
#######################################################
#                                                     #
#                        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 T0382TS393_1
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS393_1.T0382.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      K       3           -
LGA    S       2      L       4           -
LGA    K       3      D       5           -
LGA    L       4      L       6           -
LGA    D       5      H       7           -
LGA    L       6      Q       8           -
LGA    H       7      M       9           -
LGA    Q       8      T      10           -
LGA    M       9      T      11           -
LGA    T      10      Q      12           -
LGA    T      11      D      13           -
LGA    Q      12      L      14           -
LGA    D      13      V      15           -
LGA    L      14      A      16           -
LGA    V      15      L      17           -
LGA    A      16      -       -           -
LGA    L      17      -       -           -
LGA    F      18      -       -           -
LGA    A      19      -       -           -
LGA    K      20      -       -           -
LGA    V      21      -       -           -
LGA    T      22      -       -           -
LGA    V      23      -       -           -
LGA    E      24      -       -           -
LGA    Q      25      -       -           -
LGA    D      26      -       -           -
LGA    D      27      -       -           -
LGA    A      28      -       -           -
LGA    L      29      -       -           -
LGA    L      30      -       -           -
LGA    G      31      -       -           -
LGA    N      32      -       -           -
LGA    Q      33      -       -           -
LGA    I      34      -       -           -
LGA    S      35      -       -           -
LGA    R      36      -       -           -
LGA    F      37      -       -           -
LGA    N      38      -       -           -
LGA    R      39      -       -           -
LGA    L      40      F      18           #
LGA    F      41      A      19           -
LGA    G      42      K      20           -
LGA    -       -      V      21           -
LGA    V      43      T      22          4.912
LGA    M      44      V      23           #
LGA    -       -      E      24           -
LGA    A      45      Q      25          4.425
LGA    E      46      D      26          2.702
LGA    I      47      D      27          2.952
LGA    A      48      A      28          1.631
LGA    D      49      L      29          1.248
LGA    E      50      L      30          2.594
LGA    L      51      G      31          3.742
LGA    K      52      N      32          3.268
LGA    A      53      Q      33          0.814
LGA    R      54      I      34          3.803
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    D      55      F      37          2.492
LGA    G      56      N      38           #
LGA    D      57      R      39           #
LGA    Q      58      L      40           #
LGA    R      59      F      41          3.441
LGA    T      60      G      42          2.553
LGA    A      61      V      43          3.804
LGA    -       -      M      44           -
LGA    -       -      A      45           -
LGA    -       -      E      46           -
LGA    L      62      I      47          3.775
LGA    L      63      A      48           #
LGA    S      64      D      49          4.256
LGA    L      65      -       -           -
LGA    F      66      E      50          4.659
LGA    E      67      L      51           -
LGA    Y      68      -       -           -
LGA    P      69      -       -           -
LGA    N      70      K      52           #
LGA    M      71      -       -           -
LGA    Q      72      -       -           -
LGA    V      73      -       -           -
LGA    R      74      A      53           #
LGA    L      75      R      54          3.145
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    Q      76      D      57           #
LGA    A      77      Q      58          5.075
LGA    A      78      R      59          3.403
LGA    K      79      T      60          2.617
LGA    L      80      A      61          1.839
LGA    T      81      -       -           -
