
#######################################################
#                                                     #
#                        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-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307AL381_2-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      18      I      10           -
LGA    T      19      M      11           -
LGA    A      20      T      12           -
LGA    I      21      F      13           -
LGA    I      22      S      14           -
LGA    K      23      G      15           -
LGA    M      24      -       -           -
LGA    A      25      -       -           -
LGA    K      26      -       -           -
LGA    S      27      -       -           -
LGA    M      28      -       -           -
LGA    V      29      -       -           -
LGA    M      30      -       -           -
LGA    A      31      -       -           -
LGA    D      32      -       -           -
LGA    G      33      Q      16           #
LGA    K      34      E      17          3.627
LGA    -       -      L      18           -
LGA    -       -      T      19           -
LGA    I      35      A      20          3.879
LGA    K      36      I      21          2.466
LGA    P      37      I      22          2.216
LGA    A      38      K      23          2.523
LGA    E      39      M      24          2.111
LGA    I      40      A      25          0.944
LGA    A      41      K      26          1.641
LGA    V      42      S      27          1.705
LGA    M      43      M      28          0.748
LGA    T      44      V      29          0.955
LGA    R      45      M      30          1.076
LGA    E      46      A      31          0.615
LGA    F      47      D      32          3.525
LGA    M      48      G      33          4.460
LGA    R      49      K      34          3.885
LGA    F      50      I      35          1.876
LGA    G      51      K      36          2.854
LGA    I      52      P      37          3.834
LGA    -       -      A      38           -
LGA    L      53      E      39           #
LGA    Q      54      I      40          4.762
LGA    D      55      A      41          3.151
LGA    Q      56      V      42          2.701
LGA    V      57      M      43          1.981
LGA    D      58      T      44          1.117
LGA    L      59      R      45          1.321
LGA    L      60      E      46          2.253
LGA    L      61      F      47          0.938
LGA    K      62      M      48          1.774
LGA    A      63      R      49          2.427
LGA    S      64      F      50          2.363
LGA    D      65      G      51          2.090
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          4.802
LGA    A      69      A      77           #
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    S      70      E      82          2.893
LGA    Q      71      R      83          2.259
LGA    -       -      K      84           -
LGA    -       -      K      85           -
LGA    A      72      Y      86          1.741
LGA    -       -      V      87           -
LGA    -       -      A      88           -
LGA    -       -      S      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      G      92           -
LGA    -       -      V      93           -
LGA    -       -      I      94           -
LGA    -       -      M      95           -
LGA    -       -      A      96           -
LGA    -       -      S      97           -
LGA    -       -      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    -       -      I     101           -
LGA    -       -      D     102           -
LGA    -       -      D     103           -
LGA    -       -      N     104           -
LGA    -       -      E     105           -
LGA    -       -      L     106           -
LGA    -       -      A     107           -
LGA    -       -      L     108           -
LGA    -       -      W     109           -
LGA    -       -      T     110           -
LGA    -       -      L     111           -
LGA    -       -      I     112           -
LGA    -       -      S     113           -
LGA    -       -      T     114           -
LGA    -       -      L     115           -
LGA    -       -      C     116           -
LGA    -       -      G     117           -
LGA    -       -      L     118           -
LGA    V      73      P     119           #
LGA    A      74      T     120           -
LGA    -       -      M     121           -
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    L      75      N     128           #
LGA    I      76      N     129          3.512
