
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312TS393_5-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      K      10           -
LGA    G      11      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    F      12      L      16           #
LGA    L      13      D      17          4.473
LGA    L      14      Y      18           -
LGA    -       -      G      19           -
LGA    R      15      K      20           #
LGA    L      16      D      21          2.930
LGA    D      17      L      22           -
LGA    Y      18      V      23           -
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      -       -           -
LGA    H      39      R      24           #
LGA    I      40      Q      25          3.812
LGA    S      41      I      26           #
LGA    A      42      E      27          2.052
LGA    -       -      E      28           -
LGA    -       -      F      29           -
LGA    I      43      L      30          3.295
LGA    G      44      E      31          3.703
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    A      45      G      34          1.877
LGA    V      46      I      35          2.558
LGA    R      47      H      36          1.515
LGA    S      48      A      37          2.559
LGA    A      49      A      38          3.045
LGA    V      50      H      39          3.334
LGA    I      51      I      40          1.750
LGA    G      52      S      41          2.011
LGA    Y      53      A      42          3.449
LGA    Y      54      I      43          3.371
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    D      55      L      73          4.766
LGA    Q      56      -       -           -
LGA    E      57      -       -           -
LGA    K      58      -       -           -
LGA    K      59      -       -           -
LGA    E      60      -       -           -
LGA    Y      61      S      74           #
LGA    V      62      L      75           -
LGA    K      63      S      76          3.942
LGA    K      64      G      77          2.240
LGA    E      65      N      78          2.071
LGA    L      66      V      79          2.792
LGA    M      67      S      80          2.399
LGA    E      68      M      81          2.690
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    P      69      K      85          1.538
LGA    L      70      P      86          5.035
LGA    E      71      F      87           -
LGA    I      72      -       -           -
LGA    L      73      -       -           -
LGA    S      74      -       -           -
LGA    L      75      -       -           -
LGA    S      76      C      88          4.035
LGA    G      77      H      89           #
LGA    N      78      I      90          4.310
LGA    V      79      H      91          3.386
LGA    S      80      V      92          1.555
LGA    M      81      L      93          3.815
LGA    K      82      -       -           -
LGA    D      83      -       -           -
LGA    S      84      -       -           -
LGA    K      85      -       -           -
LGA    P      86      L      94          4.769
LGA    F      87      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           -
LGA    C      88      A     108           #
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      E     109          3.393
LGA    A     108      V     110          4.315
LGA    E     109      -       -           -
LGA    V     110      F     111          3.170
LGA    F     111      A     112          1.711
LGA    A     112      C     113          1.422
LGA    C     113      E     114          1.192
LGA    E     114      V     115          0.902
LGA    V     115      F     116          3.540
LGA    F     116      V     117          2.150
LGA    V     117      L     118          3.928
LGA    L     118      P     119          2.480
LGA    P     119      -       -           -
