
#######################################################
#                                                     #
#                        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  132 (  132),  selected  132 , name T0312TS393_2-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312TS393_2-D1.T0312_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G       9      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    K      10      L      13           #
LGA    G      11      L      14          4.614
LGA    F      12      R      15          5.116
LGA    -       -      L      16           -
LGA    -       -      D      17           -
LGA    -       -      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    L      13      R      24           #
LGA    L      14      Q      25          0.435
LGA    R      15      I      26          4.058
LGA    L      16      E      27          5.819
LGA    D      17      -       -           -
LGA    Y      18      -       -           -
LGA    G      19      -       -           -
LGA    K      20      -       -           -
LGA    D      21      -       -           -
LGA    L      22      -       -           -
LGA    V      23      -       -           -
LGA    R      24      -       -           -
LGA    Q      25      -       -           -
LGA    I      26      -       -           -
LGA    E      27      -       -           -
LGA    E      28      -       -           -
LGA    F      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      -       -           -
LGA    E      32      -       -           -
LGA    K      33      -       -           -
LGA    G      34      -       -           -
LGA    I      35      -       -           -
LGA    H      36      -       -           -
LGA    A      37      -       -           -
LGA    A      38      E      28          3.737
LGA    H      39      F      29           -
LGA    I      40      L      30           #
LGA    S      41      E      31          3.311
LGA    A      42      E      32          1.333
LGA    I      43      K      33          3.965
LGA    G      44      G      34          1.508
LGA    A      45      -       -           -
LGA    V      46      I      35          1.345
LGA    R      47      H      36          3.112
LGA    S      48      A      37          2.026
LGA    A      49      A      38          3.449
LGA    V      50      H      39          3.816
LGA    I      51      I      40          2.674
LGA    G      52      S      41          2.277
LGA    -       -      A      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      A      45           -
LGA    -       -      V      46           -
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    -       -      A      49           -
LGA    -       -      V      50           -
LGA    -       -      I      51           -
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    -       -      K      63           -
LGA    -       -      K      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    -       -      P      69           -
LGA    -       -      L      70           -
LGA    -       -      E      71           -
LGA    -       -      I      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    Y      53      L      75          2.868
LGA    Y      54      S      76          4.398
LGA    D      55      -       -           -
LGA    Q      56      -       -           -
LGA    E      57      -       -           -
LGA    K      58      -       -           -
LGA    K      59      -       -           -
LGA    E      60      -       -           -
LGA    Y      61      -       -           -
LGA    V      62      -       -           -
LGA    K      63      G      77          3.879
LGA    K      64      N      78          4.648
LGA    E      65      V      79           #
LGA    L      66      S      80          3.376
LGA    M      67      M      81          4.697
LGA    E      68      K      82          4.437
LGA    P      69      D      83          3.875
LGA    L      70      S      84          3.200
LGA    E      71      K      85          2.443
LGA    I      72      -       -           -
LGA    L      73      P      86          3.156
LGA    S      74      F      87          3.492
LGA    L      75      C      88          3.706
LGA    S      76      H      89          3.678
LGA    G      77      I      90          2.624
LGA    N      78      H      91          3.347
LGA    V      79      V      92          2.573
LGA    -       -      L      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      G      98           -
LGA    -       -      E      99           -
LGA    -       -      V     100           -
LGA    -       -      Y     101           -