LGA    A      77      M     130           -
LGA    R      78      K     131           -
LGA    M      79      N     132           -
LGA    D      80      -       -           -
LGA    E      81      -       -           -
LGA    E      82      -       -           -
LGA    R      83      -       -           -
LGA    K      84      -       -           -
LGA    K      85      -       -           -
LGA    Y      86      -       -           -
LGA    V      87      -       -           -
LGA    A      88      -       -           -
LGA    S      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      -       -           -
LGA    G      92      -       -           -
LGA    A      96      -       -           -
LGA    S      97      -       -           -
LGA    D      98      -       -           -
LGA    G      99      -       -           -
LGA    I     101      -       -           -
LGA    D     102      -       -           -
LGA    D     103      -       -           -
LGA    N     104      -       -           -
LGA    E     105      -       -           -
LGA    L     106      -       -           -
LGA    A     107      -       -           -
LGA    L     108      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   87  123    5.0     36    2.67     2.78     20.396     1.299

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.168227 * X  +  -0.895341 * Y  +  -0.412388 * Z  +  32.679840
  Y_new =  -0.870758 * X  +   0.331063 * Y  +  -0.363563 * Z  +  17.101353
  Z_new =   0.462040 * X  +   0.297929 * Y  +  -0.835319 * Z  +  32.592236 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.798993   -0.342600  [ DEG:   160.3705    -19.6295 ]
  Theta =  -0.480294   -2.661299  [ DEG:   -27.5188   -152.4812 ]
  Phi   =  -1.761642    1.379951  [ DEG:  -100.9346     79.0654 ]
 
# 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-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307AL381_2-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   87  123   5.0   36   2.67    2.78  20.396
REMARK  ---------------------------------------------------------- 
MOLECULE T0307AL381_2-D1
REMARK Aligment from pdb entry: 2mysB
ATOM      1  CA  LEU    18       7.257  -3.825  30.059  1.00  0.00              
ATOM      2  CA  THR    19       8.885  -2.186  32.948  1.00  0.00              
ATOM      3  CA  ALA    20      11.775  -4.628  33.120  1.00  0.00              
ATOM      4  CA  ILE    21      12.419  -4.063  29.394  1.00  0.00              
ATOM      5  CA  ILE    22      12.738  -0.434  30.266  1.00  0.00              
ATOM      6  CA  LYS    23      14.975  -0.973  33.109  1.00  0.00              
ATOM      7  CA  MET    24      17.448  -2.967  31.150  1.00  0.00              
ATOM      8  CA  ALA    25      17.091  -0.419  28.507  1.00  0.00              
ATOM      9  CA  LYS    26      17.797   2.254  31.055  1.00  0.00              
ATOM     10  CA  SER    27      20.823   0.359  32.084  1.00  0.00              
ATOM     11  CA  MET    28      22.254   0.116  28.560  1.00  0.00              
ATOM     12  CA  VAL    29      22.088   3.848  28.214  1.00  0.00              
ATOM     13  CA  MET    30      28.399   4.753  34.139  1.00  0.00              
ATOM     14  CA  ALA    31      26.266   2.611  36.480  1.00  0.00              
ATOM     15  CA  ASP    32      25.838   5.807  38.546  1.00  0.00              
ATOM     16  CA  GLY    33      22.103   5.484  38.288  1.00  0.00              
ATOM     17  CA  LYS    34      21.398   8.680  36.369  1.00  0.00              
ATOM     18  CA  ILE    35      21.225   9.241  32.602  1.00  0.00              
ATOM     19  CA  LYS    36      23.039  12.253  31.244  1.00  0.00              
ATOM     20  CA  PRO    37      24.629  13.682  28.098  1.00  0.00              
ATOM     21  CA  ALA    38      27.742  11.612  28.545  1.00  0.00              
ATOM     22  CA  GLU    39      25.810   8.363  28.556  1.00  0.00              
ATOM     23  CA  ILE    40      23.807   9.375  25.539  1.00  0.00              
ATOM     24  CA  ALA    41      26.787  10.307  23.416  1.00  0.00              
ATOM     25  CA  VAL    42      28.350   6.995  24.133  1.00  0.00              
ATOM     26  CA  MET    43      25.165   5.023  23.812  1.00  0.00              
ATOM     27  CA  THR    44      25.089   6.368  20.339  1.00  0.00              
ATOM     28  CA  ARG    45      28.728   6.029  19.498  1.00  0.00              
ATOM     29  CA  GLU    46      28.427   2.386  20.472  1.00  0.00              
ATOM     30  CA  PHE    47      25.576   2.026  18.020  1.00  0.00              