LGA    L     120      L     120          1.873
LGA    S     121      S     121          3.362
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           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  132  132    5.0     44    3.11     9.09     19.197     1.372

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.578951 * X  +  -0.732911 * Y  +  -0.357292 * Z  +  57.652191
  Y_new =   0.654660 * X  +   0.679051 * Y  +  -0.332131 * Z  +  14.934567
  Z_new =   0.486041 * X  +  -0.041617 * Y  +   0.872944 * Z  +  14.164792 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.047638    3.093954  [ DEG:    -2.7295    177.2705 ]
  Theta =  -0.507554   -2.634038  [ DEG:   -29.0807   -150.9193 ]
  Phi   =   0.846693   -2.294900  [ DEG:    48.5119   -131.4881 ]
 
# 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_5-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS393_5-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   44   3.11    9.09  19.197
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS393_5-D1
PFRMAT TS
TARGET T0312
MODEL 5
PARENT N/A
ATOM      9  CA  GLY     9      62.704  25.139   7.364  1.00 25.00           C
ATOM     10  CA  LYS    10      65.147  23.007   9.287  1.00 25.00           C
ATOM     11  CA  GLY    11      65.943  19.796  11.128  1.00 25.00           C
ATOM     12  CA  PHE    12      63.543  16.970  10.411  1.00 25.00           C
ATOM     13  CA  LEU    13      60.657  15.241   8.564  1.00 25.00           C
ATOM     14  CA  LEU    14      60.771  12.093  10.793  1.00 25.00           C
ATOM     15  CA  ARG    15      59.235   8.570  10.818  1.00 25.00           C
ATOM     16  CA  LEU    16      59.324   6.303   7.729  1.00 25.00           C
ATOM     17  CA  ASP    17      60.823   3.589   5.562  1.00 25.00           C
ATOM     18  CA  TYR    18      61.141  -0.204   5.401  1.00 25.00           C
ATOM     19  CA  GLY    19      61.067  -3.142   2.947  1.00 25.00           C
ATOM     20  CA  LYS    20      60.450  -1.954  -0.608  1.00 25.00           C
ATOM     21  CA  ASP    21      59.215   0.014  -3.652  1.00 25.00           C
ATOM     22  CA  LEU    22      58.504   3.051  -1.430  1.00 25.00           C
ATOM     23  CA  VAL    23      62.016   2.801   0.078  1.00 25.00           C
ATOM     24  CA  ARG    24      63.537   2.624  -3.432  1.00 25.00           C
ATOM     25  CA  GLN    25      61.527   5.709  -4.485  1.00 25.00           C
ATOM     26  CA  ILE    26      62.733   7.589  -1.374  1.00 25.00           C
ATOM     27  CA  GLU    27      66.354   6.625  -2.165  1.00 25.00           C
ATOM     28  CA  GLU    28      65.920   7.854  -5.766  1.00 25.00           C
ATOM     29  CA  PHE    29      64.479  11.165  -4.488  1.00 25.00           C
ATOM     30  CA  LEU    30      67.443  11.560  -2.096  1.00 25.00           C
ATOM     31  CA  GLU    31      69.884  10.885  -4.969  1.00 25.00           C
ATOM     32  CA  GLU    32      68.102  13.499  -7.128  1.00 25.00           C
ATOM     33  CA  LYS    33      68.115  17.334  -6.926  1.00 25.00           C
ATOM     34  CA  GLY    34      69.542  16.725  -3.438  1.00 25.00           C
ATOM     35  CA  ILE    35      67.743  16.189  -0.133  1.00 25.00           C
ATOM     36  CA  HIS    36      67.584  19.352   1.886  1.00 25.00           C
ATOM     37  CA  ALA    37      65.719  17.907   4.823  1.00 25.00           C
ATOM     38  CA  ALA    38      66.368  14.441   6.253  1.00 25.00           C
ATOM     39  CA  HIS    39      63.301  12.305   5.534  1.00 25.00           C
ATOM     40  CA  ILE    40      64.473   9.696   7.969  1.00 25.00           C
ATOM     41  CA  SER    41      64.298   6.485  10.079  1.00 25.00           C
ATOM     42  CA  ALA    42      65.915   7.219  13.472  1.00 25.00           C
ATOM     43  CA  ILE    43      67.271   8.783  16.716  1.00 25.00           C