LGA    L      82      L      62          3.238
LGA    A      83      L      63          1.678
LGA    V      84      S      64          4.614
LGA    A      85      L      65           #
LGA    P      86      F      66          4.513
LGA    V      87      E      67          4.487
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    K      88      R      74          1.379
LGA    A      89      L      75          2.933
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    R      90      Q      92          3.833
LGA    E      91      L      93           -
LGA    Q      92      E      94           -
LGA    -       -      A      95           -
LGA    L      93      I      96          1.738
LGA    E      94      V      97           #
LGA    A      95      S      98           #
LGA    I      96      S      99          2.623
LGA    V      97      K     100          4.503
LGA    S      98      -       -           -
LGA    S      99      -       -           -
LGA    K     100      -       -           -
LGA    W     101      W     101           #
LGA    F     102      F     102          3.327
LGA    P     103      P     103           -
LGA    Q     104      Q     104           -
LGA    A     105      A     105           -
LGA    G     106      -       -           -
LGA    D     107      -       -           -
LGA    A     108      G     106          3.157
LGA    G     109      D     107          1.431
LGA    M     110      -       -           -
LGA    C     111      A     108          2.383
LGA    L     112      G     109          2.448
LGA    D     113      M     110          2.934
LGA    L     114      C     111          2.563
LGA    L     115      L     112          1.838
LGA    D     116      D     113          3.942
LGA    D     117      L     114           -
LGA    G     118      L     115           -
LGA    T     119      D     116           -
LGA    F     120      -       -           -
LGA    K     121      -       -           -
LGA    P     122      -       -           -
LGA    K     123      D     117           #
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -
LGA    -       -      K     123           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  121    5.0     43    3.27    11.63     20.828     1.275

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.575008 * X  +  -0.818102 * Y  +  -0.008647 * Z  + -11.684336
  Y_new =  -0.142406 * X  +   0.110487 * Y  +  -0.983623 * Z  +  49.707481
  Z_new =   0.805659 * X  +  -0.564360 * Y  +  -0.180033 * Z  +   4.993762 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.879596    1.261997  [ DEG:  -107.6929     72.3071 ]
  Theta =  -0.936787   -2.204806  [ DEG:   -53.6739   -126.3261 ]
  Phi   =  -2.898819    0.242774  [ DEG:  -166.0901     13.9099 ]
 
# 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: T0382TS393_1                                  
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS393_1.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  121   5.0   43   3.27   11.63  20.828
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS393_1
PFRMAT TS
TARGET T0382
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1       5.620  57.289  17.698  1.00 25.00           C
ATOM      2  CA  SER     2       9.016  55.554  17.798  1.00 25.00           C
ATOM      3  CA  LYS     3       8.425  53.389  14.725  1.00 25.00           C
ATOM      4  CA  LEU     4       7.457  51.249  11.807  1.00 25.00           C
ATOM      5  CA  ASP     5       4.605  49.121  10.515  1.00 25.00           C
ATOM      6  CA  LEU     6       6.089  50.100   7.122  1.00 25.00           C
ATOM      7  CA  HIS     7       3.287  48.208   5.323  1.00 25.00           C
ATOM      8  CA  GLN     8       0.668  49.997   7.470  1.00 25.00           C
ATOM      9  CA  MET     9       2.271  53.377   6.653  1.00 25.00           C
ATOM     10  CA  THR    10       2.225  52.526   2.920  1.00 25.00           C
ATOM     11  CA  THR    11      -1.471  51.551   3.163  1.00 25.00           C
ATOM     12  CA  GLN    12      -2.250  54.851   4.942  1.00 25.00           C
ATOM     13  CA  ASP    13      -0.392  56.791   2.211  1.00 25.00           C
ATOM     14  CA  LEU    14      -2.368  54.927  -0.489  1.00 25.00           C
ATOM     15  CA  VAL    15      -5.647  55.745   1.309  1.00 25.00           C
