
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0307TS599_2-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307TS599_2-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      10      I      10           -
LGA    M      11      M      11           -
LGA    -       -      T      12           -
LGA    -       -      F      13           -
LGA    -       -      S      14           -
LGA    -       -      G      15           -
LGA    -       -      Q      16           -
LGA    -       -      E      17           -
LGA    T      12      L      18           #
LGA    F      13      -       -           -
LGA    S      14      -       -           -
LGA    G      15      -       -           -
LGA    Q      16      -       -           -
LGA    E      17      -       -           -
LGA    L      18      -       -           -
LGA    T      19      T      19          3.238
LGA    A      20      A      20          3.079
LGA    I      21      I      21           #
LGA    -       -      I      22           -
LGA    -       -      K      23           -
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           -
LGA    -       -      K      34           -
LGA    -       -      I      35           -
LGA    -       -      K      36           -
LGA    -       -      P      37           -
LGA    -       -      A      38           -
LGA    -       -      E      39           -
LGA    -       -      I      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      M      43           -
LGA    -       -      T      44           -
LGA    -       -      R      45           -
LGA    -       -      E      46           -
LGA    -       -      F      47           -
LGA    -       -      M      48           -
LGA    -       -      R      49           -
LGA    -       -      F      50           -
LGA    -       -      G      51           -
LGA    -       -      I      52           -
LGA    -       -      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    I      22      S      66           #
LGA    K      23      I      67          4.336
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      -       -           -
LGA    K      34      -       -           -
LGA    I      35      -       -           -
LGA    K      36      -       -           -
LGA    P      37      E      68          1.120
LGA    A      38      -       -           -
LGA    E      39      A      69          2.930
LGA    I      40      S      70          2.583
LGA    A      41      Q      71           #
LGA    -       -      A      72           -
LGA    V      42      V      73          4.316
LGA    M      43      A      74           #
LGA    T      44      -       -           -
LGA    R      45      -       -           -
LGA    E      46      -       -           -
LGA    F      47      -       -           -
LGA    M      48      -       -           -
LGA    R      49      -       -           -
LGA    F      50      -       -           -
LGA    G      51      -       -           -
LGA    I      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    D      55      -       -           -
LGA    Q      56      -       -           -
LGA    V      57      -       -           -
LGA    D      58      -       -           -
LGA    L      59      L      75           #
LGA    L      60      I      76           #
LGA    L      61      A      77          4.565
LGA    -       -      R      78           -
LGA    K      62      M      79          2.046
LGA    A      63      D      80           -
LGA    S      64      E      81           -
LGA    -       -      E      82           -
LGA    D      65      R      83          3.651
LGA    S      66      K      84           #
LGA    I      67      K      85           -
LGA    E      68      Y      86          4.055
LGA    A      69      V      87          4.021
LGA    S      70      A      88           -
LGA    Q      71      -       -           -
LGA    A      72      S      89          2.643
LGA    V      73      -       -           -
LGA    A      74      -       -           -
LGA    L      75      Y      90           #
LGA    -       -      L      91           -
LGA    -       -      G      92           -
LGA    I      76      V      93          4.992
LGA    A      77      -       -           -
LGA    R      78      -       -           -
LGA    M      79      I      94           #
