
#######################################################
#                                                     #
#                        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 (   96),  selected   24 , name T0306AL242_5
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306AL242_5.T0306.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    -       -      L       3           -
LGA    -       -      A       4           -
LGA    -       -      V       5           -
LGA    -       -      V       6           -
LGA    -       -      T       7           -
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
LGA    -       -      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    C      40      D      22          3.062
LGA    A      41      K      23          2.432
LGA    -       -      L      24           -
LGA    -       -      L      25           -
LGA    -       -      M      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      M      29           -
LGA    -       -      I      30           -
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    -       -      C      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    -       -      I      44           -
LGA    V      42      D      45          1.306
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    -       -      E      53           -
LGA    -       -      W      54           -
LGA    -       -      V      55           -
LGA    -       -      L      56           -
LGA    -       -      L      57           -
LGA    -       -      V      58           -
LGA    -       -      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    A      43      H      67          4.805
LGA    I      44      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    D      45      C      77          4.821
LGA    N      46      V      78          1.647
LGA    -       -      I      79           -
LGA    I      47      G      80          1.853
LGA    G      48      I      81          0.612
LGA    A      49      V      82          4.972
LGA    G      50      D      83          4.083
LGA    T      51      -       -           -
LGA    G      52      -       -           -
LGA    E      53      -       -           -
LGA    W      54      -       -           -
LGA    V      55      E      84           #
LGA    L      56      V      85          4.685
LGA    L      57      V      86          3.294
LGA    V      58      S      87          0.598
LGA    S      59      G      88          2.657
LGA    -       -      G      89           -
LGA    G      60      Q      90          1.243
LGA    S      61      V      91          2.821
LGA    S      62      I      92          1.672
LGA    A      63      F      93          4.160
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   95    5.0     18    3.17     0.00     12.151     0.550

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.890175 * X  +   0.132970 * Y  +   0.435783 * Z  +  28.610889
  Y_new =   0.280995 * X  +  -0.592679 * Y  +   0.754834 * Z  + -68.322144
  Z_new =   0.358650 * X  +   0.794387 * Y  +   0.490224 * Z  +  14.573411 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.017891   -2.123702  [ DEG:    58.3209   -121.6791 ]
  Theta =  -0.366821   -2.774772  [ DEG:   -21.0173   -158.9827 ]
  Phi   =   2.835829   -0.305764  [ DEG:   162.4810    -17.5190 ]
 
# 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: T0306AL242_5                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306AL242_5.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   95   5.0   18   3.17    0.00  12.151
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL242_5
REMARK Aligment from pdb entry: 1m06_J
ATOM      1  N   CYS    40      28.601  22.124  61.326  1.00  0.00              
ATOM      2  CA  CYS    40      29.021  23.089  62.390  1.00  0.00              
ATOM      3  C   CYS    40      30.183  22.520  63.202  1.00  0.00              
ATOM      4  O   CYS    40      30.325  22.785  64.397  1.00  0.00              
ATOM      5  N   ALA    41      31.016  21.722  62.547  1.00  0.00              
ATOM      6  CA  ALA    41      32.173  21.128  63.205  1.00  0.00              
ATOM      7  C   ALA    41      33.349  22.005  62.794  1.00  0.00              
ATOM      8  O   ALA    41      34.077  22.532  63.638  1.00  0.00              
ATOM      9  N   VAL    42      33.500  22.171  61.479  1.00  0.00              
ATOM     10  CA  VAL    42      34.565  22.977  60.895  1.00  0.00              
ATOM     11  C   VAL    42      34.378  24.456  61.213  1.00  0.00              
ATOM     12  O   VAL    42      35.349  25.182  61.441  1.00  0.00              
ATOM     13  N   ALA    43      33.123  24.892  61.224  1.00  0.00              
ATOM     14  CA  ALA    43      32.777  26.287  61.480  1.00  0.00              
ATOM     15  C   ALA    43      33.332  26.849  62.784  1.00  0.00              
ATOM     16  O   ALA    43      33.397  28.064  62.946  1.00  0.00              
ATOM     17  N   ILE    44      33.719  25.985  63.718  1.00  0.00              
ATOM     18  CA  ILE    44      34.266  26.463  64.988  1.00  0.00              
ATOM     19  C   ILE    44      35.791  26.634  64.894  1.00  0.00              
ATOM     20  O   ILE    44      36.391  27.454  65.604  1.00  0.00              
ATOM     21  N   ASP    45      36.414  25.851  64.017  1.00  0.00              
ATOM     22  CA  ASP    45      37.863  25.895  63.867  1.00  0.00              
ATOM     23  C   ASP    45      38.370  26.552  62.586  1.00  0.00              
ATOM     24  O   ASP    45      38.017  26.146  61.475  1.00  0.00              
ATOM     25  N   ASN    46      39.203  27.578  62.756  1.00  0.00              