ATOM     16  CA  ALA    16      -4.641  59.435   1.515  1.00 25.00           C
ATOM     17  CA  LEU    17      -3.819  59.446  -2.225  1.00 25.00           C
ATOM     18  CA  PHE    18      -7.219  57.863  -3.002  1.00 25.00           C
ATOM     19  CA  ALA    19      -8.969  60.513  -0.862  1.00 25.00           C
ATOM     20  CA  LYS    20      -7.070  63.286  -2.698  1.00 25.00           C
ATOM     21  CA  VAL    21      -8.088  61.783  -6.071  1.00 25.00           C
ATOM     22  CA  THR    22      -9.969  64.592  -7.873  1.00 25.00           C
ATOM     23  CA  VAL    23     -12.922  66.402  -9.488  1.00 25.00           C
ATOM     24  CA  GLU    24     -14.938  66.613  -6.239  1.00 25.00           C
ATOM     25  CA  GLN    25     -17.135  63.692  -7.384  1.00 25.00           C
ATOM     26  CA  ASP    26     -14.013  61.635  -8.211  1.00 25.00           C
ATOM     27  CA  ASP    27     -12.556  62.410  -4.754  1.00 25.00           C
ATOM     28  CA  ALA    28     -15.841  61.338  -3.103  1.00 25.00           C
ATOM     29  CA  LEU    29     -15.812  58.075  -5.109  1.00 25.00           C
ATOM     30  CA  LEU    30     -12.194  57.420  -4.039  1.00 25.00           C
ATOM     31  CA  GLY    31     -13.136  58.050  -0.380  1.00 25.00           C
ATOM     32  CA  ASN    32     -16.084  55.626  -0.696  1.00 25.00           C
ATOM     33  CA  GLN    33     -13.775  52.978  -2.221  1.00 25.00           C
ATOM     34  CA  ILE    34     -11.285  53.461   0.649  1.00 25.00           C
ATOM     35  CA  SER    35     -14.115  53.080   3.201  1.00 25.00           C
ATOM     36  CA  ARG    36     -15.278  49.869   1.469  1.00 25.00           C
ATOM     37  CA  PHE    37     -11.700  48.504   1.542  1.00 25.00           C
ATOM     38  CA  ASN    38     -11.436  49.330   5.273  1.00 25.00           C
ATOM     39  CA  ARG    39     -14.762  47.548   5.928  1.00 25.00           C
ATOM     40  CA  LEU    40     -13.527  44.481   3.995  1.00 25.00           C
ATOM     41  CA  PHE    41     -10.287  44.468   6.036  1.00 25.00           C
ATOM     42  CA  GLY    42     -12.303  44.679   9.285  1.00 25.00           C
ATOM     43  CA  VAL    43     -14.500  41.758   8.140  1.00 25.00           C
ATOM     44  CA  MET    44     -11.378  39.701   7.313  1.00 25.00           C
ATOM     45  CA  ALA    45      -9.921  40.476  10.769  1.00 25.00           C
ATOM     46  CA  GLU    46     -13.207  39.404  12.420  1.00 25.00           C
ATOM     47  CA  ILE    47     -13.177  36.141  10.415  1.00 25.00           C
ATOM     48  CA  ALA    48      -9.559  35.487  11.484  1.00 25.00           C
ATOM     49  CA  ASP    49     -10.501  36.116  15.143  1.00 25.00           C
ATOM     50  CA  GLU    50     -13.449  33.692  14.826  1.00 25.00           C
ATOM     51  CA  LEU    51     -11.140  31.044  13.303  1.00 25.00           C
ATOM     52  CA  LYS    52      -8.650  31.528  16.172  1.00 25.00           C
ATOM     53  CA  ALA    53      -6.080  33.186  13.816  1.00 25.00           C
ATOM     54  CA  ARG    54      -4.958  33.937  10.251  1.00 25.00           C
ATOM     55  CA  ASP    55      -6.633  35.319   7.125  1.00 25.00           C
ATOM     56  CA  GLY    56      -6.892  34.057   3.569  1.00 25.00           C
ATOM     57  CA  ASP    57      -8.792  36.662   1.524  1.00 25.00           C
ATOM     58  CA  GLN    58     -10.142  40.190   1.816  1.00 25.00           C
ATOM     59  CA  ARG    59      -7.283  42.733   1.985  1.00 25.00           C
ATOM     60  CA  THR    60      -5.259  40.660  -0.521  1.00 25.00           C
ATOM     61  CA  ALA    61      -8.278  40.507  -2.872  1.00 25.00           C
ATOM     62  CA  LEU    62      -8.711  44.303  -2.602  1.00 25.00           C
ATOM     63  CA  LEU    63      -4.998  44.807  -3.397  1.00 25.00           C
ATOM     64  CA  SER    64      -5.312  42.505  -6.442  1.00 25.00           C
ATOM     65  CA  LEU    65      -8.373  44.471  -7.641  1.00 25.00           C
ATOM     66  CA  PHE    66      -6.453  47.759  -7.231  1.00 25.00           C
ATOM     67  CA  GLU    67      -3.516  46.321  -9.226  1.00 25.00           C
ATOM     68  CA  TYR    68      -5.001  43.791 -11.674  1.00 25.00           C
ATOM     69  CA  PRO    69      -6.429  46.487 -14.024  1.00 25.00           C
