
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0360AL242_5
# Molecule2: number of CA atoms  116 (  917),  selected  116 , name T0360.pdb
# PARAMETERS: T0360AL242_5.T0360.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A      82      M       1           -
LGA    R      83      T       2           -
LGA    G      84      Q       3           -
LGA    G      85      E       4           -
LGA    K      86      T       5           -
LGA    -       -      A       6           -
LGA    -       -      L       7           -
LGA    -       -      G       8           -
LGA    -       -      A       9           -
LGA    -       -      A      10           -
LGA    -       -      L      11           -
LGA    -       -      K      12           -
LGA    -       -      S      13           -
LGA    -       -      A      14           -
LGA    -       -      V      15           -
LGA    -       -      Q      16           -
LGA    -       -      T      17           -
LGA    -       -      M      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      K      21           -
LGA    -       -      K      22           -
LGA    -       -      Q      23           -
LGA    -       -      T      24           -
LGA    -       -      E      25           -
LGA    -       -      M      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      D      29           -
LGA    -       -      H      30           -
LGA    -       -      I      31           -
LGA    -       -      Y      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      Y      35           -
LGA    -       -      D      36           -
LGA    -       -      V      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      R      40           -
LGA    -       -      F      41           -
LGA    -       -      K      42           -
LGA    R      87      P      43           #
LGA    F      88      L      44           #
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    D      89      G      47           #
LGA    L      90      I      48          2.477
LGA    -       -      D      49           -
LGA    -       -      Q      50           -
LGA    N      91      D      51          4.718
LGA    N      92      L      52          2.081
LGA    R      93      I      53          2.771
LGA    -       -      A      54           -
LGA    -       -      A      55           -
LGA    -       -      L      56           -
LGA    -       -      P      57           -
LGA    -       -      Q      58           -
LGA    -       -      Y      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      A      62           -
LGA    F      94      L      63          5.002
LGA    -       -      I      64           -
LGA    K      95      A      65          2.275
LGA    -       -      R      66           -
LGA    -       -      V      67           -
LGA    G      96      L      68          2.543
LGA    E      97      A      69          2.543
LGA    -       -      N      70           -
LGA    -       -      H      71           -
LGA    V      98      C      72          0.569
LGA    T      99      R      73          2.154
LGA    P     100      R      74          0.823
LGA    E     101      P      75          1.084
LGA    E     102      R      76          1.522
LGA    Q     103      Y      77          1.915
LGA    A     104      L      78          2.944
LGA    I     105      K      79          2.543
LGA    A     106      A      80          0.953
LGA    Q     107      L      81          3.723
LGA    -       -      A      82           -
LGA    N     108      R      83           #
LGA    H     109      G      84          2.447
LGA    P     110      G      85          4.899
LGA    F     111      K      86          3.807
LGA    V     112      R      87          4.641
LGA    Q     113      F      88           #
LGA    -       -      D      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    -       -      N      92           -
LGA    -       -      R      93           -
LGA    Q     114      F      94          2.114
LGA    A     115      K      95          3.874
LGA    L     116      G      96           #
LGA    Q     117      E      97           -
LGA    Q     118      V      98           -
LGA    -       -      T      99           -
LGA    -       -      P     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -
LGA    -       -      Q     103           -
LGA    -       -      A     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      Q     107           -