ATOM     26  CA  ASN    46      39.773  28.296  61.619  1.00  0.00              
ATOM     27  C   ASN    46      40.568  27.332  60.757  1.00  0.00              
ATOM     28  O   ASN    46      41.454  26.632  61.251  1.00  0.00              
ATOM     29  N   ILE    47      40.278  27.297  59.452  1.00  0.00              
ATOM     30  CA  ILE    47      40.965  26.414  58.511  1.00  0.00              
ATOM     31  C   ILE    47      42.481  26.310  58.700  1.00  0.00              
ATOM     32  O   ILE    47      43.103  27.106  59.414  1.00  0.00              
ATOM     33  N   GLY    48      43.058  25.317  58.037  1.00  0.00              
ATOM     34  CA  GLY    48      44.474  25.029  58.134  1.00  0.00              
ATOM     35  C   GLY    48      45.327  25.639  57.030  1.00  0.00              
ATOM     36  O   GLY    48      46.523  25.854  57.228  1.00  0.00              
ATOM     37  N   ALA    49      44.728  25.918  55.876  1.00  0.00              
ATOM     38  CA  ALA    49      45.482  26.468  54.749  1.00  0.00              
ATOM     39  C   ALA    49      46.669  25.539  54.466  1.00  0.00              
ATOM     40  O   ALA    49      47.785  25.998  54.208  1.00  0.00              
ATOM     41  N   GLY    50      46.420  24.232  54.526  1.00  0.00              
ATOM     42  CA  GLY    50      47.457  23.226  54.297  1.00  0.00              
ATOM     43  C   GLY    50      47.684  22.985  52.791  1.00  0.00              
ATOM     44  O   GLY    50      48.786  22.597  52.373  1.00  0.00              
ATOM     45  N   THR    51      46.648  23.227  51.985  1.00  0.00              
ATOM     46  CA  THR    51      46.744  23.059  50.529  1.00  0.00              
ATOM     47  C   THR    51      47.636  24.154  49.949  1.00  0.00              
ATOM     48  O   THR    51      47.674  25.265  50.467  1.00  0.00              
ATOM     49  N   GLY    52      48.361  23.843  48.880  1.00  0.00              
ATOM     50  CA  GLY    52      49.226  24.848  48.285  1.00  0.00              
ATOM     51  C   GLY    52      50.656  24.787  48.781  1.00  0.00              
ATOM     52  O   GLY    52      51.037  23.863  49.509  1.00  0.00              
ATOM     53  N   GLU    53      51.447  25.781  48.396  1.00  0.00              
ATOM     54  CA  GLU    53      52.854  25.825  48.780  1.00  0.00              
ATOM     55  C   GLU    53      53.109  26.536  50.094  1.00  0.00              
ATOM     56  O   GLU    53      52.169  26.899  50.797  1.00  0.00              
ATOM     57  N   TRP    54      54.391  26.731  50.410  1.00  0.00              
ATOM     58  CA  TRP    54      54.810  27.390  51.646  1.00  0.00              
ATOM     59  C   TRP    54      54.665  28.890  51.516  1.00  0.00              
ATOM     60  O   TRP    54      55.034  29.465  50.482  1.00  0.00              
ATOM     61  N   VAL    55      54.138  29.518  52.570  1.00  0.00              
ATOM     62  CA  VAL    55      53.916  30.966  52.596  1.00  0.00              
ATOM     63  C   VAL    55      54.790  31.704  53.595  1.00  0.00              
ATOM     64  O   VAL    55      55.249  32.814  53.342  1.00  0.00              
ATOM     65  N   LEU    56      55.019  31.074  54.732  1.00  0.00              
ATOM     66  CA  LEU    56      55.755  31.750  55.813  1.00  0.00              
ATOM     67  C   LEU    56      57.206  31.395  55.971  1.00  0.00              
ATOM     68  O   LEU    56      57.565  30.295  56.391  1.00  0.00              
ATOM     69  N   LEU    57      58.039  32.351  55.609  1.00  0.00              
ATOM     70  CA  LEU    57      59.450  32.203  55.840  1.00  0.00              
ATOM     71  C   LEU    57      59.716  33.166  56.978  1.00  0.00              
ATOM     72  O   LEU    57      59.436  34.354  56.868  1.00  0.00              
ATOM     73  N   VAL    58      60.258  32.660  58.072  1.00  0.00              
ATOM     74  CA  VAL    58      60.466  33.479  59.231  1.00  0.00              
ATOM     75  C   VAL    58      61.864  33.286  59.813  1.00  0.00              
ATOM     76  O   VAL    58      62.151  33.726  60.917  1.00  0.00              
ATOM     77  N   SER    59      62.730  32.628  59.058  1.00  0.00              
ATOM     78  CA  SER    59      64.088  32.405  59.519  1.00  0.00              
ATOM     79  C   SER    59      64.403  30.963  59.870  1.00  0.00              
ATOM     80  O   SER    59      65.572  30.557  59.922  1.00  0.00              
ATOM     81  N   GLY    60      63.359  30.175  60.111  1.00  0.00              
ATOM     82  CA  GLY    60      63.557  28.780  60.463  1.00  0.00              
ATOM     83  C   GLY    60      62.271  28.186  60.985  1.00  0.00              
ATOM     84  O   GLY    60      61.195  28.692  60.674  1.00  0.00              
ATOM     85  N   SER    61      62.374  27.118  61.773  1.00  0.00              
ATOM     86  CA  SER    61      61.191  26.466  62.323  1.00  0.00              
ATOM     87  C   SER    61      60.652  27.213  63.527  1.00  0.00              
ATOM     88  O   SER    61      61.392  27.573  64.442  1.00  0.00              
ATOM     89  N   SER    62      59.352  27.468  63.502  1.00  0.00              
ATOM     90  CA  SER    62      58.682  28.173  64.585  1.00  0.00              
ATOM     91  C   SER    62      57.372  27.456  64.796  1.00  0.00              
ATOM     92  O   SER    62      56.594  27.313  63.861  1.00  0.00              
ATOM     93  N   ALA    63      57.130  26.994  66.015  1.00  0.00              
ATOM     94  CA  ALA    63      55.891  26.293  66.303  1.00  0.00              
ATOM     95  C   ALA    63      54.679  27.221  66.441  1.00  0.00              
ATOM     96  O   ALA    63      54.861  28.465  66.503  1.00  0.00              
END