LGA    D      80      M      95           -
LGA    E      81      A      96           -
LGA    E      82      S      97          4.419
LGA    R      83      D      98          3.527
LGA    K      84      G      99          3.207
LGA    K      85      D     100          4.203
LGA    Y      86      -       -           -
LGA    V      87      I     101          2.367
LGA    A      88      -       -           -
LGA    S      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      D     102          3.958
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      D     103          2.411
LGA    L     108      N     104          1.553
LGA    W     109      E     105          0.620
LGA    T     110      L     106          1.277
LGA    L     111      A     107          1.267
LGA    I     112      L     108          0.545
LGA    S     113      W     109          0.762
LGA    T     114      T     110          0.852
LGA    L     115      L     111          0.656
LGA    C     116      I     112          0.834
LGA    G     117      S     113          0.848
LGA    L     118      T     114           -
LGA    -       -      L     115           -
LGA    -       -      C     116           -
LGA    -       -      G     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      T     120           -
LGA    P     119      M     121           #
LGA    T     120      T     122           #
LGA    M     121      V     123          4.858
LGA    T     122      M     124           -
LGA    V     123      E     125           -
LGA    M     124      A     126           -
LGA    E     125      I     127           -
LGA    A     126      N     128           -
LGA    I     127      N     129           -
LGA    N     128      M     130           -
LGA    N     129      K     131           -
LGA    M     130      N     132           -
LGA    K     131      -       -           -
LGA    N     132      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  123    5.0     32    3.05    15.62     17.339     1.017

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.462848 * X  +   0.880124 * Y  +  -0.105611 * Z  +  21.055937
  Y_new =  -0.002502 * X  +   0.117843 * Y  +   0.993029 * Z  +   3.251892
  Z_new =   0.886434 * X  +   0.459885 * Y  +  -0.052342 * Z  +  28.207909 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.684123   -1.457469  [ DEG:    96.4932    -83.5068 ]
  Theta =  -1.089584   -2.052009  [ DEG:   -62.4286   -117.5714 ]
  Phi   =  -3.136188    0.005405  [ DEG:  -179.6903      0.3097 ]
 
# 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: T0307TS599_2-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS599_2-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  123   5.0   32   3.05   15.62  17.339
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS599_2-D1
PFRMAT TS                                                                       
TARGET T0307                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM     10  CA  ILE    10      21.792   1.019  33.334  1.00  0.00              
ATOM     11  CA  MET    11      23.780   2.900  30.760  1.00  0.00              
ATOM     12  CA  THR    12      23.038   6.554  30.251  1.00  0.00              
ATOM     13  CA  PHE    13      24.596   8.692  27.572  1.00  0.00              
ATOM     14  CA  SER    14      22.670  11.759  26.438  1.00  0.00              
ATOM     15  CA  GLY    15      25.189  14.442  27.382  1.00  0.00              
ATOM     16  CA  GLN    16      23.592  15.322  30.712  1.00  0.00              
ATOM     17  CA  GLU    17      22.550  11.979  32.073  1.00  0.00              
ATOM     18  CA  LEU    18      25.535   9.746  31.474  1.00  0.00              
ATOM     19  CA  THR    19      27.766  12.447  33.048  1.00  0.00              
ATOM     20  CA  ALA    20      25.522  12.478  36.115  1.00  0.00              
ATOM     21  CA  ILE    21      25.701   8.663  36.380  1.00  0.00              
ATOM     22  CA  ILE    22      29.515   8.703  36.140  1.00  0.00              
ATOM     23  CA  LYS    23      29.830  11.369  38.834  1.00  0.00              
ATOM     24  CA  MET    24      27.517   9.283  41.072  1.00  0.00              
ATOM     25  CA  ALA    25      29.604   6.157  40.408  1.00  0.00              
ATOM     26  CA  LYS    26      32.843   7.683  41.513  1.00  0.00              
