
#######################################################
#                                                     #
#                        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   95 (   95),  selected   95 , name T0306TS599_3
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS599_3.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    K       2      -       -           -
LGA    L       3      -       -           -
LGA    A       4      -       -           -
LGA    V       5      -       -           -
LGA    V       6      -       -           -
LGA    T       7      -       -           -
LGA    G       8      -       -           -
LGA    Q       9      -       -           -
LGA    I      10      -       -           -
LGA    V      11      -       -           -
LGA    C      12      -       -           -
LGA    T      13      -       -           -
LGA    V      14      -       -           -
LGA    R      15      -       -           -
LGA    H      16      -       -           -
LGA    H      17      -       -           -
LGA    G      18      -       -           -
LGA    L      19      -       -           -
LGA    A      20      -       -           -
LGA    H      21      -       -           -
LGA    D      22      -       -           -
LGA    K      23      -       -           -
LGA    L      24      M       1          2.707
LGA    L      25      K       2           #
LGA    M      26      L       3           #
LGA    V      27      A       4           -
LGA    E      28      V       5           -
LGA    M      29      V       6           -
LGA    -       -      T       7           -
LGA    -       -      G       8           -
LGA    I      30      Q       9           #
LGA    D      31      -       -           -
LGA    P      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      I      10          4.181
LGA    N      35      V      11          2.203
LGA    P      36      C      12          4.893
LGA    D      37      T      13           #
LGA    -       -      V      14           -
LGA    G      38      R      15           #
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    Q      39      K      23           #
LGA    C      40      L      24           #
LGA    A      41      L      25          5.359
LGA    V      42      M      26           #
LGA    A      43      V      27          3.044
LGA    I      44      E      28          4.038
LGA    D      45      M      29          2.870
LGA    N      46      -       -           -
LGA    I      47      -       -           -
LGA    G      48      -       -           -
LGA    A      49      -       -           -
LGA    G      50      -       -           -
LGA    T      51      -       -           -
LGA    G      52      I      30          5.114
LGA    E      53      D      31          3.956
LGA    W      54      P      32           #
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    V      55      C      40           #
LGA    L      56      A      41           #
LGA    -       -      V      42           -
LGA    L      57      A      43           #
LGA    V      58      I      44           #
LGA    S      59      D      45          1.792
LGA    G      60      N      46          1.842
LGA    S      61      I      47          3.418
LGA    S      62      G      48          2.032
LGA    A      63      A      49           #
LGA    R      64      G      50          3.411
LGA    Q      65      -       -           -
LGA    A      66      -       -           -
LGA    H      67      -       -           -
LGA    K      68      -       -           -
LGA    S      69      -       -           -
LGA    E      70      T      51          3.213
LGA    T      71      G      52          2.184
LGA    S      72      E      53          1.781
LGA    P      73      W      54          0.669
LGA    V      74      V      55          0.495
LGA    D      75      L      56          3.241
LGA    L      76      L      57          3.323
LGA    C      77      V      58          3.301
LGA    V      78      S      59          2.741
LGA    I      79      G      60          3.762
LGA    G      80      S      61          2.405
LGA    I      81      S      62          0.560
LGA    V      82      A      63          1.927
LGA    D      83      R      64          1.246
LGA    E      84      Q      65          3.382
LGA    V      85      A      66          4.568
LGA    V      86      H      67          2.523
LGA    S      87      K      68          3.482
LGA    G      88      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    -       -      C      77           -
