
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0304AL381_3-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304AL381_3-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    L      97      C      29          2.011
LGA    T      98      F      30          2.187
LGA    C      99      G      31          1.251
LGA    K     100      A      32          0.541
LGA    A     101      R      33          1.171
LGA    D     102      L      34          1.636
LGA    T     103      V      35          0.874
LGA    L     104      Q      36          4.087
LGA    S     105      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    -       -      P      67           -
LGA    -       -      L      68           -
LGA    -       -      L      69           -
LGA    -       -      M      70           -
LGA    -       -      K      71           -
LGA    -       -      Q      72           -
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    -       -      L      75           -
LGA    -       -      M      76           -
LGA    -       -      L      77           -
LGA    -       -      T      78           -
LGA    -       -      S      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    S     106      P      84          4.385
LGA    C     107      R      85          3.444
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    D     108      D     108          3.121
LGA    Y     109      Y     109          1.261
LGA    V     110      V     110          0.893
LGA    Y     111      Y     111          1.692
LGA    L     112      L     112          2.186
LGA    A     113      A     113          1.567
LGA    V     114      V     114          1.479
LGA    Y     115      Y     115          0.598
LGA    P     116      P     116          0.496
LGA    T     117      T     117          1.415

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  101    5.0     20    2.12    50.00     15.762     0.899

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.192592 * X  +  -0.207459 * Y  +  -0.959098 * Z  + 119.722992
  Y_new =  -0.161931 * X  +  -0.957277 * Y  +   0.239582 * Z  +  17.486830
  Z_new =  -0.967826 * X  +   0.201450 * Y  +   0.150769 * Z  + 124.903305 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.928306   -2.213287  [ DEG:    53.1880   -126.8120 ]
  Theta =   1.316441    1.825152  [ DEG:    75.4265    104.5735 ]
  Phi   =  -2.442463    0.699130  [ DEG:  -139.9428     40.0572 ]
 
