
#######################################################
#                                                     #
#                        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  146 (  146),  selected  146 , name T0312TS168_2
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312TS168_2.T0312.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    K       2      K       2           -
LGA    -       -      V       3           -
LGA    -       -      F       4           -
LGA    -       -      E       5           -
LGA    -       -      F       6           -
LGA    -       -      E       7           -
LGA    -       -      V       8           -
LGA    -       -      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    V       3      F      12           #
LGA    F       4      L      13          2.769
LGA    E       5      L      14          2.736
LGA    F       6      R      15          1.453
LGA    -       -      L      16           -
LGA    E       7      D      17          4.237
LGA    V       8      Y      18           -
LGA    G       9      G      19           -
LGA    K      10      K      20           -
LGA    G      11      D      21           -
LGA    F      12      -       -           -
LGA    L      13      L      22          5.006
LGA    -       -      V      23           -
LGA    -       -      R      24           -
LGA    L      14      Q      25          0.778
LGA    R      15      I      26          4.476
LGA    L      16      E      27           #
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          3.858
LGA    H      39      -       -           -
LGA    I      40      -       -           -
LGA    S      41      F      29           #
LGA    -       -      L      30           -
LGA    A      42      E      31          2.709
LGA    I      43      E      32          4.512
LGA    G      44      K      33          3.622
LGA    A      45      G      34          2.167
LGA    V      46      I      35          0.919
LGA    R      47      H      36          2.088
LGA    S      48      A      37          3.029
LGA    A      49      A      38          4.022
LGA    V      50      H      39          3.959
LGA    I      51      I      40          2.496
LGA    G      52      S      41          2.303
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          3.320
LGA    Y      54      S      76          4.265
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          3.604
LGA    K      64      N      78          4.583
LGA    E      65      V      79           -
LGA    L      66      S      80          3.834
LGA    M      67      M      81          5.345
LGA    E      68      K      82          3.511
LGA    P      69      D      83          3.314
LGA    L      70      S      84          2.305
LGA    E      71      K      85          1.458
LGA    I      72      P      86          4.480
LGA    L      73      -       -           -
LGA    S      74      F      87          3.570
LGA    L      75      C      88          3.388
LGA    S      76      H      89          3.622
LGA    G      77      I      90          2.857
LGA    N      78      H      91          2.846
LGA    V      79      V      92          2.454
LGA    S      80      L      93          3.785
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    M      81      G     103          1.128
LGA    K      82      H     104           #
LGA    D      83      -       -           -
LGA    S      84      -       -           -
LGA    K      85      -       -           -
LGA    P      86      -       -           -
LGA    F      87      L     105          3.267
LGA    C      88      F     106          4.926
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      S     107           #
LGA    S     107      A     108          1.999
LGA    A     108      E     109          3.885
LGA    E     109      V     110          4.071
LGA    V     110      F     111          4.689
LGA    F     111      A     112          4.232
LGA    A     112      C     113          1.737
LGA    C     113      E     114          1.572
LGA    E     114      V     115          1.662
LGA    V     115      F     116          1.021
LGA    F     116      -       -           -
LGA    V     117      V     117          4.631
LGA    L     118      L     118          2.544
LGA    P     119      P     119          2.525
LGA    L     120      L     120          0.902
LGA    S     121      S     121          2.959
LGA    G     122      G     122           -
LGA    E     123      E     123           -