ATOM     27  CA  SER    27      31.380   9.017  44.826  1.00  0.00              
ATOM     28  CA  MET    28      29.915   5.510  45.408  1.00  0.00              
ATOM     29  CA  VAL    29      32.776   3.240  44.678  1.00  0.00              
ATOM     30  CA  MET    30      32.887  -0.064  42.859  1.00  0.00              
ATOM     31  CA  ALA    31      35.566  -2.463  44.173  1.00  0.00              
ATOM     32  CA  ASP    32      35.927  -5.010  41.492  1.00  0.00              
ATOM     33  CA  GLY    33      36.252  -2.562  38.677  1.00  0.00              
ATOM     34  CA  LYS    34      33.004  -3.608  37.098  1.00  0.00              
ATOM     35  CA  ILE    35      31.546  -0.336  36.015  1.00  0.00              
ATOM     36  CA  LYS    36      33.795   1.987  33.972  1.00  0.00              
ATOM     37  CA  PRO    37      33.022   5.661  34.130  1.00  0.00              
ATOM     38  CA  ALA    38      31.931   6.006  30.460  1.00  0.00              
ATOM     39  CA  GLU    39      29.566   3.082  30.457  1.00  0.00              
ATOM     40  CA  ILE    40      27.781   3.064  33.732  1.00  0.00              
ATOM     41  CA  ALA    41      26.247  -0.242  34.945  1.00  0.00              
ATOM     42  CA  VAL    42      24.100  -0.460  38.014  1.00  0.00              
ATOM     43  CA  MET    43      23.308  -3.798  39.711  1.00  0.00              
ATOM     44  CA  THR    44      21.671  -3.403  43.098  1.00  0.00              
ATOM     45  CA  ARG    45      22.866  -6.476  45.024  1.00  0.00              
ATOM     46  CA  GLU    46      26.274  -5.949  43.472  1.00  0.00              
ATOM     47  CA  PHE    47      26.577  -2.368  44.819  1.00  0.00              
ATOM     48  CA  MET    48      25.671  -3.083  48.395  1.00  0.00              
ATOM     49  CA  ARG    49      28.110  -6.083  48.228  1.00  0.00              
ATOM     50  CA  PHE    50      31.058  -4.145  46.772  1.00  0.00              
ATOM     51  CA  GLY    51      30.784  -1.502  49.432  1.00  0.00              
ATOM     52  CA  ILE    52      30.071   1.723  47.632  1.00  0.00              
ATOM     53  CA  LEU    53      27.682   3.104  50.308  1.00  0.00              
ATOM     54  CA  GLN    54      24.668   0.924  49.761  1.00  0.00              
ATOM     55  CA  ASP    55      22.081   3.454  50.935  1.00  0.00              
ATOM     56  CA  GLN    56      23.813   6.147  48.849  1.00  0.00              
ATOM     57  CA  VAL    57      23.715   4.008  45.686  1.00  0.00              
ATOM     58  CA  ASP    58      19.995   3.186  46.104  1.00  0.00              
ATOM     59  CA  LEU    59      19.336   6.924  46.471  1.00  0.00              
ATOM     60  CA  LEU    60      21.363   7.718  43.342  1.00  0.00              
ATOM     61  CA  LEU    61      19.619   4.982  41.330  1.00  0.00              
ATOM     62  CA  LYS    62      16.149   6.153  42.359  1.00  0.00              
ATOM     63  CA  ALA    63      16.829   9.833  41.586  1.00  0.00              
ATOM     64  CA  SER    64      18.372   9.211  38.150  1.00  0.00              
ATOM     65  CA  ASP    65      15.456   6.964  37.093  1.00  0.00              
ATOM     66  CA  SER    66      12.725   9.469  38.029  1.00  0.00              
ATOM     67  CA  ILE    67      14.202  12.412  36.055  1.00  0.00              
ATOM     68  CA  GLU    68      14.844  10.047  33.151  1.00  0.00              
ATOM     69  CA  ALA    69      11.398   8.420  32.812  1.00  0.00              
ATOM     70  CA  SER    70       9.447  11.635  32.532  1.00  0.00              
ATOM     71  CA  GLN    71      11.816  12.955  29.822  1.00  0.00              
ATOM     72  CA  ALA    72      11.606   9.715  27.852  1.00  0.00              
ATOM     73  CA  VAL    73       7.820   9.322  27.625  1.00  0.00              
ATOM     74  CA  ALA    74       7.536  12.944  26.468  1.00  0.00              
ATOM     75  CA  LEU    75      10.235  12.668  23.792  1.00  0.00              
ATOM     76  CA  ILE    76       8.799   9.450  22.295  1.00  0.00              
ATOM     77  CA  ALA    77       5.316  10.850  22.314  1.00  0.00              
ATOM     78  CA  ARG    78       6.148  14.110  20.639  1.00  0.00              
ATOM     79  CA  MET    79       8.445  12.752  17.903  1.00  0.00              