LGA    G      89      V      78           #
LGA    Q      90      I      79           #
LGA    V      91      G      80           -
LGA    I      92      I      81           -
LGA    F      93      V      82           -
LGA    H      94      D      83           -
LGA    K      95      E      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   95   95    5.0     33    3.15     6.06     22.081     1.016

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.922402 * X  +  -0.245687 * Y  +  -0.298013 * Z  +  38.452629
  Y_new =   0.298137 * X  +  -0.037599 * Y  +   0.953782 * Z  +  31.355753
  Z_new =  -0.245537 * X  +  -0.968620 * Y  +   0.038567 * Z  +  65.534851 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.531001    1.610592  [ DEG:   -87.7199     92.2801 ]
  Theta =   0.248074    2.893519  [ DEG:    14.2136    165.7864 ]
  Phi   =   0.312619   -2.828973  [ DEG:    17.9118   -162.0882 ]
 
# 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: T0306TS599_3                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS599_3.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   95   95   5.0   33   3.15    6.06  22.081
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS599_3
PFRMAT TS                                                                       
TARGET T0306                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      28.482  47.623  71.895  1.00  0.00              
ATOM      2  CA  LYS     2      26.944  45.437  69.121  1.00  0.00              
ATOM      3  CA  LEU     3      27.425  42.420  67.087  1.00  0.00              
ATOM      4  CA  ALA     4      29.146  44.474  63.847  1.00  0.00              
ATOM      5  CA  VAL     5      30.996  46.669  66.366  1.00  0.00              
ATOM      6  CA  VAL     6      32.550  43.496  67.868  1.00  0.00              
ATOM      7  CA  THR     7      33.382  41.510  64.757  1.00  0.00              
ATOM      8  CA  GLY     8      34.879  44.559  62.950  1.00  0.00              
ATOM      9  CA  GLN     9      37.007  45.575  65.920  1.00  0.00              
ATOM     10  CA  ILE    10      38.823  42.477  66.872  1.00  0.00              
ATOM     11  CA  VAL    11      42.443  42.825  67.416  1.00  0.00              
ATOM     12  CA  CYS    12      44.411  39.672  68.040  1.00  0.00              
ATOM     13  CA  THR    13      48.239  39.636  68.204  1.00  0.00              
ATOM     14  CA  VAL    14      49.739  36.499  66.609  1.00  0.00              
ATOM     15  CA  ARG    15      53.528  36.910  66.384  1.00  0.00              
ATOM     16  CA  HIS    16      53.707  40.727  66.373  1.00  0.00              
ATOM     17  CA  HIS    17      54.595  41.186  62.666  1.00  0.00              
ATOM     18  CA  GLY    18      51.677  38.935  61.558  1.00  0.00              
ATOM     19  CA  LEU    19      49.194  40.868  63.681  1.00  0.00              
ATOM     20  CA  ALA    20      50.109  44.378  62.481  1.00  0.00              
ATOM     21  CA  HIS    21      46.737  45.751  61.542  1.00  0.00              
ATOM     22  CA  ASP    22      45.125  42.349  60.729  1.00  0.00              
ATOM     23  CA  LYS    23      42.241  41.627  62.985  1.00  0.00              
ATOM     24  CA  LEU    24      42.153  38.155  64.545  1.00  0.00              
ATOM     25  CA  LEU    25      39.122  37.183  66.663  1.00  0.00              
ATOM     26  CA  MET    26      39.227  34.110  68.728  1.00  0.00              
ATOM     27  CA  VAL    27      36.017  32.325  69.605  1.00  0.00              
ATOM     28  CA  GLU    28      35.911  29.764  72.352  1.00  0.00              
ATOM     29  CA  MET    29      33.404  26.991  72.090  1.00  0.00              
ATOM     30  CA  ILE    30      33.283  24.590  74.886  1.00  0.00              
ATOM     31  CA  ASP    31      29.710  23.275  74.776  1.00  0.00              
ATOM     32  CA  PRO    32      29.008  22.749  78.466  1.00  0.00              
ATOM     33  CA  GLN    33      29.469  19.024  78.618  1.00  0.00              
ATOM     34  CA  GLY    34      32.522  19.048  76.283  1.00  0.00              
ATOM     35  CA  ASN    35      30.604  17.798  73.226  1.00  0.00              
ATOM     36  CA  PRO    36      31.294  19.228  69.855  1.00  0.00              
ATOM     37  CA  ASP    37      28.102  21.127  68.916  1.00  0.00              
ATOM     38  CA  GLY    38      28.280  20.767  65.180  1.00  0.00              
ATOM     39  CA  GLN    39      29.134  24.171  63.869  1.00  0.00              
ATOM     40  CA  CYS    40      32.551  25.872  63.587  1.00  0.00              