ATOM     70  CA  ASN    70      -9.495  48.276 -15.486  1.00 25.00           C
ATOM     71  CA  MET    71     -10.762  45.128 -17.227  1.00 25.00           C
ATOM     72  CA  GLN    72     -14.331  46.503 -17.027  1.00 25.00           C
ATOM     73  CA  VAL    73     -15.555  43.181 -15.567  1.00 25.00           C
ATOM     74  CA  ARG    74     -12.741  43.256 -12.971  1.00 25.00           C
ATOM     75  CA  LEU    75     -13.674  46.849 -12.029  1.00 25.00           C
ATOM     76  CA  GLN    76     -17.344  45.822 -11.648  1.00 25.00           C
ATOM     77  CA  ALA    77     -16.316  42.882  -9.418  1.00 25.00           C
ATOM     78  CA  ALA    78     -14.183  45.227  -7.269  1.00 25.00           C
ATOM     79  CA  LYS    79     -17.132  47.650  -6.941  1.00 25.00           C
ATOM     80  CA  LEU    80     -19.421  44.760  -5.901  1.00 25.00           C
ATOM     81  CA  THR    81     -16.857  43.638  -3.286  1.00 25.00           C
ATOM     82  CA  LEU    82     -16.639  47.213  -1.930  1.00 25.00           C
ATOM     83  CA  ALA    83     -20.458  47.391  -1.711  1.00 25.00           C
ATOM     84  CA  VAL    84     -20.530  44.050   0.161  1.00 25.00           C
ATOM     85  CA  ALA    85     -17.865  45.330   2.596  1.00 25.00           C
ATOM     86  CA  PRO    86     -19.899  48.522   3.181  1.00 25.00           C
ATOM     87  CA  VAL    87     -23.037  46.430   3.847  1.00 25.00           C
ATOM     88  CA  LYS    88     -21.094  44.261   6.334  1.00 25.00           C
ATOM     89  CA  ALA    89     -19.810  47.403   8.110  1.00 25.00           C
ATOM     90  CA  ARG    90     -23.380  48.777   8.310  1.00 25.00           C
ATOM     91  CA  GLU    91     -24.604  45.455   9.770  1.00 25.00           C
ATOM     92  CA  GLN    92     -21.790  45.530  12.366  1.00 25.00           C
ATOM     93  CA  LEU    93     -22.722  49.123  13.309  1.00 25.00           C
ATOM     94  CA  GLU    94     -26.393  48.096  13.689  1.00 25.00           C
ATOM     95  CA  ALA    95     -25.365  45.156  15.918  1.00 25.00           C
ATOM     96  CA  ILE    96     -23.232  47.501  18.067  1.00 25.00           C
ATOM     97  CA  VAL    97     -26.180  49.923  18.396  1.00 25.00           C
ATOM     98  CA  SER    98     -28.469  47.034  19.437  1.00 25.00           C
ATOM     99  CA  SER    99     -25.905  45.912  22.051  1.00 25.00           C
ATOM    100  CA  LYS   100     -23.701  46.671  25.106  1.00 25.00           C
ATOM    101  CA  TRP   101     -20.704  44.436  24.403  1.00 25.00           C
ATOM    102  CA  PHE   102     -18.428  45.514  21.543  1.00 25.00           C
ATOM    103  CA  PRO   103     -16.596  47.612  24.091  1.00 25.00           C
ATOM    104  CA  GLN   104     -14.860  49.606  26.769  1.00 25.00           C
ATOM    105  CA  ALA   105     -11.839  50.396  24.622  1.00 25.00           C
ATOM    106  CA  GLY   106      -8.163  50.857  23.917  1.00 25.00           C
ATOM    107  CA  ASP   107      -9.361  51.529  20.327  1.00 25.00           C
ATOM    108  CA  ALA   108     -11.153  51.300  16.940  1.00 25.00           C
ATOM    109  CA  GLY   109     -11.272  49.519  13.581  1.00 25.00           C
ATOM    110  CA  MET   110     -11.013  50.101   9.805  1.00 25.00           C
ATOM    111  CA  CYS   111     -14.736  50.991   9.661  1.00 25.00           C
ATOM    112  CA  LEU   112     -14.286  53.446  12.566  1.00 25.00           C
ATOM    113  CA  ASP   113     -11.303  55.051  10.778  1.00 25.00           C
ATOM    114  CA  LEU   114     -13.373  55.386   7.573  1.00 25.00           C
ATOM    115  CA  LEU   115     -16.221  57.012   9.551  1.00 25.00           C
ATOM    116  CA  ASP   116     -16.317  60.325  11.474  1.00 25.00           C
ATOM    117  CA  ASP   117     -18.568  62.766  13.344  1.00 25.00           C
ATOM    118  CA  GLY   118     -19.887  66.212  14.148  1.00 25.00           C
ATOM    119  CA  THR   119     -17.682  68.351  16.475  1.00 25.00           C
ATOM    120  CA  PHE   120     -14.205  68.812  15.022  1.00 25.00           C
ATOM    121  CA  LYS   121     -12.929  69.704  18.497  1.00 25.00           C
ATOM    122  CA  PRO   122      -9.155  70.419  18.170  1.00 25.00           C
ATOM    123  CA  LYS   123      -7.337  69.332  15.031  1.00 25.00           C
TER
END
