.00  0.00              
ATOM     49  N   PHE    91      35.118  45.430  -9.793  1.00  0.00              
ATOM     50  CA  PHE    91      34.350  45.284  -8.563  1.00  0.00              
ATOM     51  C   PHE    91      34.606  46.487  -7.673  1.00  0.00              
ATOM     52  O   PHE    91      35.705  47.031  -7.658  1.00  0.00              
ATOM     53  N   CYS    92      33.583  46.853  -6.931  1.00  0.00              
ATOM     54  CA ACYS    92      33.737  47.823  -5.856  1.00  0.00              
ATOM     55  CA BCYS    92      33.718  47.827  -5.863  1.00  0.00              
ATOM     56  C   CYS    92      33.307  47.141  -4.569  1.00  0.00              
ATOM     57  O   CYS    92      32.264  46.480  -4.542  1.00  0.00              
ATOM     58  N   MET    93      34.112  47.322  -3.525  1.00  0.00              
ATOM     59  CA  MET    93      33.729  46.859  -2.188  1.00  0.00              
ATOM     60  C   MET    93      33.308  48.114  -1.461  1.00  0.00              
ATOM     61  O   MET    93      34.057  49.117  -1.444  1.00  0.00              
ATOM     62  N   LEU    94      32.112  48.077  -0.869  1.00  0.00              
ATOM     63  CA  LEU    94      31.601  49.252  -0.141  1.00  0.00              
ATOM     64  C   LEU    94      31.268  48.762   1.265  1.00  0.00              
ATOM     65  O   LEU    94      30.518  47.789   1.402  1.00  0.00              
ATOM     66  N   GLY    95      31.799  49.449   2.270  1.00  0.00              
ATOM     67  CA  GLY    95      31.405  49.183   3.663  1.00  0.00              
ATOM     68  C   GLY    95      30.713  50.463   4.114  1.00  0.00              
ATOM     69  O   GLY    95      31.324  51.549   4.073  1.00  0.00              
ATOM     70  N   VAL    96      29.443  50.363   4.506  1.00  0.00              
ATOM     71  CA  VAL    96      28.720  51.582   4.865  1.00  0.00              
ATOM     72  C   VAL    96      27.864  51.394   6.111  1.00  0.00              
ATOM     73  O   VAL    96      27.263  50.325   6.310  1.00  0.00              
ATOM     74  N   CYS    97      27.796  52.422   6.962  1.00  0.00              
ATOM     75  CA  CYS    97      26.700  52.404   7.951  1.00  0.00              
ATOM     76  C   CYS    97      25.393  52.449   7.207  1.00  0.00              
ATOM     77  O   CYS    97      25.278  53.137   6.192  1.00  0.00              
ATOM     78  N   SER    98      24.380  51.817   7.763  1.00  0.00              
ATOM     79  CA  SER    98      23.082  51.813   7.098  1.00  0.00              
ATOM     80  C   SER    98      22.463  53.208   6.970  1.00  0.00              
ATOM     81  O   SER    98      21.644  53.440   6.053  1.00  0.00              
ATOM     82  N   ASN    99      22.888  54.139   7.830  1.00  0.00              
ATOM     83  CA  ASN    99      22.475  55.546   7.768  1.00  0.00              
ATOM     84  C   ASN    99      22.707  56.151   6.404  1.00  0.00              
ATOM     85  O   ASN    99      22.065  57.133   6.048  1.00  0.00              
ATOM     86  N   MET   100      23.690  55.614   5.704  1.00  0.00              
ATOM     87  CA  MET   100      24.103  56.233   4.441  1.00  0.00              
ATOM     88  C   MET   100      23.746  55.462   3.206  1.00  0.00              
ATOM     89  O   MET   100      24.096  55.902   2.080  1.00  0.00              
ATOM     90  N   ARG   101      23.016  54.358   3.380  1.00  0.00              
ATOM     91  CA  ARG   101      22.628  53.594   2.217  1.00  0.00              
ATOM     92  C   ARG   101      21.826  54.443   1.210  1.00  0.00              
ATOM     93  O   ARG   101      22.097  54.398  -0.014  1.00  0.00              
ATOM     94  N   ALA   102      20.801  55.175   1.675  1.00  0.00              
ATOM     95  CA  ALA   102      20.013  55.962   0.715  1.00  0.00              
ATOM     96  C   ALA   102      20.845  57.004  -0.048  1.00  0.00              
ATOM     97  O   ALA   102      20.556  57.316  -1.228  1.00  0.00              
ATOM     98  N   ASP   103      21.875  57.548   0.588  1.00  0.00              
ATOM     99  CA  ASP   103      22.800  58.472  -0.067  1.00  0.00              
ATOM    100  C   ASP   103      23.500  57.841  -1.267  1.00  0.00              
ATOM    101  O   ASP   103      23.700  58.503  -2.298  1.00  0.00              
ATOM    102  N   LEU   104      23.832  56.561  -1.154  1.00  0.00              