ATOM     31  CA  MET    48      27.532   3.647  15.223  1.00  0.00              
ATOM     32  CA  ARG    49      26.301   7.208  15.323  1.00  0.00              
ATOM     33  CA  PHE    50      29.219   9.579  15.749  1.00  0.00              
ATOM     34  CA  GLY    51      27.760  12.683  14.183  1.00  0.00              
ATOM     35  CA  ILE    52      26.101  13.790  17.380  1.00  0.00              
ATOM     36  CA  LEU    53      25.331  17.440  17.932  1.00  0.00              
ATOM     37  CA  GLN    54      24.721  18.731  21.427  1.00  0.00              
ATOM     38  CA  ASP    55      21.447  20.388  20.488  1.00  0.00              
ATOM     39  CA  GLN    56      20.247  16.880  19.934  1.00  0.00              
ATOM     40  CA  VAL    57      21.692  15.533  23.112  1.00  0.00              
ATOM     41  CA  ASP    58      20.191  18.550  24.868  1.00  0.00              
ATOM     42  CA  LEU    59      16.852  18.312  23.232  1.00  0.00              
ATOM     43  CA  LEU    60      16.398  14.840  24.576  1.00  0.00              
ATOM     44  CA  LEU    61      17.415  15.943  27.997  1.00  0.00              
ATOM     45  CA  LYS    62      15.167  18.883  28.184  1.00  0.00              
ATOM     46  CA  ALA    63      12.211  16.495  28.083  1.00  0.00              
ATOM     47  CA  SER    64      12.555  16.327  31.807  1.00  0.00              
ATOM     48  CA  ASP    65      12.925  18.832  34.684  1.00  0.00              
ATOM     49  CA  SER    66      15.108  16.615  36.838  1.00  0.00              
ATOM     50  CA  ILE    67      16.891  11.558  34.632  1.00  0.00              
ATOM     51  CA  GLU    68      16.855   8.678  37.029  1.00  0.00              
ATOM     52  CA  ALA    69      14.622   5.606  36.464  1.00  0.00              
ATOM     53  CA  SER    70      11.420   7.042  37.777  1.00  0.00              
ATOM     54  CA  GLN    71      11.748  10.234  35.736  1.00  0.00              
ATOM     55  CA  ALA    72      12.520   8.150  32.695  1.00  0.00              
ATOM     56  CA  VAL    73       9.740   5.656  33.210  1.00  0.00              
ATOM     57  CA  ALA    74       7.371   8.519  33.901  1.00  0.00              
ATOM     58  CA  LEU    75       8.585  10.385  30.859  1.00  0.00              
ATOM     59  CA  ILE    76       7.973   7.389  28.684  1.00  0.00              
ATOM     60  CA  ALA    77      -8.489 -11.608  16.806  1.00  0.00              
ATOM     61  CA  ARG    78     -11.938 -10.452  17.766  1.00  0.00              
ATOM     62  CA  MET    79     -12.366  -8.787  14.396  1.00  0.00              
ATOM     63  CA  ASP    80     -11.033 -11.959  12.853  1.00  0.00              
ATOM     64  CA  GLU    81     -13.526 -13.848  15.025  1.00  0.00              
ATOM     65  CA  GLU    82     -13.360 -16.343  12.221  1.00  0.00              
ATOM     66  CA  ARG    83     -10.129  -6.136   4.754  1.00  0.00              
ATOM     67  CA  LYS    84      -9.414  -2.422   4.119  1.00  0.00              
ATOM     68  CA  LYS    85     -13.030  -1.264   3.979  1.00  0.00              
ATOM     69  CA  TYR    86     -14.125  -3.519   6.805  1.00  0.00              
ATOM     70  CA  VAL    87     -11.999  -1.586   9.266  1.00  0.00              
ATOM     71  CA  ALA    88     -12.120   1.667   7.375  1.00  0.00              
ATOM     72  CA  SER    89     -15.826   1.937   8.222  1.00  0.00              
ATOM     73  CA  TYR    90     -15.445   0.577  11.708  1.00  0.00              
ATOM     74  CA  LEU    91     -12.842   3.097  12.876  1.00  0.00              
ATOM     75  CA  GLY    92     -15.096   5.784  11.464  1.00  0.00              
ATOM     76  CA  ALA    96     -18.428   4.276  12.645  1.00  0.00              
ATOM     77  CA  SER    97     -17.605   3.957  16.270  1.00  0.00              
ATOM     78  CA  ASP    98     -14.929   4.595  18.814  1.00  0.00              
ATOM     79  CA  GLY    99     -14.008   7.971  17.353  1.00  0.00              
ATOM     80  CA  ILE   101     -11.773   8.334  14.269  1.00  0.00              
ATOM     81  CA  ASP   102     -11.044  10.869  11.502  1.00  0.00              
ATOM     82  CA  ASP   103     -10.130  10.474   7.797  1.00  0.00              
ATOM     83  CA  ASN   104      -6.932  12.515   7.930  1.00  0.00              
ATOM     84  CA  GLU   105      -6.137   9.837  10.515  1.00  0.00              
ATOM     85  CA  LEU   106      -6.944   6.818   8.338  1.00  0.00              
ATOM     86  CA  ALA   107      -5.045   7.547   5.118  1.00  0.00              
ATOM     87  CA  LEU   108      -2.020   8.120   7.292  1.00  0.00              
END