ATOM     41  CA  ALA    41      34.577  26.088  66.741  1.00  0.00              
ATOM     42  CA  VAL    42      37.190  28.720  67.290  1.00  0.00              
ATOM     43  CA  ALA    43      39.536  28.137  70.131  1.00  0.00              
ATOM     44  CA  ILE    44      41.652  30.943  71.508  1.00  0.00              
ATOM     45  CA  ASP    45      44.475  30.069  73.844  1.00  0.00              
ATOM     46  CA  ASN    46      46.136  32.502  75.956  1.00  0.00              
ATOM     47  CA  ILE    47      43.601  33.906  78.219  1.00  0.00              
ATOM     48  CA  GLY    48      44.358  37.674  78.054  1.00  0.00              
ATOM     49  CA  ALA    49      44.803  37.985  74.286  1.00  0.00              
ATOM     50  CA  GLY    50      48.449  38.747  73.991  1.00  0.00              
ATOM     51  CA  THR    51      51.004  38.399  71.274  1.00  0.00              
ATOM     52  CA  GLY    52      52.181  34.833  70.988  1.00  0.00              
ATOM     53  CA  GLU    53      48.836  33.350  72.054  1.00  0.00              
ATOM     54  CA  TRP    54      47.823  30.365  69.988  1.00  0.00              
ATOM     55  CA  VAL    55      44.747  30.294  67.841  1.00  0.00              
ATOM     56  CA  LEU    56      43.067  26.992  66.970  1.00  0.00              
ATOM     57  CA  LEU    57      40.505  26.834  64.190  1.00  0.00              
ATOM     58  CA  VAL    58      38.193  23.896  63.787  1.00  0.00              
ATOM     59  CA  SER    59      35.925  23.930  60.711  1.00  0.00              
ATOM     60  CA  GLY    60      33.544  21.243  60.046  1.00  0.00              
ATOM     61  CA  SER    61      35.358  19.033  57.607  1.00  0.00              
ATOM     62  CA  SER    62      38.613  17.371  57.576  1.00  0.00              
ATOM     63  CA  ALA    63      38.025  14.237  59.555  1.00  0.00              
ATOM     64  CA  ARG    64      40.669  15.097  62.221  1.00  0.00              
ATOM     65  CA  GLN    65      39.307  18.617  62.730  1.00  0.00              
ATOM     66  CA  ALA    66      35.697  17.452  63.166  1.00  0.00              
ATOM     67  CA  HIS    67      36.096  14.645  65.758  1.00  0.00              
ATOM     68  CA  LYS    68      38.679  16.383  67.846  1.00  0.00              
ATOM     69  CA  SER    69      42.221  15.200  67.987  1.00  0.00              
ATOM     70  CA  GLU    70      44.200  15.567  64.825  1.00  0.00              
ATOM     71  CA  THR    71      46.489  18.423  65.617  1.00  0.00              
ATOM     72  CA  SER    72      46.220  20.825  62.672  1.00  0.00              
ATOM     73  CA  PRO    73      47.126  24.452  63.545  1.00  0.00              
ATOM     74  CA  VAL    74      44.555  26.996  62.965  1.00  0.00              
ATOM     75  CA  ASP    75      46.024  30.340  63.339  1.00  0.00              
ATOM     76  CA  LEU    76      43.250  32.822  63.658  1.00  0.00              
ATOM     77  CA  CYS    77      39.588  31.965  64.414  1.00  0.00              
ATOM     78  CA  VAL    78      36.930  34.429  63.433  1.00  0.00              
ATOM     79  CA  ILE    79      33.786  34.462  65.295  1.00  0.00              
ATOM     80  CA  GLY    80      31.096  36.827  64.155  1.00  0.00              
ATOM     81  CA  ILE    81      32.141  36.919  60.545  1.00  0.00              
ATOM     82  CA  VAL    82      32.323  33.084  60.205  1.00  0.00              
ATOM     83  CA  ASP    83      28.995  32.691  61.963  1.00  0.00              
ATOM     84  CA  GLU    84      27.324  35.240  59.829  1.00  0.00              
ATOM     85  CA  VAL    85      28.328  33.745  56.547  1.00  0.00              
ATOM     86  CA  VAL    86      29.091  30.175  56.607  1.00  0.00              
ATOM     87  CA  SER    87      29.139  28.293  53.573  1.00  0.00              
ATOM     88  CA  GLY    88      30.105  24.840  53.996  1.00  0.00              
ATOM     89  CA  GLY    89      33.239  25.570  56.119  1.00  0.00              
ATOM     90  CA  GLN    90      34.160  28.372  53.969  1.00  0.00              
ATOM     91  CA  VAL    91      33.963  31.462  55.720  1.00  0.00              
ATOM     92  CA  ILE    92      32.824  34.390  54.006  1.00  0.00              
ATOM     93  CA  PHE    93      33.170  37.555  55.581  1.00  0.00              
ATOM     94  CA  HIS    94      34.823  41.188  55.903  1.00  0.00              
ATOM     95  CA  LYS    95      37.675  43.446  58.018  1.00  0.00              
TER                                                                             
END