LGA    S      80      G     102          3.502
LGA    M      81      G     103          1.938
LGA    K      82      H     104          5.259
LGA    D      83      -       -           -
LGA    S      84      -       -           -
LGA    K      85      -       -           -
LGA    P      86      -       -           -
LGA    F      87      L     105          2.948
LGA    C      88      F     106           #
LGA    H      89      -       -           -
LGA    I      90      -       -           -
LGA    H      91      -       -           -
LGA    V      92      -       -           -
LGA    L      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      -       -           -
LGA    K      96      -       -           -
LGA    D      97      -       -           -
LGA    G      98      -       -           -
LGA    E      99      -       -           -
LGA    V     100      -       -           -
LGA    Y     101      -       -           -
LGA    G     102      -       -           -
LGA    G     103      -       -           -
LGA    H     104      -       -           -
LGA    L     105      -       -           -
LGA    F     106      -       -           -
LGA    S     107      S     107          4.372
LGA    A     108      A     108          3.411
LGA    E     109      E     109          2.219
LGA    V     110      V     110          2.094
LGA    F     111      F     111          3.502
LGA    A     112      A     112          4.329
LGA    C     113      C     113          2.415
LGA    E     114      E     114          3.674
LGA    V     115      V     115          2.740
LGA    F     116      F     116          3.094
LGA    V     117      V     117          4.262
LGA    L     118      L     118          1.462
LGA    P     119      P     119          2.957
LGA    L     120      L     120          1.718
LGA    -       -      S     121           -
LGA    S     121      G     122           #
LGA    G     122      E     123           -
LGA    E     123      A     124           -
LGA    A     124      P     125           -
LGA    P     125      E     126           -
LGA    E     126      R     127           -
LGA    R     127      A     128           -
LGA    A     128      F     129           -
LGA    F     129      D     130           -
LGA    D     130      E     131           -
LGA    E     131      Q     132           -
LGA    Q     132      T     133           -
LGA    T     133      G     134           -
LGA    G     134      L     135           -
LGA    L     135      F     136           -
LGA    F     136      L     137           -
LGA    L     137      W     138           -
LGA    W     138      L     139           -
LGA    L     139      E     140           -
LGA    E     140      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  132  132    5.0     52    3.43    36.54     20.346     1.473

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.277588 * X  +  -0.918680 * Y  +   0.281020 * Z  +  57.635292
  Y_new =  -0.250319 * X  +   0.213247 * Y  +   0.944387 * Z  +  12.740221
  Z_new =  -0.927516 * X  +  -0.332495 * Y  +  -0.170768 * Z  +  15.949511 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.045262    1.096331  [ DEG:  -117.1849     62.8151 ]
  Theta =   1.187711    1.953882  [ DEG:    68.0508    111.9492 ]
  Phi   =  -0.733789    2.407804  [ DEG:   -42.0430    137.9570 ]
 
# 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: T0312TS393_2-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS393_2-D1.T0312_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  132  132   5.0   52   3.43   36.54  20.346
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS393_2-D1
PFRMAT TS
TARGET T0312
MODEL 2
PARENT N/A
ATOM      9  CA  GLY     9      58.719  25.253  10.476  1.00 25.00           C
ATOM     10  CA  LYS    10      61.597  23.688  12.491  1.00 25.00           C
ATOM     11  CA  GLY    11      61.825  19.977  11.569  1.00 25.00           C
ATOM     12  CA  PHE    12      60.500  16.561  12.742  1.00 25.00           C
ATOM     13  CA  LEU    13      58.786  13.933  10.641  1.00 25.00           C
ATOM     14  CA  LEU    14      61.444  11.229   9.916  1.00 25.00           C
ATOM     15  CA  ARG    15      63.894   8.676  11.394  1.00 25.00           C
ATOM     16  CA  LEU    16      62.435   6.199   8.991  1.00 25.00           C
ATOM     17  CA  ASP    17      64.355   3.354   7.254  1.00 25.00           C
ATOM     18  CA  TYR    18      65.781   0.651   4.992  1.00 25.00           C
ATOM     19  CA  GLY    19      64.637  -1.909   2.421  1.00 25.00           C
ATOM     20  CA  LYS    20      66.718  -0.547  -0.380  1.00 25.00           C
ATOM     21  CA  ASP    21      64.206   1.093  -2.762  1.00 25.00           C