LGA    -       -      N     108           -
LGA    -       -      H     109           -
LGA    -       -      P     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      Q     113           -
LGA    -       -      Q     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37  116    5.0     24    2.97     4.17     14.076     0.782

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.941446 * X  +  -0.150510 * Y  +   0.301706 * Z  +   9.193688
  Y_new =  -0.262873 * X  +  -0.232688 * Y  +  -0.936351 * Z  +  52.124241
  Z_new =   0.211133 * X  +  -0.960835 * Y  +   0.179498 * Z  +   5.611198 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.386110    1.755483  [ DEG:   -79.4183    100.5817 ]
  Theta =  -0.212734   -2.928859  [ DEG:   -12.1888   -167.8112 ]
  Phi   =  -2.869304    0.272288  [ DEG:  -164.3990     15.6010 ]
 
# 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: T0360AL242_5                                  
REMARK     2: T0360.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0360AL242_5.T0360.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37  116   5.0   24   2.97    4.17  14.076
REMARK  ---------------------------------------------------------- 
MOLECULE T0360AL242_5
REMARK Aligment from pdb entry: 2auh_B
ATOM      1  N   ALA    82     -62.527  21.422 -17.667  1.00  0.00              
ATOM      2  CA  ALA    82     -62.210  21.619 -19.122  1.00  0.00              
ATOM      3  C   ALA    82     -62.378  20.297 -19.882  1.00  0.00              
ATOM      4  O   ALA    82     -62.436  20.274 -21.117  1.00  0.00              
ATOM      5  N   ARG    83     -62.451  19.208 -19.116  1.00  0.00              
ATOM      6  CA  ARG    83     -62.620  17.850 -19.631  1.00  0.00              
ATOM      7  C   ARG    83     -63.608  17.821 -20.805  1.00  0.00              
ATOM      8  O   ARG    83     -64.374  18.766 -21.003  1.00  0.00              
ATOM      9  N   GLY    84     -63.603  16.744 -21.585  1.00  0.00              
ATOM     10  CA  GLY    84     -64.488  16.678 -22.744  1.00  0.00              
ATOM     11  C   GLY    84     -65.343  15.420 -22.856  1.00  0.00              
ATOM     12  O   GLY    84     -66.565  15.503 -22.982  1.00  0.00              
ATOM     13  N   GLY    85     -64.697  14.259 -22.820  1.00  0.00              
ATOM     14  CA  GLY    85     -65.399  12.986 -22.904  1.00  0.00              
ATOM     15  C   GLY    85     -65.810  12.569 -21.506  1.00  0.00              
ATOM     16  O   GLY    85     -65.202  12.978 -20.527  1.00  0.00              
ATOM     17  N   LYS    86     -66.846  11.751 -21.410  1.00  0.00              
ATOM     18  CA  LYS    86     -67.317  11.265 -20.125  1.00  0.00              
ATOM     19  C   LYS    86     -67.592   9.780 -20.273  1.00  0.00              
ATOM     20  O   LYS    86     -67.951   9.316 -21.351  1.00  0.00              
ATOM     21  N   ARG    87     -67.425   9.022 -19.202  1.00  0.00              
ATOM     22  CA  ARG    87     -67.683   7.597 -19.292  1.00  0.00              
ATOM     23  C   ARG    87     -69.170   7.318 -19.085  1.00  0.00              
ATOM     24  O   ARG    87     -69.767   7.806 -18.134  1.00  0.00              
ATOM     25  N   PHE    88     -69.761   6.533 -19.977  1.00  0.00              
ATOM     26  CA  PHE    88     -71.171   6.182 -19.871  1.00  0.00              
ATOM     27  C   PHE    88     -71.382   4.696 -20.144  1.00  0.00              
ATOM     28  O   PHE    88     -70.437   3.972 -20.454  1.00  0.00              
ATOM     29  N   ASP    89     -72.637   4.260 -20.031  1.00  0.00              
ATOM     30  CA  ASP    89     -73.022   2.870 -20.279  1.00  0.00              
ATOM     31  C   ASP    89     -74.464   2.764 -20.763  1.00  0.00              
ATOM     32  O   ASP    89     -75.390   3.162 -20.058  1.00  0.00              
ATOM     33  N   LEU    90     -74.655   2.215 -21.959  1.00  0.00              
ATOM     34  CA  LEU    90     -75.993   2.073 -22.518  1.00  0.00              
ATOM     35  C   LEU    90     -76.577   0.661 -22.467  1.00  0.00              
ATOM     36  O   LEU    90     -77.661   0.402 -23.007  1.00  0.00              
ATOM     37  N   ASN    91     -75.848  -0.240 -21.812  1.00  0.00              
ATOM     38  CA  ASN    91     -76.262  -1.632 -21.641  1.00  0.00              
ATOM     39  C   ASN    91     -77.356  -1.639 -20.606  1.00  0.00              
