
#######################################################
#                                                     #
#                        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   87 (   87),  selected   87 , name T0307AL381_2
# Molecule2: number of CA atoms  132 ( 1005),  selected  132 , name T0307.pdb
# PARAMETERS: T0307AL381_2.T0307.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      18      M       1           -
LGA    T      19      G       2           -
LGA    A      20      L       3           -
LGA    I      21      G       4           -
LGA    I      22      R       5           -
LGA    K      23      Q       6           -
LGA    M      24      S       7           -
LGA    A      25      L       8           -
LGA    K      26      N       9           -
LGA    S      27      I      10           -
LGA    M      28      M      11           -
LGA    V      29      T      12           -
LGA    M      30      F      13           -
LGA    A      31      S      14           -
LGA    D      32      G      15           -
LGA    G      33      Q      16           #
LGA    K      34      E      17          3.312
LGA    -       -      L      18           -
LGA    -       -      T      19           -
LGA    I      35      A      20          2.924
LGA    K      36      I      21          2.878
LGA    P      37      I      22          2.427
LGA    A      38      K      23          3.153
LGA    E      39      M      24          2.851
LGA    I      40      A      25          1.247
LGA    A      41      K      26          1.773
LGA    V      42      S      27          2.199
LGA    M      43      M      28          1.567
LGA    T      44      V      29          1.225
LGA    R      45      M      30          0.964
LGA    E      46      A      31          0.933
LGA    F      47      D      32          3.220
LGA    M      48      G      33          4.155
LGA    R      49      K      34          3.974
LGA    F      50      I      35          1.772
LGA    G      51      K      36          2.079
LGA    I      52      P      37          3.708
LGA    -       -      A      38           -
LGA    L      53      E      39          5.695
LGA    Q      54      I      40          4.145
LGA    D      55      A      41          2.451
LGA    Q      56      V      42          1.791
LGA    V      57      M      43          1.467
LGA    D      58      T      44          1.361
LGA    L      59      R      45          2.488
LGA    L      60      E      46          3.039
LGA    L      61      F      47          1.603
LGA    K      62      M      48          2.588
LGA    A      63      R      49          3.211
LGA    S      64      F      50          2.514
LGA    D      65      G      51          2.760
LGA    S      66      I      52           #
LGA    I      67      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    -       -      D      58           -
LGA    -       -      L      59           -
LGA    -       -      L      60           -
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      S      64           -
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    E      68      I      76          3.920
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    A      69      M      79          3.127
LGA    S      70      D      80          2.966
LGA    -       -      E      81           -
LGA    Q      71      E      82          5.159
LGA    A      72      R      83          3.439
LGA    V      73      K      84          2.332
LGA    A      74      K      85          4.010
LGA    L      75      Y      86          1.984
LGA    -       -      V      87           -
LGA    -       -      A      88           -
LGA    I      76      S      89          4.480
LGA    A      77      Y      90           -
LGA    R      78      L      91           -
LGA    M      79      G      92           -
LGA    D      80      V      93           -
LGA    E      81      I      94           -
LGA    E      82      M      95           -
LGA    R      83      A      96           -
LGA    K      84      S      97           -
LGA    K      85      D      98           -
LGA    Y      86      G      99           -
LGA    V      87      D     100           -
LGA    A      88      I     101           -
LGA    S      89      D     102           -
LGA    Y      90      D     103           -
LGA    L      91      N     104           -