LGA    A     124      A     124           -
LGA    P     125      P     125           -
LGA    E     126      E     126           -
LGA    R     127      R     127           -
LGA    A     128      A     128           -
LGA    F     129      F     129           -
LGA    D     130      D     130           -
LGA    E     131      E     131           -
LGA    Q     132      Q     132           -
LGA    T     133      T     133           -
LGA    G     134      G     134           -
LGA    L     135      L     135           -
LGA    F     136      F     136           -
LGA    L     137      L     137           -
LGA    W     138      W     138           -
LGA    L     139      L     139           -
LGA    E     140      E     140           -
LGA    H     141      -       -           -
LGA    H     142      -       -           -
LGA    H     143      -       -           -
LGA    H     144      -       -           -
LGA    H     145      -       -           -
LGA    H     146      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  146  140    5.0     54    3.32    18.52     19.953     1.579

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.192500 * X  +  -0.912187 * Y  +   0.361743 * Z  +  58.063286
  Y_new =  -0.283615 * X  +   0.301187 * Y  +   0.910411 * Z  +  12.846412
  Z_new =  -0.939418 * X  +  -0.277850 * Y  +  -0.200732 * Z  +  15.956589 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.196429    0.945164  [ DEG:  -125.8461     54.1539 ]
  Theta =   1.220928    1.920665  [ DEG:    69.9540    110.0460 ]
  Phi   =  -0.974484    2.167109  [ DEG:   -55.8338    124.1662 ]
 
# 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: T0312TS168_2                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS168_2.T0312.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  146  140   5.0   54   3.32   18.52  19.953
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS168_2
PFRMAT TS
TARGET T0312
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      53.778  25.489  24.450  1.00 25.00           C
ATOM      2  CA  LYS     2      56.260  24.779  21.691  1.00 25.00           C
ATOM      3  CA  VAL     3      54.335  21.527  21.140  1.00 25.00           C
ATOM      4  CA  PHE     4      55.995  21.578  17.721  1.00 25.00           C
ATOM      5  CA  GLU     5      56.571  20.728  14.107  1.00 25.00           C
ATOM      6  CA  PHE     6      56.671  18.896  10.817  1.00 25.00           C
ATOM      7  CA  GLU     7      55.800  20.456   7.457  1.00 25.00           C
ATOM      8  CA  VAL     8      58.859  22.710   7.651  1.00 25.00           C
ATOM      9  CA  GLY     9      60.032  25.148  10.256  1.00 25.00           C
ATOM     10  CA  LYS    10      62.863  23.319  12.110  1.00 25.00           C
ATOM     11  CA  GLY    11      62.664  19.598  11.227  1.00 25.00           C
ATOM     12  CA  PHE    12      61.084  16.339  12.526  1.00 25.00           C
ATOM     13  CA  LEU    13      58.990  13.879  10.571  1.00 25.00           C
ATOM     14  CA  LEU    14      61.316  10.919   9.720  1.00 25.00           C
ATOM     15  CA  ARG    15      63.590   8.146  11.078  1.00 25.00           C
ATOM     16  CA  LEU    16      61.744   5.809   8.804  1.00 25.00           C
ATOM     17  CA  ASP    17      63.261   2.773   6.991  1.00 25.00           C
ATOM     18  CA  TYR    18      64.267  -0.075   4.681  1.00 25.00           C
ATOM     19  CA  GLY    19      62.716  -2.528   2.221  1.00 25.00           C
ATOM     20  CA  LYS    20      64.741  -1.400  -0.721  1.00 25.00           C
ATOM     21  CA  ASP    21      62.258   0.463  -2.965  1.00 25.00           C
ATOM     22  CA  LEU    22      61.414   2.850  -0.090  1.00 25.00           C
ATOM     23  CA  VAL    23      65.143   3.485   0.510  1.00 25.00           C
ATOM     24  CA  ARG    24      65.646   4.205  -3.218  1.00 25.00           C
ATOM     25  CA  GLN    25      62.696   6.647  -3.169  1.00 25.00           C
ATOM     26  CA  ILE    26      64.172   8.406  -0.103  1.00 25.00           C
ATOM     27  CA  GLU    27      67.562   8.680  -1.862  1.00 25.00           C
ATOM     28  CA  GLU    28      65.862  10.154  -4.962  1.00 25.00           C
ATOM     29  CA  PHE    29      64.016  12.695  -2.771  1.00 25.00           C
ATOM     30  CA  LEU    30      67.310  13.666  -1.078  1.00 25.00           C
ATOM     31  CA  GLU    31      68.967  14.115  -4.502  1.00 25.00           C
ATOM     32  CA  GLU    32      66.050  16.316  -5.651  1.00 25.00           C