ATOM    103  CA  LEU   104      24.608  55.908  -2.209  1.00  0.00              
ATOM    104  C   LEU   104      23.852  54.893  -3.050  1.00  0.00              
ATOM    105  O   LEU   104      24.435  54.343  -4.002  1.00  0.00              
ATOM    106  N   GLU   105      22.565  54.697  -2.754  1.00  0.00              
ATOM    107  CA  GLU   105      21.782  53.667  -3.394  1.00  0.00              
ATOM    108  C   GLU   105      21.851  53.750  -4.932  1.00  0.00              
ATOM    109  O   GLU   105      22.167  52.767  -5.606  1.00  0.00              
ATOM    110  N   ALA   106      21.599  54.930  -5.484  1.00  0.00              
ATOM    111  CA  ALA   106      21.593  55.041  -6.938  1.00  0.00              
ATOM    112  C   ALA   106      22.976  54.885  -7.548  1.00  0.00              
ATOM    113  O   ALA   106      23.090  54.430  -8.697  1.00  0.00              
ATOM    114  N   ILE   107      24.025  55.253  -6.801  1.00  0.00              
ATOM    115  CA  ILE   107      25.383  55.020  -7.288  1.00  0.00              
ATOM    116  C   ILE   107      25.809  53.564  -7.303  1.00  0.00              
ATOM    117  O   ILE   107      26.427  53.117  -8.273  1.00  0.00              
ATOM    118  N   LEU   108      25.337  52.774  -6.352  1.00  0.00              
ATOM    119  CA  LEU   108      25.236  51.339  -6.522  1.00  0.00              
ATOM    120  C   LEU   108      24.545  50.782  -7.701  1.00  0.00              
ATOM    121  O   LEU   108      25.073  49.885  -8.387  1.00  0.00              
ATOM    122  N   PRO   109      23.330  51.249  -7.896  1.00  0.00              
ATOM    123  CA  PRO   109      22.576  50.790  -9.040  1.00  0.00              
ATOM    124  C   PRO   109      23.319  51.054 -10.352  1.00  0.00              
ATOM    125  O   PRO   109      23.386  50.156 -11.197  1.00  0.00              
ATOM    126  N   GLU   110      23.871  52.261 -10.505  1.00  0.00              
ATOM    127  CA  GLU   110      24.534  52.633 -11.760  1.00  0.00              
ATOM    128  C   GLU   110      25.809  51.842 -11.977  1.00  0.00              
ATOM    129  O   GLU   110      26.126  51.452 -13.116  1.00  0.00              
ATOM    130  N   ARG   111      26.495  51.526 -10.885  1.00  0.00              
ATOM    131  CA  ARG   111      27.673  50.677 -10.962  1.00  0.00              
ATOM    132  C   ARG   111      27.313  49.262 -11.451  1.00  0.00              
ATOM    133  O   ARG   111      27.938  48.717 -12.378  1.00  0.00              
ATOM    134  N   PHE   112      26.296  48.670 -10.835  1.00  0.00              
ATOM    135  CA  PHE   112      25.813  47.338 -11.248  1.00  0.00              
ATOM    136  C   PHE   112      25.407  47.319 -12.716  1.00  0.00              
ATOM    137  O   PHE   112      25.635  46.315 -13.414  1.00  0.00              
ATOM    138  N   ILE   113      24.780  48.410 -13.153  1.00  0.00              
ATOM    139  CA  ILE   113      24.275  48.452 -14.548  1.00  0.00              
ATOM    140  C   ILE   113      25.405  48.455 -15.607  1.00  0.00              
ATOM    141  O   ILE   113      25.166  48.130 -16.787  1.00  0.00              
ATOM    142  N   PHE   114      26.634  48.803 -15.208  1.00  0.00              
ATOM    143  CA  PHE   114      27.788  48.691 -16.112  1.00  0.00              
ATOM    144  C   PHE   114      28.372  47.265 -16.123  1.00  0.00              
ATOM    145  O   PHE   114      29.340  47.013 -16.843  1.00  0.00              
ATOM    146  N   THR   115      27.819  46.355 -15.311  1.00  0.00              
ATOM    147  CA  THR   115      28.364  44.982 -15.250  1.00  0.00              
ATOM    148  C   THR   115      29.442  44.791 -14.171  1.00  0.00              
ATOM    149  O   THR   115      30.032  43.702 -14.055  1.00  0.00              
ATOM    150  N   GLU   116      29.678  45.840 -13.380  1.00  0.00              
ATOM    151  CA  GLU   116      30.656  45.798 -12.285  1.00  0.00              
ATOM    152  C   GLU   116      30.010  45.163 -11.061  1.00  0.00              
ATOM    153  O   GLU   116      28.821  45.418 -10.740  1.00  0.00              
ATOM    154  N   ASP   117      30.766  44.291 -10.398  1.00  0.00              
ATOM    155  CA  ASP   117      30.240  43.697  -9.153  1.00  0.00              
ATOM    156  C   ASP   117      30.219  44.711  -8.021  1.00  0.00              
ATOM    157  O   ASP   117      31.204  45.459  -7.858  1.00  0.00              
END