ATOM     44  CA  GLY    44      69.770  11.131  18.298  1.00 25.00           C
ATOM     45  CA  ALA    45      71.731  13.848  20.213  1.00 25.00           C
ATOM     46  CA  VAL    46      69.745  13.023  23.390  1.00 25.00           C
ATOM     47  CA  ARG    47      70.073   9.293  23.529  1.00 25.00           C
ATOM     48  CA  SER    48      66.689   7.806  22.464  1.00 25.00           C
ATOM     49  CA  ALA    49      63.099   9.025  22.173  1.00 25.00           C
ATOM     50  CA  VAL    50      59.301   9.255  22.205  1.00 25.00           C
ATOM     51  CA  ILE    51      57.214  12.101  20.950  1.00 25.00           C
ATOM     52  CA  GLY    52      53.917  10.321  21.492  1.00 25.00           C
ATOM     53  CA  TYR    53      50.761  12.462  21.126  1.00 25.00           C
ATOM     54  CA  TYR    54      47.452  13.534  19.544  1.00 25.00           C
ATOM     55  CA  ASP    55      44.349  12.460  21.575  1.00 25.00           C
ATOM     56  CA  GLN    56      40.680  13.021  22.445  1.00 25.00           C
ATOM     57  CA  GLU    57      39.669  15.289  25.330  1.00 25.00           C
ATOM     58  CA  LYS    58      41.759  14.852  28.452  1.00 25.00           C
ATOM     59  CA  LYS    59      42.574  11.196  29.197  1.00 25.00           C
ATOM     60  CA  GLU    60      44.555   8.166  28.078  1.00 25.00           C
ATOM     61  CA  TYR    61      47.382   8.012  25.512  1.00 25.00           C
ATOM     62  CA  VAL    62      49.538   4.821  25.429  1.00 25.00           C
ATOM     63  CA  LYS    63      53.312   5.176  24.821  1.00 25.00           C
ATOM     64  CA  LYS    64      56.930   4.488  23.833  1.00 25.00           C
ATOM     65  CA  GLU    65      60.767   4.424  23.626  1.00 25.00           C
ATOM     66  CA  LEU    66      62.902   4.269  20.482  1.00 25.00           C
ATOM     67  CA  MET    67      65.868   2.205  21.692  1.00 25.00           C
ATOM     68  CA  GLU    68      68.598   2.560  19.108  1.00 25.00           C
ATOM     69  CA  PRO    69      71.565   4.720  18.274  1.00 25.00           C
ATOM     70  CA  LEU    70      72.664   7.348  15.774  1.00 25.00           C
ATOM     71  CA  GLU    71      71.309   9.524  13.008  1.00 25.00           C
ATOM     72  CA  ILE    72      69.650  12.944  13.581  1.00 25.00           C
ATOM     73  CA  LEU    73      66.217  12.211  12.030  1.00 25.00           C
ATOM     74  CA  SER    74      63.357  11.496  14.434  1.00 25.00           C
ATOM     75  CA  LEU    75      62.069   9.023  17.063  1.00 25.00           C
ATOM     76  CA  SER    76      59.521   6.619  15.563  1.00 25.00           C
ATOM     77  CA  GLY    77      56.582   7.946  17.526  1.00 25.00           C
ATOM     78  CA  ASN    78      53.372   6.215  16.280  1.00 25.00           C
ATOM     79  CA  VAL    79      51.392   6.219  19.521  1.00 25.00           C
ATOM     80  CA  SER    80      47.927   5.300  18.238  1.00 25.00           C
ATOM     81  CA  MET    81      46.869   1.593  18.263  1.00 25.00           C
ATOM     82  CA  LYS    82      44.447  -1.147  17.189  1.00 25.00           C
ATOM     83  CA  ASP    83      41.597  -0.391  14.813  1.00 25.00           C
ATOM     84  CA  SER    84      43.609   2.349  13.135  1.00 25.00           C
ATOM     85  CA  LYS    85      46.038   5.258  13.243  1.00 25.00           C
ATOM     86  CA  PRO    86      48.762   7.798  12.588  1.00 25.00           C
ATOM     87  CA  PHE    87      50.698  10.520  14.427  1.00 25.00           C
ATOM     88  CA  CYS    88      54.047   9.818  12.830  1.00 25.00           C
ATOM     89  CA  HIS    89      56.925  11.844  14.396  1.00 25.00           C
ATOM     90  CA  ILE    90      59.514  13.426  16.667  1.00 25.00           C
ATOM     91  CA  HIS    91      62.605  14.534  18.663  1.00 25.00           C