LGA    G      92      E     105           -
LGA    A      96      L     106           -
LGA    S      97      A     107           -
LGA    D      98      L     108           -
LGA    G      99      W     109           -
LGA    I     101      T     110           -
LGA    D     102      L     111           -
LGA    D     103      I     112           -
LGA    N     104      S     113           -
LGA    E     105      T     114           -
LGA    L     106      L     115           -
LGA    A     107      C     116           -
LGA    L     108      G     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      T     120           -
LGA    -       -      M     121           -
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   87  132    5.0     41    2.97     2.44     19.741     1.336

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.043795 * X  +  -0.904623 * Y  +  -0.423957 * Z  +  32.683731
  Y_new =  -0.855306 * X  +   0.253247 * Y  +  -0.452015 * Z  +  18.289587
  Z_new =   0.516268 * X  +   0.342817 * Y  +  -0.784821 * Z  +  31.721020 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.729762   -0.411830  [ DEG:   156.4039    -23.5961 ]
  Theta =  -0.542488   -2.599104  [ DEG:   -31.0823   -148.9177 ]
  Phi   =  -1.621956    1.519637  [ DEG:   -92.9312     87.0688 ]
 
# 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: T0307AL381_2                                  
REMARK     2: T0307.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307AL381_2.T0307.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   87  132   5.0   41   2.97    2.44  19.741
REMARK  ---------------------------------------------------------- 
MOLECULE T0307AL381_2
REMARK Aligment from pdb entry: 2mysB
ATOM      1  CA  LEU    18       9.542  -5.268  32.042  1.00  0.00              
ATOM      2  CA  THR    19      11.167  -3.305  34.722  1.00  0.00              
ATOM      3  CA  ALA    20      14.307  -5.420  34.815  1.00  0.00              
ATOM      4  CA  ILE    21      14.645  -5.009  31.029  1.00  0.00              
ATOM      5  CA  ILE    22      14.629  -1.322  31.692  1.00  0.00              
ATOM      6  CA  LYS    23      17.089  -1.460  34.394  1.00  0.00              
ATOM      7  CA  MET    24      19.630  -3.298  32.371  1.00  0.00              
ATOM      8  CA  ALA    25      18.833  -0.958  29.633  1.00  0.00              
ATOM      9  CA  LYS    26      19.410   1.917  31.986  1.00  0.00              
ATOM     10  CA  SER    27      22.682   0.408  32.896  1.00  0.00              
ATOM     11  CA  MET    28      23.901   0.111  29.297  1.00  0.00              
ATOM     12  CA  VAL    29      23.315   3.780  28.775  1.00  0.00              
ATOM     13  CA  MET    30      29.860   5.675  34.188  1.00  0.00              
ATOM     14  CA  ALA    31      28.125   3.462  36.779  1.00  0.00              
ATOM     15  CA  ASP    32      27.490   6.711  38.706  1.00  0.00              
ATOM     16  CA  GLY    33      23.802   5.988  38.726  1.00  0.00              
ATOM     17  CA  LYS    34      22.637   8.978  36.702  1.00  0.00              
ATOM     18  CA  ILE    35      22.162   9.299  32.933  1.00  0.00              
ATOM     19  CA  LYS    36      23.551  12.399  31.300  1.00  0.00              
ATOM     20  CA  PRO    37      24.774  13.801  27.982  1.00  0.00              
ATOM     21  CA  ALA    38      28.112  12.094  28.313  1.00  0.00              
ATOM     22  CA  GLU    39      26.545   8.668  28.625  1.00  0.00              
ATOM     23  CA  ILE    40      24.255   9.291  25.708  1.00  0.00              
ATOM     24  CA  ALA    41      26.974  10.402  23.337  1.00  0.00              
ATOM     25  CA  VAL    42      28.926   7.317  24.110  1.00  0.00              
ATOM     26  CA  MET    43      25.957   5.010  24.113  1.00  0.00              
ATOM     27  CA  THR    44      25.515   6.138  20.590  1.00  0.00              
ATOM     28  CA  ARG    45      29.107   6.129  19.515  1.00  0.00              
ATOM     29  CA  GLU    46      29.262   2.537  20.691  1.00  0.00              
ATOM     30  CA  PHE    47      26.314   1.742  18.466  1.00  0.00              
ATOM     31  CA  MET    48      27.901   3.393  15.461  1.00  0.00              
ATOM     32  CA  ARG    49      26.304   6.806  15.466  1.00  0.00              
ATOM     33  CA  PHE    50      28.972   9.488  15.565  1.00  0.00              