ATOM     22  CA  LEU    22      62.952   3.344   0.072  1.00 25.00           C
ATOM     23  CA  VAL    23      66.555   4.337   0.910  1.00 25.00           C
ATOM     24  CA  ARG    24      67.214   5.154  -2.773  1.00 25.00           C
ATOM     25  CA  GLN    25      64.038   7.291  -2.892  1.00 25.00           C
ATOM     26  CA  ILE    26      65.138   9.146   0.274  1.00 25.00           C
ATOM     27  CA  GLU    27      68.587   9.778  -1.266  1.00 25.00           C
ATOM     28  CA  GLU    28      66.944  11.119  -4.456  1.00 25.00           C
ATOM     29  CA  PHE    29      64.722  13.435  -2.367  1.00 25.00           C
ATOM     30  CA  LEU    30      67.792  14.704  -0.462  1.00 25.00           C
ATOM     31  CA  GLU    31      69.605  15.361  -3.771  1.00 25.00           C
ATOM     32  CA  GLU    32      66.560  17.277  -5.086  1.00 25.00           C
ATOM     33  CA  LYS    33      68.682  20.412  -5.154  1.00 25.00           C
ATOM     34  CA  GLY    34      69.219  20.105  -1.373  1.00 25.00           C
ATOM     35  CA  ILE    35      67.233  19.382   1.811  1.00 25.00           C
ATOM     36  CA  HIS    36      68.376  18.043   5.248  1.00 25.00           C
ATOM     37  CA  ALA    37      65.065  16.700   6.576  1.00 25.00           C
ATOM     38  CA  ALA    38      66.078  13.370   8.119  1.00 25.00           C
ATOM     39  CA  HIS    39      68.339  10.838   6.452  1.00 25.00           C
ATOM     40  CA  ILE    40      70.474  11.392   9.569  1.00 25.00           C
ATOM     41  CA  SER    41      72.755  12.240  12.474  1.00 25.00           C
ATOM     42  CA  ALA    42      69.910  14.397  13.835  1.00 25.00           C
ATOM     43  CA  ILE    43      68.297  12.870  16.981  1.00 25.00           C
ATOM     44  CA  GLY    44      71.817  13.916  18.102  1.00 25.00           C
ATOM     45  CA  ALA    45      71.746  14.102  21.911  1.00 25.00           C
ATOM     46  CA  VAL    46      68.487  12.070  22.013  1.00 25.00           C
ATOM     47  CA  ARG    47      69.458   9.978  25.037  1.00 25.00           C
ATOM     48  CA  SER    48      67.596   6.889  23.807  1.00 25.00           C
ATOM     49  CA  ALA    49      63.905   7.350  23.168  1.00 25.00           C
ATOM     50  CA  VAL    50      60.264   6.849  23.977  1.00 25.00           C
ATOM     51  CA  ILE    51      57.182   9.055  23.926  1.00 25.00           C
ATOM     52  CA  GLY    52      54.044  11.071  23.377  1.00 25.00           C
ATOM     53  CA  TYR    53      52.619   8.160  21.310  1.00 25.00           C
ATOM     54  CA  TYR    54      48.828   8.601  21.713  1.00 25.00           C
ATOM     55  CA  ASP    55      45.119   7.754  21.699  1.00 25.00           C
ATOM     56  CA  GLN    56      42.387   5.225  20.793  1.00 25.00           C
ATOM     57  CA  GLU    57      40.224   7.680  22.745  1.00 25.00           C
ATOM     58  CA  LYS    58      40.301   7.579  26.519  1.00 25.00           C
ATOM     59  CA  LYS    59      43.418   7.604  28.785  1.00 25.00           C
ATOM     60  CA  GLU    60      45.210   4.497  27.539  1.00 25.00           C
ATOM     61  CA  TYR    61      47.695   3.446  24.852  1.00 25.00           C
ATOM     62  CA  VAL    62      51.278   2.055  25.156  1.00 25.00           C
ATOM     63  CA  LYS    63      54.689   3.063  23.788  1.00 25.00           C
ATOM     64  CA  LYS    64      58.236   2.195  22.789  1.00 25.00           C
ATOM     65  CA  GLU    65      60.891  -0.091  21.343  1.00 25.00           C
ATOM     66  CA  LEU    66      63.594   2.411  22.241  1.00 25.00           C
ATOM     67  CA  MET    67      65.934  -0.445  23.058  1.00 25.00           C
ATOM     68  CA  GLU    68      68.929   1.912  22.926  1.00 25.00           C
ATOM     69  CA  PRO    69      70.332   0.451  19.738  1.00 25.00           C
ATOM     70  CA  LEU    70      72.431   3.679  19.619  1.00 25.00           C
ATOM     71  CA  GLU    71      72.201   6.256  16.850  1.00 25.00           C
ATOM     72  CA  ILE    72      70.649   9.708  16.185  1.00 25.00           C
ATOM     73  CA  LEU    73      67.435   7.615  15.911  1.00 25.00           C
ATOM     74  CA  SER    74      64.250   5.647  15.449  1.00 25.00           C
ATOM     75  CA  LEU    75      62.711   8.116  17.943  1.00 25.00           C
ATOM     76  CA  SER    76      59.812   5.878  18.840  1.00 25.00           C
ATOM     77  CA  GLY    77      56.130   6.381  18.112  1.00 25.00           C
ATOM     78  CA  ASN    78      55.265   2.660  18.170  1.00 25.00           C
ATOM     79  CA  VAL    79      51.703   4.028  18.569  1.00 25.00           C
ATOM     80  CA  SER    80      48.749   1.655  18.016  1.00 25.00           C
ATOM     81  CA  MET    81      50.541  -1.676  17.588  1.00 25.00           C