# 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: T0304AL381_3-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL381_3-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21  101   5.0   20   2.12   50.00  15.762
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL381_3-D1
REMARK Aligment from pdb entry: 1rerA
ATOM      1  N   LEU    97      38.219  24.447  34.203  1.00  0.00              
ATOM      2  CA  LEU    97      38.877  24.961  35.384  1.00  0.00              
ATOM      3  C   LEU    97      38.984  23.893  36.453  1.00  0.00              
ATOM      4  O   LEU    97      38.090  23.055  36.593  1.00  0.00              
ATOM      5  N   THR    98      40.084  23.912  37.198  1.00  0.00              
ATOM      6  CA  THR    98      40.261  22.932  38.258  1.00  0.00              
ATOM      7  C   THR    98      41.105  23.434  39.425  1.00  0.00              
ATOM      8  O   THR    98      42.278  23.827  39.257  1.00  0.00              
ATOM      9  N   CYS    99      40.500  23.401  40.617  1.00  0.00              
ATOM     10  CA  CYS    99      41.158  23.865  41.833  1.00  0.00              
ATOM     11  C   CYS    99      41.833  22.745  42.598  1.00  0.00              
ATOM     12  O   CYS    99      41.313  21.627  42.677  1.00  0.00              
ATOM     13  N   LYS   100      42.979  23.053  43.187  1.00  0.00              
ATOM     14  CA  LYS   100      43.712  22.040  43.938  1.00  0.00              
ATOM     15  C   LYS   100      44.512  22.699  45.051  1.00  0.00              
ATOM     16  O   LYS   100      45.524  23.369  44.799  1.00  0.00              
ATOM     17  N   ALA   101      44.081  22.500  46.289  1.00  0.00              
ATOM     18  CA  ALA   101      44.787  23.111  47.407  1.00  0.00              
ATOM     19  C   ALA   101      45.933  22.259  47.942  1.00  0.00              
ATOM     20  O   ALA   101      45.697  21.173  48.471  1.00  0.00              
ATOM     21  N   ASP   102      47.166  22.755  47.818  1.00  0.00              
ATOM     22  CA  ASP   102      48.339  22.009  48.295  1.00  0.00              
ATOM     23  C   ASP   102      48.380  22.028  49.809  1.00  0.00              
ATOM     24  O   ASP   102      47.922  21.091  50.486  1.00  0.00              
ATOM     25  N   THR   103      48.951  23.107  50.335  1.00  0.00              
ATOM     26  CA  THR   103      49.041  23.298  51.774  1.00  0.00              
ATOM     27  C   THR   103      48.139  24.436  52.174  1.00  0.00              
ATOM     28  O   THR   103      47.835  25.324  51.361  1.00  0.00              
ATOM     29  N   LEU   104      47.713  24.378  53.431  1.00  0.00              
ATOM     30  CA  LEU   104      46.836  25.375  54.012  1.00  0.00              
ATOM     31  C   LEU   104      46.907  25.459  55.538  1.00  0.00              
ATOM     32  O   LEU   104      46.817  24.454  56.252  1.00  0.00              
ATOM     33  N   SER   105      45.511  32.392  59.683  1.00  0.00              
ATOM     34  CA  SER   105      46.742  33.146  59.461  1.00  0.00              
ATOM     35  C   SER   105      46.721  33.794  58.074  1.00  0.00              
ATOM     36  O   SER   105      46.435  33.139  57.073  1.00  0.00              
ATOM     37  N   SER   106      47.023  35.087  58.036  1.00  0.00              
ATOM     38  CA  SER   106      47.038  35.863  56.805  1.00  0.00              
ATOM     39  C   SER   106      47.575  35.088  55.613  1.00  0.00              
ATOM     40  O   SER   106      48.785  34.879  55.473  1.00  0.00              
ATOM     41  N   CYS   107      46.631  34.661  54.772  1.00  0.00              
ATOM     42  CA  CYS   107      46.889  33.901  53.548  1.00  0.00              
ATOM     43  C   CYS   107      47.783  32.693  53.762  1.00  0.00              
ATOM     44  O   CYS   107      48.884  32.606  53.209  1.00  0.00              
ATOM     45  N   ASP   108      47.289  31.752  54.553  1.00  0.00              
ATOM     46  CA  ASP   108      48.065  30.565  54.840  1.00  0.00              
ATOM     47  C   ASP   108      47.817  29.426  53.875  1.00  0.00              
ATOM     48  O   ASP   108      48.441  28.369  53.982  1.00  0.00              
ATOM     49  N   TYR   109      46.917  29.643  52.928  1.00  0.00              
ATOM     50  CA  TYR   109      46.603  28.605  51.973  1.00  0.00              
ATOM     51  C   TYR   109      47.177  28.886  50.607  1.00  0.00              
ATOM     52  O   TYR   109      47.492  30.027  50.272  1.00  0.00              
ATOM     53  N   VAL   110      47.299  27.830  49.812  1.00  0.00              
ATOM     54  CA  VAL   110      47.851  27.936  48.473  1.00  0.00              
ATOM     55  C   VAL   110      47.054  27.113  47.461  1.00  0.00              
ATOM     56  O   VAL   110      47.094  25.882  47.471  1.00  0.00              
ATOM     57  N   TYR   111      46.330  27.812  46.592  1.00  0.00              
ATOM     58  CA  TYR   111      45.506  27.181  45.573  1.00  0.00              
ATOM     59  C   TYR   111      46.264  27.105  44.270  1.00  0.00              
ATOM     60  O   TYR   111      47.144  27.914  44.006  1.00  0.00              
ATOM     61  N   LEU   112      45.920  26.125  43.451  1.00  0.00              
ATOM     62  CA  LEU   112      46.567  25.974  42.161  1.00  0.00              
ATOM     63  C   LEU   112      45.507  25.637  41.132  1.00  0.00              
ATOM     64  O   LEU   112      44.801  24.620  41.242  1.00  0.00              
ATOM     65  N   ALA   113      45.390  26.486  40.122  1.00  0.00              
ATOM     66  CA  ALA   113      44.371  26.246  39.127  1.00  0.00              
ATOM     67  C   ALA   113      44.918  25.711  37.828  1.00  0.00              
ATOM     68  O   ALA   113      45.861  26.272  37.268  1.00  0.00              
ATOM     69  N   VAL   114      44.335  24.611  37.354  1.00  0.00              
ATOM     70  CA  VAL   114      44.750  24.025  36.085  1.00  0.00              
ATOM     71  C   VAL   114      43.655  24.432  35.111  1.00  0.00              
ATOM     72  O   VAL   114      42.480  24.593  35.505  1.00  0.00              
ATOM     73  N   TYR   115      44.012  24.583  33.840  1.00  0.00              
ATOM     74  CA  TYR   115      43.008  25.017  32.876  1.00  0.00              
ATOM     75  C   TYR   115      43.487  24.960  31.431  1.00  0.00              
ATOM     76  O   TYR   115      44.583  24.459  31.119  1.00  0.00              
ATOM     77  N   PRO   116      42.635  25.494  30.559  1.00  0.00              
ATOM     78  CA  PRO   116      42.915  25.581  29.131  1.00  0.00              
ATOM     79  C   PRO   116      42.475  26.949  28.635  1.00  0.00              
ATOM     80  O   PRO   116      41.336  27.383  28.861  1.00  0.00              
ATOM     81  N   THR   117      43.384  27.628  27.957  1.00  0.00              
ATOM     82  CA  THR   117      43.082  28.938  27.423  1.00  0.00              
ATOM     83  C   THR   117      43.100  28.914  25.895  1.00  0.00              
ATOM     84  O   THR   117      43.613  27.970  25.278  1.00  0.00              
END