ATOM     34  CA  GLY    51      27.090  12.328  13.950  1.00  0.00              
ATOM     35  CA  ILE    52      25.532  13.441  17.195  1.00  0.00              
ATOM     36  CA  LEU    53      24.412  17.016  17.614  1.00  0.00              
ATOM     37  CA  GLN    54      23.894  18.438  21.073  1.00  0.00              
ATOM     38  CA  ASP    55      20.408  19.690  20.283  1.00  0.00              
ATOM     39  CA  GLN    56      19.557  16.050  19.994  1.00  0.00              
ATOM     40  CA  VAL    57      21.340  15.046  23.126  1.00  0.00              
ATOM     41  CA  ASP    58      19.640  17.988  24.828  1.00  0.00              
ATOM     42  CA  LEU    59      16.248  17.311  23.445  1.00  0.00              
ATOM     43  CA  LEU    60      16.256  13.895  24.991  1.00  0.00              
ATOM     44  CA  LEU    61      17.367  15.293  28.272  1.00  0.00              
ATOM     45  CA  LYS    62      14.834  17.990  28.467  1.00  0.00              
ATOM     46  CA  ALA    63      12.151  15.307  28.695  1.00  0.00              
ATOM     47  CA  SER    64      12.750  15.391  32.389  1.00  0.00              
ATOM     48  CA  ASP    65      13.033  18.083  35.103  1.00  0.00              
ATOM     49  CA  SER    66      15.575  16.233  37.208  1.00  0.00              
ATOM     50  CA  ILE    67      17.744  11.269  35.141  1.00  0.00              
ATOM     51  CA  GLU    68      18.172   8.544  37.679  1.00  0.00              
ATOM     52  CA  ALA    69      16.249   5.230  37.428  1.00  0.00              
ATOM     53  CA  SER    70      13.004   6.400  38.888  1.00  0.00              
ATOM     54  CA  GLN    71      12.855   9.485  36.669  1.00  0.00              
ATOM     55  CA  ALA    72      13.649   7.319  33.692  1.00  0.00              
ATOM     56  CA  VAL    73      11.191   4.585  34.526  1.00  0.00              
ATOM     57  CA  ALA    74       8.578   7.222  35.236  1.00  0.00              
ATOM     58  CA  LEU    75       9.387   9.025  32.025  1.00  0.00              
ATOM     59  CA  ILE    76       8.961   5.861  30.053  1.00  0.00              
ATOM     60  CA  ALA    77      -6.100 -15.394  20.337  1.00  0.00              
ATOM     61  CA  ARG    78      -9.584 -14.547  21.477  1.00  0.00              
ATOM     62  CA  MET    79     -10.405 -13.133  18.066  1.00  0.00              
ATOM     63  CA  ASP    80      -8.841 -16.234  16.595  1.00  0.00              
ATOM     64  CA  GLU    81     -10.972 -18.242  19.030  1.00  0.00              
ATOM     65  CA  GLU    82     -10.721 -20.865  16.352  1.00  0.00              
ATOM     66  CA  ARG    83      -9.090 -10.826   8.168  1.00  0.00              
ATOM     67  CA  LYS    84      -8.820  -7.102   7.298  1.00  0.00              
ATOM     68  CA  LYS    85     -12.540  -6.334   7.353  1.00  0.00              
ATOM     69  CA  TYR    86     -13.203  -8.523  10.359  1.00  0.00              
ATOM     70  CA  VAL    87     -11.142  -6.242  12.564  1.00  0.00              
ATOM     71  CA  ALA    88     -11.733  -3.134  10.523  1.00  0.00              
ATOM     72  CA  SER    89     -15.384  -3.200  11.614  1.00  0.00              
ATOM     73  CA  TYR    90     -14.637  -4.309  15.128  1.00  0.00              
ATOM     74  CA  LEU    91     -12.249  -1.471  15.982  1.00  0.00              
ATOM     75  CA  GLY    92     -14.864   0.882  14.597  1.00  0.00              
ATOM     76  CA  ALA    96     -17.932  -0.891  16.084  1.00  0.00              
ATOM     77  CA  SER    97     -16.848  -0.914  19.654  1.00  0.00              
ATOM     78  CA  ASP    98     -14.098   0.145  21.968  1.00  0.00              
ATOM     79  CA  GLY    99     -13.640   3.508  20.276  1.00  0.00              
ATOM     80  CA  ILE   101     -11.660   3.922  17.029  1.00  0.00              
ATOM     81  CA  ASP   102     -11.387   6.354  14.093  1.00  0.00              
ATOM     82  CA  ASP   103     -10.676   5.842  10.357  1.00  0.00              
ATOM     83  CA  ASN   104      -7.713   8.208  10.162  1.00  0.00              
ATOM     84  CA  GLU   105      -6.471   5.780  12.818  1.00  0.00              
ATOM     85  CA  LEU   106      -7.088   2.573  10.859  1.00  0.00              
ATOM     86  CA  ALA   107      -5.490   3.307   7.480  1.00  0.00              
ATOM     87  CA  LEU   108      -2.410   4.315   9.405  1.00  0.00              
END