ATOM     40  O   ASN    91     -77.062  -1.623 -19.413  1.00  0.00              
ATOM     41  N   ASN    92     -78.608  -1.659 -21.040  1.00  0.00              
ATOM     42  CA  ASN    92     -79.686  -1.661 -20.070  1.00  0.00              
ATOM     43  C   ASN    92     -80.754  -0.639 -20.377  1.00  0.00              
ATOM     44  O   ASN    92     -80.470   0.423 -20.933  1.00  0.00              
ATOM     45  N   ARG    93     -81.985  -0.967 -19.997  1.00  0.00              
ATOM     46  CA  ARG    93     -83.148  -0.121 -20.236  1.00  0.00              
ATOM     47  C   ARG    93     -82.854   1.370 -20.134  1.00  0.00              
ATOM     48  O   ARG    93     -83.234   2.138 -21.017  1.00  0.00              
ATOM     49  N   PHE    94     -82.172   1.780 -19.071  1.00  0.00              
ATOM     50  CA  PHE    94     -81.882   3.192 -18.887  1.00  0.00              
ATOM     51  C   PHE    94     -80.443   3.623 -19.190  1.00  0.00              
ATOM     52  O   PHE    94     -79.486   2.859 -19.024  1.00  0.00              
ATOM     53  N   LYS    95     -80.310   4.868 -19.644  1.00  0.00              
ATOM     54  CA  LYS    95     -79.018   5.465 -19.968  1.00  0.00              
ATOM     55  C   LYS    95     -78.221   5.557 -18.669  1.00  0.00              
ATOM     56  O   LYS    95     -78.708   5.137 -17.628  1.00  0.00              
ATOM     57  N   GLY    96     -77.010   6.104 -18.708  1.00  0.00              
ATOM     58  CA  GLY    96     -76.228   6.205 -17.477  1.00  0.00              
ATOM     59  C   GLY    96     -74.809   6.771 -17.569  1.00  0.00              
ATOM     60  O   GLY    96     -73.962   6.230 -18.281  1.00  0.00              
ATOM     61  N   GLU    97     -74.551   7.862 -16.851  1.00  0.00              
ATOM     62  CA  GLU    97     -73.206   8.419 -16.797  1.00  0.00              
ATOM     63  C   GLU    97     -72.617   7.691 -15.596  1.00  0.00              
ATOM     64  O   GLU    97     -73.092   7.882 -14.473  1.00  0.00              
ATOM     65  N   VAL    98     -71.601   6.857 -15.831  1.00  0.00              
ATOM     66  CA  VAL    98     -70.965   6.074 -14.762  1.00  0.00              
ATOM     67  C   VAL    98     -70.572   6.934 -13.578  1.00  0.00              
ATOM     68  O   VAL    98     -69.793   7.887 -13.717  1.00  0.00              
ATOM     69  N   THR    99     -71.112   6.567 -12.416  1.00  0.00              
ATOM     70  CA  THR    99     -70.910   7.303 -11.178  1.00  0.00              
ATOM     71  C   THR    99     -69.723   6.945 -10.287  1.00  0.00              
ATOM     72  O   THR    99     -69.225   7.791  -9.558  1.00  0.00              
ATOM     73  N   PRO   100     -69.263   5.706 -10.331  1.00  0.00              
ATOM     74  CA  PRO   100     -68.142   5.330  -9.481  1.00  0.00              
ATOM     75  C   PRO   100     -66.817   5.735 -10.102  1.00  0.00              
ATOM     76  O   PRO   100     -66.498   5.335 -11.220  1.00  0.00              
ATOM     77  N   GLU   101     -66.018   6.531  -9.373  1.00  0.00              
ATOM     78  CA  GLU   101     -64.727   6.969  -9.893  1.00  0.00              
ATOM     79  C   GLU   101     -63.909   5.837 -10.483  1.00  0.00              
ATOM     80  O   GLU   101     -63.479   5.916 -11.630  1.00  0.00              
ATOM     81  N   GLU   102     -63.698   4.774  -9.713  1.00  0.00              
ATOM     82  CA  GLU   102     -62.889   3.676 -10.219  1.00  0.00              
ATOM     83  C   GLU   102     -63.495   2.919 -11.388  1.00  0.00              
ATOM     84  O   GLU   102     -62.755   2.430 -12.244  1.00  0.00              
ATOM     85  N   GLN   103     -64.823   2.817 -11.442  1.00  0.00              
ATOM     86  CA  GLN   103     -65.454   2.100 -12.562  1.00  0.00              
ATOM     87  C   GLN   103     -65.379   2.931 -13.833  1.00  0.00              
ATOM     88  O   GLN   103     -64.996   2.438 -14.883  1.00  0.00              
ATOM     89  N   ALA   104     -65.753   4.198 -13.721  1.00  0.00              
ATOM     90  CA  ALA   104     -65.731   5.111 -14.849  1.00  0.00              
ATOM     91  C   ALA   104     -64.342   5.195 -15.450  1.00  0.00              
ATOM     92  O   ALA   104     -64.174   5.304 -16.655  1.00  0.00              
ATOM     93  N   ILE   105     -63.340   5.142 -14.597  1.00  0.00              