ATOM     92  CA  VAL    92      64.510  16.191  15.764  1.00 25.00           C
ATOM     93  CA  LEU    93      67.693  15.758  17.740  1.00 25.00           C
ATOM     94  CA  LEU    94      68.865  18.992  16.051  1.00 25.00           C
ATOM     95  CA  GLY    95      71.962  17.293  14.735  1.00 25.00           C
ATOM     96  CA  LYS    96      74.844  18.542  16.851  1.00 25.00           C
ATOM     97  CA  ASP    97      72.928  21.491  18.343  1.00 25.00           C
ATOM     98  CA  GLY    98      71.303  18.977  20.741  1.00 25.00           C
ATOM     99  CA  GLU    99      68.022  20.399  22.110  1.00 25.00           C
ATOM    100  CA  VAL   100      65.280  20.168  19.479  1.00 25.00           C
ATOM    101  CA  TYR   101      62.451  21.779  17.481  1.00 25.00           C
ATOM    102  CA  GLY   102      61.758  20.519  13.898  1.00 25.00           C
ATOM    103  CA  GLY   103      59.585  17.389  13.615  1.00 25.00           C
ATOM    104  CA  HIS   104      56.666  16.020  11.563  1.00 25.00           C
ATOM    105  CA  LEU   105      56.131  13.140   9.138  1.00 25.00           C
ATOM    106  CA  PHE   106      55.125   9.995   7.250  1.00 25.00           C
ATOM    107  CA  SER   107      51.448   9.828   8.087  1.00 25.00           C
ATOM    108  CA  ALA   108      48.580  11.122   6.031  1.00 25.00           C
ATOM    109  CA  GLU   109      49.751  14.350   4.284  1.00 25.00           C
ATOM    110  CA  VAL   110      52.858  15.722   5.900  1.00 25.00           C
ATOM    111  CA  PHE   111      52.100  17.433   9.207  1.00 25.00           C
ATOM    112  CA  ALA   112      51.872  14.575  11.731  1.00 25.00           C
ATOM    113  CA  CYS   113      52.818  17.123  14.294  1.00 25.00           C
ATOM    114  CA  GLU   114      55.546  16.720  16.878  1.00 25.00           C
ATOM    115  CA  VAL   115      58.358  18.804  18.310  1.00 25.00           C
ATOM    116  CA  PHE   116      58.906  16.875  21.578  1.00 25.00           C
ATOM    117  CA  VAL   117      62.077  18.462  22.924  1.00 25.00           C
ATOM    118  CA  LEU   118      65.067  16.371  23.999  1.00 25.00           C
ATOM    119  CA  PRO   119      67.275  17.503  26.810  1.00 25.00           C
ATOM    120  CA  LEU   120      67.353  13.905  27.882  1.00 25.00           C
ATOM    121  CA  SER   121      67.542  13.597  31.666  1.00 25.00           C
ATOM    122  CA  GLY   122      64.367  11.510  31.769  1.00 25.00           C
ATOM    123  CA  GLU   123      62.385  13.466  29.162  1.00 25.00           C
ATOM    124  CA  ALA   124      59.865  13.830  26.413  1.00 25.00           C
ATOM    125  CA  PRO   125      58.996  17.434  27.221  1.00 25.00           C
ATOM    126  CA  GLU   126      55.600  18.397  25.705  1.00 25.00           C
ATOM    127  CA  ARG   127      52.353  18.953  23.718  1.00 25.00           C
ATOM    128  CA  ALA   128      50.632  18.318  20.387  1.00 25.00           C
ATOM    129  CA  PHE   129      48.090  18.670  17.583  1.00 25.00           C
ATOM    130  CA  ASP   130      46.362  21.212  19.773  1.00 25.00           C
ATOM    131  CA  GLU   131      43.098  23.142  19.631  1.00 25.00           C
ATOM    132  CA  GLN   132      39.698  21.826  18.552  1.00 25.00           C
ATOM    133  CA  THR   133      40.448  20.456  15.098  1.00 25.00           C
ATOM    134  CA  GLY   134      42.185  23.781  14.534  1.00 25.00           C
ATOM    135  CA  LEU   135      41.484  27.244  13.013  1.00 25.00           C
ATOM    136  CA  PHE   136      42.100  30.411  10.999  1.00 25.00           C
ATOM    137  CA  LEU   137      40.550  33.480   9.348  1.00 25.00           C
ATOM    138  CA  TRP   138      43.941  35.143   9.564  1.00 25.00           C
ATOM    139  CA  LEU   139      45.428  38.339   8.062  1.00 25.00           C
ATOM    140  CA  GLU   140      47.215  41.664   8.525  1.00 25.00           C
TER
END
