
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0304AL381_3
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304AL381_3.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# 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    -       -      D      16           -
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          1.477
LGA    T      98      F      30          1.696
LGA    C      99      G      31          1.044
LGA    K     100      A      32          1.020
LGA    A     101      R      33          1.503
LGA    D     102      L      34          1.636
LGA    T     103      V      35          1.508
LGA    L     104      Q      36          4.045
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    -       -      P      84           -
LGA    S     106      R      85          3.564
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    C     107      S     106          2.521
LGA    D     108      C     107          1.556
LGA    Y     109      D     108          3.684
LGA    -       -      Y     109           -
LGA    V     110      V     110          0.314
LGA    Y     111      Y     111          1.108
LGA    L     112      L     112          1.603
LGA    A     113      A     113          1.088
LGA    V     114      V     114          1.047
LGA    Y     115      Y     115          0.453
LGA    P     116      P     116          1.061
LGA    T     117      T     117          2.506
LGA    P     118      P     118          2.151
LGA    -       -      E     119           -
LGA    E     119      M     120          3.926
LGA    -       -      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  107    5.0     22    2.13    40.91     18.299     0.987

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.177703 * X  +  -0.000750 * Y  +  -0.984084 * Z  + 121.474991
  Y_new =  -0.165791 * X  +  -0.985683 * Y  +   0.030689 * Z  +  30.608274
  Z_new =  -0.970018 * X  +   0.168606 * Y  +   0.175034 * Z  + 123.527161 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.766694   -2.374899  [ DEG:    43.9283   -136.0717 ]
  Theta =   1.325305    1.816287  [ DEG:    75.9344    104.0656 ]
  Phi   =  -2.390859    0.750734  [ DEG:  -136.9861     43.0139 ]
 
# 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                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL381_3.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  107   5.0   22   2.13   40.91  18.299
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL381_3
REMARK Aligment from pdb entry: 1rerA
ATOM      1  N   LEU    97      38.183  23.581  34.471  1.00  0.00              
ATOM      2  CA  LEU    97      38.748  24.179  35.660  1.00  0.00              
ATOM      3  C   LEU    97      39.098  23.122  36.686  1.00  0.00              
ATOM      4  O   LEU    97      38.399  22.113  36.809  1.00  0.00              
ATOM      5  N   THR    98      40.187  23.343  37.414  1.00  0.00              
ATOM      6  CA  THR    98      40.588  22.386  38.433  1.00  0.00              
ATOM      7  C   THR    98      41.337  23.013  39.605  1.00  0.00              
ATOM      8  O   THR    98      42.399  23.645  39.433  1.00  0.00              
ATOM      9  N   CYS    99      40.780  22.815  40.804  1.00  0.00              
ATOM     10  CA  CYS    99      41.357  23.364  42.026  1.00  0.00              
ATOM     11  C   CYS    99      42.266  22.383  42.737  1.00  0.00              
ATOM     12  O   CYS    99      41.990  21.180  42.783  1.00  0.00              
ATOM     13  N   LYS   100      43.338  22.902  43.319  1.00  0.00              
ATOM     14  CA  LYS   100      44.281  22.038  44.020  1.00  0.00              
ATOM     15  C   LYS   100      44.954  22.810  45.144  1.00  0.00              
ATOM     16  O   LYS   100      45.800  23.684  44.900  1.00  0.00              
ATOM     17  N   ALA   101      44.603  22.485  46.380  1.00  0.00              
ATOM     18  CA  ALA   101      45.194  23.191  47.509  1.00  0.00              
ATOM     19  C   ALA   101      46.502  22.578  47.993  1.00  0.00              
ATOM     20  O   ALA   101      46.508  21.450  48.485  1.00  0.00              
ATOM     21  N   ASP   102      47.604  23.322  47.868  1.00  0.00              
ATOM     22  CA  ASP   102      48.916  22.819  48.298  1.00  0.00              
ATOM     23  C   ASP   102      48.988  22.796  49.810  1.00  0.00              
ATOM     24  O   ASP   102      48.749  21.762  50.459  1.00  0.00              
ATOM     25  N   THR   103      49.336  23.952  50.368  1.00  0.00              
ATOM     26  CA  THR   103      49.418  24.109  51.811  1.00  0.00              
ATOM     27  C   THR   103      48.310  25.021  52.267  1.00  0.00              
ATOM     28  O   THR   103      47.811  25.854  51.494  1.00  0.00              
ATOM     29  N   LEU   104      47.935  24.835  53.529  1.00  0.00              
ATOM     30  CA  LEU   104      46.886  25.608  54.161  1.00  0.00              