ATOM     94  CA  ILE   105     -61.973   5.235 -15.073  1.00  0.00              
ATOM     95  C   ILE   105     -61.551   3.982 -15.830  1.00  0.00              
ATOM     96  O   ILE   105     -60.538   3.986 -16.529  1.00  0.00              
ATOM     97  N   ALA   106     -62.334   2.918 -15.691  1.00  0.00              
ATOM     98  CA  ALA   106     -62.036   1.652 -16.356  1.00  0.00              
ATOM     99  C   ALA   106     -62.557   1.635 -17.777  1.00  0.00              
ATOM    100  O   ALA   106     -61.943   1.041 -18.658  1.00  0.00              
ATOM    101  N   GLN   107     -63.693   2.291 -17.994  1.00  0.00              
ATOM    102  CA  GLN   107     -64.330   2.345 -19.304  1.00  0.00              
ATOM    103  C   GLN   107     -63.348   2.534 -20.455  1.00  0.00              
ATOM    104  O   GLN   107     -63.397   1.813 -21.451  1.00  0.00              
ATOM    105  N   ASN   108     -62.458   3.504 -20.316  1.00  0.00              
ATOM    106  CA  ASN   108     -61.460   3.776 -21.342  1.00  0.00              
ATOM    107  C   ASN   108     -60.887   2.490 -21.971  1.00  0.00              
ATOM    108  O   ASN   108     -61.241   2.114 -23.093  1.00  0.00              
ATOM    109  N   HIS   109     -60.001   1.828 -21.234  1.00  0.00              
ATOM    110  CA  HIS   109     -59.352   0.607 -21.698  1.00  0.00              
ATOM    111  C   HIS   109     -60.301  -0.391 -22.331  1.00  0.00              
ATOM    112  O   HIS   109     -59.991  -0.987 -23.363  1.00  0.00              
ATOM    113  N   PRO   110     -61.455  -0.565 -21.697  1.00  0.00              
ATOM    114  CA  PRO   110     -62.464  -1.508 -22.159  1.00  0.00              
ATOM    115  C   PRO   110     -63.103  -1.139 -23.500  1.00  0.00              
ATOM    116  O   PRO   110     -63.267  -2.004 -24.361  1.00  0.00              
ATOM    117  N   PHE   111     -63.463   0.130 -23.689  1.00  0.00              
ATOM    118  CA  PHE   111     -64.078   0.535 -24.951  1.00  0.00              
ATOM    119  C   PHE   111     -63.080   0.207 -26.042  1.00  0.00              
ATOM    120  O   PHE   111     -63.451  -0.058 -27.179  1.00  0.00              
ATOM    121  N   VAL   112     -61.804   0.219 -25.677  1.00  0.00              
ATOM    122  CA  VAL   112     -60.750  -0.070 -26.631  1.00  0.00              
ATOM    123  C   VAL   112     -60.735  -1.519 -27.061  1.00  0.00              
ATOM    124  O   VAL   112     -60.813  -1.816 -28.251  1.00  0.00              
ATOM    125  N   GLN   113     -60.620  -2.422 -26.093  1.00  0.00              
ATOM    126  CA  GLN   113     -60.614  -3.855 -26.376  1.00  0.00              
ATOM    127  C   GLN   113     -61.888  -4.215 -27.139  1.00  0.00              
ATOM    128  O   GLN   113     -61.839  -4.811 -28.218  1.00  0.00              
ATOM    129  N   GLN   114     -63.023  -3.840 -26.556  1.00  0.00              
ATOM    130  CA  GLN   114     -64.332  -4.095 -27.135  1.00  0.00              
ATOM    131  C   GLN   114     -64.373  -3.784 -28.628  1.00  0.00              
ATOM    132  O   GLN   114     -65.124  -4.411 -29.375  1.00  0.00              
ATOM    133  N   ALA   115     -63.573  -2.814 -29.062  1.00  0.00              
ATOM    134  CA  ALA   115     -63.526  -2.457 -30.475  1.00  0.00              
ATOM    135  C   ALA   115     -62.582  -3.390 -31.230  1.00  0.00              
ATOM    136  O   ALA   115     -62.866  -3.777 -32.366  1.00  0.00              
ATOM    137  N   LEU   116     -61.464  -3.749 -30.601  1.00  0.00              
ATOM    138  CA  LEU   116     -60.493  -4.656 -31.214  1.00  0.00              
ATOM    139  C   LEU   116     -61.277  -5.802 -31.848  1.00  0.00              
ATOM    140  O   LEU   116     -61.027  -6.183 -32.993  1.00  0.00              
ATOM    141  N   GLN   117     -62.231  -6.332 -31.083  1.00  0.00              
ATOM    142  CA  GLN   117     -63.085  -7.426 -31.527  1.00  0.00              
ATOM    143  C   GLN   117     -64.089  -7.008 -32.608  1.00  0.00              
ATOM    144  O   GLN   117     -65.291  -6.872 -32.340  1.00  0.00              
ATOM    145  N   GLN   118     -63.589  -6.807 -33.824  1.00  0.00              
ATOM    146  CA  GLN   118     -64.418  -6.417 -34.965  1.00  0.00              
ATOM    147  C   GLN   118     -63.579  -5.705 -36.025  1.00  0.00              
ATOM    148  O   GLN   118     -62.394  -6.078 -36.160  1.00  0.00              
END