ATOM     82  CA  LYS    82      49.770  -5.401  17.941  1.00 25.00           C
ATOM     83  CA  ASP    83      46.210  -6.434  16.863  1.00 25.00           C
ATOM     84  CA  SER    84      46.834  -4.125  13.884  1.00 25.00           C
ATOM     85  CA  LYS    85      48.905  -1.148  12.674  1.00 25.00           C
ATOM     86  CA  PRO    86      51.105   1.948  12.874  1.00 25.00           C
ATOM     87  CA  PHE    87      54.070   4.241  13.520  1.00 25.00           C
ATOM     88  CA  CYS    88      57.622   4.892  12.422  1.00 25.00           C
ATOM     89  CA  HIS    89      59.523   7.752  13.953  1.00 25.00           C
ATOM     90  CA  ILE    90      60.152  11.442  14.860  1.00 25.00           C
ATOM     91  CA  HIS    91      63.588  12.930  14.494  1.00 25.00           C
ATOM     92  CA  VAL    92      65.328  16.305  14.353  1.00 25.00           C
ATOM     93  CA  LEU    93      64.671  19.716  15.941  1.00 25.00           C
ATOM     94  CA  LEU    94      67.525  20.330  18.271  1.00 25.00           C
ATOM     95  CA  GLY    95      70.604  18.142  18.143  1.00 25.00           C
ATOM     96  CA  LYS    96      73.961  19.027  19.641  1.00 25.00           C
ATOM     97  CA  ASP    97      72.179  19.391  23.017  1.00 25.00           C
ATOM     98  CA  GLY    98      68.625  19.579  24.324  1.00 25.00           C
ATOM     99  CA  GLU    99      66.936  16.990  22.108  1.00 25.00           C
ATOM    100  CA  VAL   100      64.645  15.959  19.324  1.00 25.00           C
ATOM    101  CA  TYR   101      61.131  15.162  18.265  1.00 25.00           C
ATOM    102  CA  GLY   102      60.988  12.312  20.776  1.00 25.00           C
ATOM    103  CA  GLY   103      57.666  11.395  19.174  1.00 25.00           C
ATOM    104  CA  HIS   104      54.787  11.026  16.699  1.00 25.00           C
ATOM    105  CA  LEU   105      55.063   9.953  13.120  1.00 25.00           C
ATOM    106  CA  PHE   106      56.185   8.832   9.672  1.00 25.00           C
ATOM    107  CA  SER   107      52.961   6.783   9.270  1.00 25.00           C
ATOM    108  CA  ALA   108      50.334   6.860   6.460  1.00 25.00           C
ATOM    109  CA  GLU   109      51.841   8.885   3.617  1.00 25.00           C
ATOM    110  CA  VAL   110      54.123  11.281   5.486  1.00 25.00           C
ATOM    111  CA  PHE   111      51.434  12.054   8.020  1.00 25.00           C
ATOM    112  CA  ALA   112      52.909  13.982  10.938  1.00 25.00           C
ATOM    113  CA  CYS   113      53.000  15.842  14.252  1.00 25.00           C
ATOM    114  CA  GLU   114      56.318  15.854  16.086  1.00 25.00           C
ATOM    115  CA  VAL   115      56.412  16.340  19.848  1.00 25.00           C
ATOM    116  CA  PHE   116      58.122  19.468  21.295  1.00 25.00           C
ATOM    117  CA  VAL   117      61.661  19.171  22.653  1.00 25.00           C
ATOM    118  CA  LEU   118      62.510  15.763  24.142  1.00 25.00           C
ATOM    119  CA  PRO   119      65.054  16.648  26.801  1.00 25.00           C
ATOM    120  CA  LEU   120      65.606  13.629  29.094  1.00 25.00           C
ATOM    121  CA  SER   121      67.014  13.597  32.628  1.00 25.00           C
ATOM    122  CA  GLY   122      63.494  12.902  33.862  1.00 25.00           C
ATOM    123  CA  GLU   123      61.142  11.707  31.210  1.00 25.00           C
ATOM    124  CA  ALA   124      59.098  12.331  28.080  1.00 25.00           C
ATOM    125  CA  PRO   125      57.802  15.469  26.449  1.00 25.00           C
ATOM    126  CA  GLU   126      54.235  15.800  24.997  1.00 25.00           C
ATOM    127  CA  ARG   127      51.686  15.984  22.221  1.00 25.00           C
ATOM    128  CA  ALA   128      50.592  13.213  19.948  1.00 25.00           C
ATOM    129  CA  PHE   129      47.854  14.437  17.537  1.00 25.00           C
ATOM    130  CA  ASP   130      45.027  15.264  15.107  1.00 25.00           C
ATOM    131  CA  GLU   131      42.800  14.909  11.993  1.00 25.00           C
ATOM    132  CA  GLN   132      39.125  15.017  12.786  1.00 25.00           C
ATOM    133  CA  THR   133      39.848  17.277  15.700  1.00 25.00           C
ATOM    134  CA  GLY   134      42.545  19.260  17.591  1.00 25.00           C
ATOM    135  CA  LEU   135      40.052  21.991  18.519  1.00 25.00           C
ATOM    136  CA  PHE   136      37.369  24.649  18.064  1.00 25.00           C
ATOM    137  CA  LEU   137      37.052  26.723  21.219  1.00 25.00           C
ATOM    138  CA  TRP   138      34.895  28.774  23.596  1.00 25.00           C
ATOM    139  CA  LEU   139      34.838  29.180  27.334  1.00 25.00           C
ATOM    140  CA  GLU   140      35.274  30.351  30.867  1.00 25.00           C
TER
END