ATOM     31  C   LEU   104      46.973  25.654  55.688  1.00  0.00              
ATOM     32  O   LEU   104      47.109  24.628  56.364  1.00  0.00              
ATOM     33  N   SER   105      44.275  32.005  60.112  1.00  0.00              
ATOM     34  CA  SER   105      45.318  33.005  59.898  1.00  0.00              
ATOM     35  C   SER   105      45.132  33.680  58.538  1.00  0.00              
ATOM     36  O   SER   105      44.963  33.014  57.518  1.00  0.00              
ATOM     37  N   SER   106      45.159  35.008  58.544  1.00  0.00              
ATOM     38  CA  SER   106      44.986  35.811  57.343  1.00  0.00              
ATOM     39  C   SER   106      45.642  35.205  56.114  1.00  0.00              
ATOM     40  O   SER   106      46.866  35.255  55.947  1.00  0.00              
ATOM     41  N   CYS   107      44.788  34.620  55.272  1.00  0.00              
ATOM     42  CA  CYS   107      45.168  33.971  54.017  1.00  0.00              
ATOM     43  C   CYS   107      46.296  32.968  54.171  1.00  0.00              
ATOM     44  O   CYS   107      47.378  33.129  53.598  1.00  0.00              
ATOM     45  N   ASP   108      46.026  31.919  54.934  1.00  0.00              
ATOM     46  CA  ASP   108      47.036  30.910  55.163  1.00  0.00              
ATOM     47  C   ASP   108      47.007  29.777  54.161  1.00  0.00              
ATOM     48  O   ASP   108      47.837  28.869  54.217  1.00  0.00              
ATOM     49  N   TYR   109      46.059  29.834  53.237  1.00  0.00              
ATOM     50  CA  TYR   109      45.944  28.787  52.248  1.00  0.00              
ATOM     51  C   TYR   109      46.415  29.226  50.885  1.00  0.00              
ATOM     52  O   TYR   109      46.480  30.418  50.588  1.00  0.00              
ATOM     53  N   VAL   110      46.734  28.245  50.049  1.00  0.00              
ATOM     54  CA  VAL   110      47.220  28.508  48.706  1.00  0.00              
ATOM     55  C   VAL   110      46.587  27.572  47.677  1.00  0.00              
ATOM     56  O   VAL   110      46.880  26.377  47.640  1.00  0.00              
ATOM     57  N   TYR   111      45.713  28.135  46.846  1.00  0.00              
ATOM     58  CA  TYR   111      45.014  27.381  45.818  1.00  0.00              
ATOM     59  C   TYR   111      45.740  27.507  44.501  1.00  0.00              
ATOM     60  O   TYR   111      46.428  28.489  44.254  1.00  0.00              
ATOM     61  N   LEU   112      45.587  26.506  43.651  1.00  0.00              
ATOM     62  CA  LEU   112      46.221  26.535  42.346  1.00  0.00              
ATOM     63  C   LEU   112      45.229  26.021  41.322  1.00  0.00              
ATOM     64  O   LEU   112      44.751  24.877  41.405  1.00  0.00              
ATOM     65  N   ALA   113      44.916  26.860  40.347  1.00  0.00              
ATOM     66  CA  ALA   113      43.945  26.448  39.361  1.00  0.00              
ATOM     67  C   ALA   113      44.561  26.081  38.033  1.00  0.00              
ATOM     68  O   ALA   113      45.354  26.844  37.480  1.00  0.00              
ATOM     69  N   VAL   114      44.205  24.902  37.528  1.00  0.00              
ATOM     70  CA  VAL   114      44.703  24.456  36.231  1.00  0.00              
ATOM     71  C   VAL   114      43.524  24.660  35.291  1.00  0.00              
ATOM     72  O   VAL   114      42.352  24.561  35.709  1.00  0.00              
ATOM     73  N   TYR   115      43.813  24.925  34.021  1.00  0.00              
ATOM     74  CA  TYR   115      42.719  25.173  33.090  1.00  0.00              
ATOM     75  C   TYR   115      43.166  25.265  31.637  1.00  0.00              
ATOM     76  O   TYR   115      44.334  25.013  31.289  1.00  0.00              
ATOM     77  N   PRO   116      42.201  25.640  30.799  1.00  0.00              
ATOM     78  CA  PRO   116      42.424  25.831  29.371  1.00  0.00              
ATOM     79  C   PRO   116      41.699  27.094  28.934  1.00  0.00              
ATOM     80  O   PRO   116      40.501  27.275  29.195  1.00  0.00              
ATOM     81  N   THR   117      42.432  27.969  28.268  1.00  0.00              
ATOM     82  CA  THR   117      41.854  29.205  27.788  1.00  0.00              
ATOM     83  C   THR   117      41.841  29.237  26.260  1.00  0.00              
ATOM     84  O   THR   117      42.523  28.440  25.599  1.00  0.00              
ATOM     85  N   PRO   118      41.053  30.157  25.713  1.00  0.00              
ATOM     86  CA  PRO   118      40.959  30.324  24.277  1.00  0.00              
ATOM     87  C   PRO   118      41.782  31.549  23.864  1.00  0.00              
ATOM     88  O   PRO   118      42.257  31.627  22.730  1.00  0.00              
ATOM     89  N   GLU   119      41.970  32.488  24.791  1.00  0.00              
ATOM     90  CA  GLU   119      42.733  33.717  24.515  1.00  0.00              
ATOM     91  C   GLU   119      43.390  34.242  25.796  1.00  0.00              
ATOM     92  O   GLU   119      42.705  34.397  26.804  1.00  0.00              
END