ATOM     33  CA  LYS    33      68.464  19.222  -5.893  1.00 25.00           C
ATOM     34  CA  GLY    34      69.204  18.892  -2.149  1.00 25.00           C
ATOM     35  CA  ILE    35      67.361  18.394   1.162  1.00 25.00           C
ATOM     36  CA  HIS    36      68.580  16.974   4.539  1.00 25.00           C
ATOM     37  CA  ALA    37      65.243  15.977   6.088  1.00 25.00           C
ATOM     38  CA  ALA    38      66.017  12.574   7.610  1.00 25.00           C
ATOM     39  CA  HIS    39      67.907   9.817   5.841  1.00 25.00           C
ATOM     40  CA  ILE    40      70.279  10.178   8.812  1.00 25.00           C
ATOM     41  CA  SER    41      72.810  10.817  11.558  1.00 25.00           C
ATOM     42  CA  ALA    42      70.284  13.257  13.063  1.00 25.00           C
ATOM     43  CA  ILE    43      68.729  11.922  16.324  1.00 25.00           C
ATOM     44  CA  GLY    44      72.399  12.620  17.210  1.00 25.00           C
ATOM     45  CA  ALA    45      72.587  12.841  21.013  1.00 25.00           C
ATOM     46  CA  VAL    46      69.155  11.144  21.345  1.00 25.00           C
ATOM     47  CA  ARG    47      70.104   8.988  24.331  1.00 25.00           C
ATOM     48  CA  SER    48      67.872   6.091  23.261  1.00 25.00           C
ATOM     49  CA  ALA    49      64.211   6.913  22.846  1.00 25.00           C
ATOM     50  CA  VAL    50      60.596   6.782  23.885  1.00 25.00           C
ATOM     51  CA  ILE    51      57.751   9.284  23.996  1.00 25.00           C
ATOM     52  CA  GLY    52      54.799  11.598  23.614  1.00 25.00           C
ATOM     53  CA  TYR    53      52.966   8.828  21.680  1.00 25.00           C
ATOM     54  CA  TYR    54      49.271   9.648  22.310  1.00 25.00           C
ATOM     55  CA  ASP    55      45.503   9.174  22.538  1.00 25.00           C
ATOM     56  CA  GLN    56      42.482   6.924  21.837  1.00 25.00           C
ATOM     57  CA  GLU    57      40.699   9.596  23.886  1.00 25.00           C
ATOM     58  CA  LYS    58      41.004   9.516  27.648  1.00 25.00           C
ATOM     59  CA  LYS    59      44.244   9.247  29.717  1.00 25.00           C
ATOM     60  CA  GLU    60      45.638   5.968  28.405  1.00 25.00           C
ATOM     61  CA  TYR    61      47.833   4.655  25.584  1.00 25.00           C
ATOM     62  CA  VAL    62      51.272   2.916  25.684  1.00 25.00           C
ATOM     63  CA  LYS    63      54.673   3.569  24.094  1.00 25.00           C
ATOM     64  CA  LYS    64      58.048   2.345  22.889  1.00 25.00           C
ATOM     65  CA  GLU    65      60.367  -0.205  21.313  1.00 25.00           C
ATOM     66  CA  LEU    66      63.355   2.022  22.008  1.00 25.00           C
ATOM     67  CA  MET    67      65.448  -1.047  22.717  1.00 25.00           C
ATOM     68  CA  GLU    68      68.647   0.999  22.367  1.00 25.00           C
ATOM     69  CA  PRO    69      69.696  -0.618  19.119  1.00 25.00           C
ATOM     70  CA  LEU    70      72.092   2.384  18.826  1.00 25.00           C
ATOM     71  CA  GLU    71      71.943   4.951  16.042  1.00 25.00           C
ATOM     72  CA  ILE    72      70.702   8.535  15.427  1.00 25.00           C
ATOM     73  CA  LEU    73      67.286   6.770  15.381  1.00 25.00           C
ATOM     74  CA  SER    74      63.899   5.127  15.144  1.00 25.00           C
ATOM     75  CA  LEU    75      62.772   7.755  17.695  1.00 25.00           C
ATOM     76  CA  SER    76      59.728   5.824  18.800  1.00 25.00           C
ATOM     77  CA  GLY    77      56.075   6.685  18.295  1.00 25.00           C
ATOM     78  CA  ASN    78      54.852   3.069  18.457  1.00 25.00           C
ATOM     79  CA  VAL    79      51.475   4.788  19.057  1.00 25.00           C
ATOM     80  CA  SER    80      48.271   2.717  18.721  1.00 25.00           C
ATOM     81  CA  MET    81      49.695  -0.779  18.228  1.00 25.00           C
ATOM     82  CA  LYS    82      48.583  -4.406  18.679  1.00 25.00           C
ATOM     83  CA  ASP    83      44.877  -5.088  17.838  1.00 25.00           C
ATOM     84  CA  SER    84      45.538  -2.874  14.795  1.00 25.00           C
ATOM     85  CA  LYS    85      47.813  -0.127  13.418  1.00 25.00           C
ATOM     86  CA  PRO    86      50.317   2.735  13.440  1.00 25.00           C
ATOM     87  CA  PHE    87      53.528   4.726  13.869  1.00 25.00           C
ATOM     88  CA  CYS    88      57.051   5.013  12.544  1.00 25.00           C
ATOM     89  CA  HIS    89      59.318   7.680  13.916  1.00 25.00           C