ATOM     80  CA  ASP    80       6.346   9.960  16.626  1.00  0.00              
ATOM     81  CA  GLU    81       6.044  10.065  12.854  1.00  0.00              
ATOM     82  CA  GLU    82       9.729  10.996  12.351  1.00  0.00              
ATOM     83  CA  ARG    83      10.827   8.274  14.728  1.00  0.00              
ATOM     84  CA  LYS    84       8.761   5.585  12.952  1.00  0.00              
ATOM     85  CA  LYS    85      10.185   6.545   9.611  1.00  0.00              
ATOM     86  CA  TYR    86      13.828   6.598  10.799  1.00  0.00              
ATOM     87  CA  VAL    87      13.471   3.253  12.514  1.00  0.00              
ATOM     88  CA  ALA    88      11.855   1.581   9.455  1.00  0.00              
ATOM     89  CA  SER    89      14.526   2.776   7.090  1.00  0.00              
ATOM     90  CA  TYR    90      17.421   1.678   9.220  1.00  0.00              
ATOM     91  CA  LEU    91      15.899  -1.765   9.860  1.00  0.00              
ATOM     92  CA  GLY    92      15.187  -2.331   6.137  1.00  0.00              
ATOM     93  CA  VAL    93      18.985  -1.843   5.686  1.00  0.00              
ATOM     94  CA  ILE    94      20.291  -3.661   8.694  1.00  0.00              
ATOM     95  CA  MET    95      23.383  -2.297  10.315  1.00  0.00              
ATOM     96  CA  ALA    96      25.003  -4.217  13.129  1.00  0.00              
ATOM     97  CA  SER    97      28.472  -3.172  14.332  1.00  0.00              
ATOM     98  CA  ASP    98      30.489  -6.187  13.194  1.00  0.00              
ATOM     99  CA  GLY    99      29.043  -6.085   9.670  1.00  0.00              
ATOM    100  CA  ASP   100      27.372  -9.493   9.668  1.00  0.00              
ATOM    101  CA  ILE   101      23.820  -8.576   8.991  1.00  0.00              
ATOM    102  CA  ASP   102      21.716  -9.824   6.189  1.00  0.00              
ATOM    103  CA  ASP   103      20.258  -7.232   3.906  1.00  0.00              
ATOM    104  CA  ASN   104      16.736  -7.316   5.400  1.00  0.00              
ATOM    105  CA  GLU   105      17.811  -7.736   9.010  1.00  0.00              
ATOM    106  CA  LEU   106      19.635  -6.267  11.931  1.00  0.00              
ATOM    107  CA  ALA   107      18.911  -2.751  13.257  1.00  0.00              
ATOM    108  CA  LEU   108      21.627  -0.921  15.085  1.00  0.00              
ATOM    109  CA  TRP   109      19.825   1.630  17.311  1.00  0.00              
ATOM    110  CA  THR   110      17.434  -1.240  18.071  1.00  0.00              
ATOM    111  CA  LEU   111      20.207  -3.541  19.307  1.00  0.00              
ATOM    112  CA  ILE   112      21.803  -0.831  21.460  1.00  0.00              
ATOM    113  CA  SER   113      18.536   0.411  22.836  1.00  0.00              
ATOM    114  CA  THR   114      17.511  -3.062  23.903  1.00  0.00              
ATOM    115  CA  LEU   115      20.742  -3.850  25.629  1.00  0.00              
ATOM    116  CA  CYS   116      20.912  -0.608  27.530  1.00  0.00              
ATOM    117  CA  GLY   117      17.228  -0.366  28.578  1.00  0.00              
ATOM    118  CA  LEU   118      16.845   2.952  26.836  1.00  0.00              
ATOM    119  CA  PRO   119      13.541   4.064  25.483  1.00  0.00              
ATOM    120  CA  THR   120      13.627   3.740  21.738  1.00  0.00              
ATOM    121  CA  MET   121      12.820   7.317  20.661  1.00  0.00              
ATOM    122  CA  THR   122      15.398   8.837  23.080  1.00  0.00              
ATOM    123  CA  VAL   123      18.209   6.542  21.999  1.00  0.00              
ATOM    124  CA  MET   124      17.561   7.134  18.267  1.00  0.00              
ATOM    125  CA  GLU   125      17.715  10.884  18.729  1.00  0.00              
ATOM    126  CA  ALA   126      20.998  10.569  20.671  1.00  0.00              
ATOM    127  CA  ILE   127      22.586   8.316  18.049  1.00  0.00              
ATOM    128  CA  ASN   128      21.601  10.730  15.226  1.00  0.00              
ATOM    129  CA  ASN   129      23.062  13.661  17.087  1.00  0.00              
ATOM    130  CA  MET   130      26.435  12.031  17.860  1.00  0.00              
ATOM    131  CA  LYS   131      26.643  11.026  13.783  1.00  0.00              
ATOM    132  CA  ASN   132      25.850  14.653  12.856  1.00  0.00              
TER                                                                             
END