ATOM     90  CA  ILE    90      60.366  11.296  14.731  1.00 25.00           C
ATOM     91  CA  HIS    91      63.902  12.432  14.133  1.00 25.00           C
ATOM     92  CA  VAL    92      65.955  15.615  13.838  1.00 25.00           C
ATOM     93  CA  LEU    93      65.740  19.086  15.417  1.00 25.00           C
ATOM     94  CA  LEU    94      68.782  19.430  17.558  1.00 25.00           C
ATOM     95  CA  GLY    95      71.615  16.946  17.269  1.00 25.00           C
ATOM     96  CA  LYS    96      75.131  17.504  18.544  1.00 25.00           C
ATOM     97  CA  ASP    97      73.610  18.068  22.019  1.00 25.00           C
ATOM     98  CA  GLY    98      70.181  18.619  23.540  1.00 25.00           C
ATOM     99  CA  GLU    99      68.108  16.194  21.469  1.00 25.00           C
ATOM    100  CA  VAL   100      65.556  15.376  18.847  1.00 25.00           C
ATOM    101  CA  TYR   101      61.920  14.925  18.017  1.00 25.00           C
ATOM    102  CA  GLY   102      61.654  12.122  20.572  1.00 25.00           C
ATOM    103  CA  GLY   103      58.163  11.529  19.192  1.00 25.00           C
ATOM    104  CA  HIS   104      55.112  11.430  16.905  1.00 25.00           C
ATOM    105  CA  LEU   105      55.054  10.308  13.330  1.00 25.00           C
ATOM    106  CA  PHE   106      55.841   9.056   9.835  1.00 25.00           C
ATOM    107  CA  SER   107      52.411   7.335   9.661  1.00 25.00           C
ATOM    108  CA  ALA   108      49.633   7.652   7.019  1.00 25.00           C
ATOM    109  CA  GLU   109      51.150   9.496   4.060  1.00 25.00           C
ATOM    110  CA  VAL   110      53.772  11.667   5.752  1.00 25.00           C
ATOM    111  CA  PHE   111      51.338  12.722   8.437  1.00 25.00           C
ATOM    112  CA  ALA   112      53.177  14.515  11.230  1.00 25.00           C
ATOM    113  CA  CYS   113      53.660  16.382  14.507  1.00 25.00           C
ATOM    114  CA  GLU   114      57.071  16.077  16.132  1.00 25.00           C
ATOM    115  CA  VAL   115      57.450  16.579  19.873  1.00 25.00           C
ATOM    116  CA  PHE   116      59.549  19.532  21.169  1.00 25.00           C
ATOM    117  CA  VAL   117      63.120  18.894  22.310  1.00 25.00           C
ATOM    118  CA  LEU   118      63.720  15.430  23.789  1.00 25.00           C
ATOM    119  CA  PRO   119      66.500  16.077  26.274  1.00 25.00           C
ATOM    120  CA  LEU   120      66.895  13.035  28.569  1.00 25.00           C
ATOM    121  CA  SER   121      68.513  12.890  32.009  1.00 25.00           C
ATOM    122  CA  GLY   122      65.026  12.557  33.468  1.00 25.00           C
ATOM    123  CA  GLU   123      62.405  11.583  30.983  1.00 25.00           C
ATOM    124  CA  ALA   124      60.239  12.384  27.978  1.00 25.00           C
ATOM    125  CA  PRO   125      59.160  15.623  26.387  1.00 25.00           C
ATOM    126  CA  GLU   126      55.559  16.297  25.154  1.00 25.00           C
ATOM    127  CA  ARG   127      52.871  16.713  22.539  1.00 25.00           C
ATOM    128  CA  ALA   128      51.367  14.048  20.377  1.00 25.00           C
ATOM    129  CA  PHE   129      48.617  15.521  18.123  1.00 25.00           C
ATOM    130  CA  ASP   130      45.739  16.607  15.862  1.00 25.00           C
ATOM    131  CA  GLU   131      43.296  16.452  12.897  1.00 25.00           C
ATOM    132  CA  GLN   132      39.707  16.932  13.915  1.00 25.00           C
ATOM    133  CA  THR   133      40.832  19.129  16.747  1.00 25.00           C
ATOM    134  CA  GLY   134      43.825  20.848  18.440  1.00 25.00           C
ATOM    135  CA  LEU   135      41.678  23.821  19.484  1.00 25.00           C
ATOM    136  CA  PHE   136      39.248  26.729  19.159  1.00 25.00           C
ATOM    137  CA  LEU   137      39.337  28.848  22.299  1.00 25.00           C
ATOM    138  CA  TRP   138      37.547  31.122  24.776  1.00 25.00           C
ATOM    139  CA  LEU   139      37.766  31.559  28.505  1.00 25.00           C
ATOM    140  CA  GLU   140      38.538  32.707  31.988  1.00 25.00           C
ATOM    141  CA  HIS   141      41.252  35.335  32.363  1.00 25.00           C
ATOM    142  CA  HIS   142      41.574  37.195  29.011  1.00 25.00           C
ATOM    143  CA  HIS   143      41.333  39.961  26.434  1.00 25.00           C
ATOM    144  CA  HIS   144      39.407  41.890  23.769  1.00 25.00           C
ATOM    145  CA  HIS   145      41.482  45.074  23.728  1.00 25.00           C
ATOM    146  CA  HIS   146      45.072  44.142  22.961  1.00 25.00           C
TER
END
