
#######################################################
#                                                     #
#                        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 T0312TS393_4
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312TS393_4.T0312.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      V       3           -
LGA    -       -      F       4           -
LGA    -       -      E       5           -
LGA    -       -      F       6           -
LGA    -       -      E       7           -
LGA    -       -      V       8           -
LGA    M       1      G       9          1.414
LGA    K       2      K      10          1.219
LGA    V       3      G      11          2.325
LGA    F       4      F      12          2.398
LGA    E       5      L      13          3.554
LGA    F       6      L      14          4.502
LGA    E       7      R      15          3.250
LGA    V       8      L      16          2.213
LGA    -       -      D      17           -
LGA    -       -      Y      18           -
LGA    G       9      G      19          4.190
LGA    -       -      K      20           -
LGA    K      10      D      21          1.369
LGA    G      11      L      22          1.827
LGA    F      12      V      23          4.114
LGA    -       -      R      24           -
LGA    L      13      Q      25          4.521
LGA    L      14      I      26          3.347
LGA    R      15      E      27           #
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    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      E      28          4.543
LGA    A      38      F      29          2.456
LGA    H      39      L      30          2.816
LGA    I      40      E      31          1.737
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      G      34           -
LGA    -       -      I      35           -
LGA    S      41      H      36           #
LGA    A      42      A      37           -
LGA    I      43      A      38           -
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    L      75      -       -           -
LGA    S      76      H      39           #
LGA    G      77      I      40          3.434
LGA    N      78      S      41          4.869
LGA    V      79      A      42           -
LGA    S      80      I      43           -
LGA    M      81      G      44           -
LGA    K      82      A      45           -
LGA    D      83      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    S      84      L      73          4.619
LGA    K      85      S      74          2.574
LGA    P      86      L      75          3.989
LGA    F      87      S      76          4.331
LGA    C      88      G      77           #
LGA    H      89      -       -           -
LGA    I      90      -       -           -
LGA    H      91      -       -           -
LGA    V      92      N      78           #
LGA    -       -      V      79           -
LGA    -       -      S      80           -
LGA    -       -      M      81           -
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    L      93      P      86          2.810
LGA    L      94      F      87           #
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      C      88           #
LGA    H     104      H      89           -
LGA    L     105      I      90           #
LGA    F     106      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           -
LGA    -       -      A     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    S     107      C     113          4.574
LGA    A     108      E     114          1.011
LGA    E     109      V     115          4.655
LGA    V     110      F     116          2.479
LGA    F     111      V     117          3.765
LGA    A     112      L     118          4.449
LGA    C     113      P     119          3.847
LGA    E     114      L     120          4.956
LGA    V     115      S     121           #
LGA    -       -      G     122           -
LGA    -       -      E     123           -
LGA    F     116      A     124          4.516
LGA    V     117      P     125          1.964
LGA    L     118      E     126          3.251
LGA    P     119      R     127          2.876
LGA    L     120      A     128          3.112
LGA    S     121      F     129          3.236
LGA    G     122      D     130          2.768
LGA    -       -      E     131           -
LGA    -       -      Q     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      L     135           -
LGA    -       -      F     136           -
LGA    E     123      L     137          1.100
LGA    A     124      W     138          3.841
LGA    P     125      L     139           -
LGA    E     126      E     140           -
LGA    R     127      -       -           -
LGA    A     128      -       -           -
LGA    F     129      -       -           -
LGA    D     130      -       -           -
LGA    E     131      -       -           -
LGA    Q     132      -       -           -
LGA    T     133      -       -           -
LGA    G     134      -       -           -
LGA    L     135      -       -           -
LGA    F     136      -       -           -
LGA    L     137      -       -           -
LGA    W     138      -       -           -
LGA    L     139      -       -           -
LGA    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     42    3.41     7.14     15.863     1.197

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.315844 * X  +   0.386454 * Y  +  -0.866542 * Z  +  61.102478
  Y_new =  -0.147951 * X  +   0.922181 * Y  +   0.357341 * Z  +  10.680608
  Z_new =   0.937205 * X  +   0.015342 * Y  +   0.348441 * Z  +  19.821697 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.044001   -3.097592  [ DEG:     2.5211   -177.4789 ]
  Theta =  -1.214528   -1.927064  [ DEG:   -69.5873   -110.4127 ]
  Phi   =  -0.438074    2.703518  [ DEG:   -25.0998    154.9002 ]
 
# 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_4                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS393_4.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   42   3.41    7.14  15.863
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS393_4
PFRMAT TS
TARGET T0312
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      67.074  18.764  29.847  1.00 25.00           C
ATOM      2  CA  LYS     2      66.248  19.559  26.194  1.00 25.00           C
ATOM      3  CA  VAL     3      63.857  18.815  23.301  1.00 25.00           C
ATOM      4  CA  PHE     4      62.298  17.844  19.939  1.00 25.00           C
ATOM      5  CA  GLU     5      59.981  17.792  16.938  1.00 25.00           C
ATOM      6  CA  PHE     6      59.941  15.084  14.279  1.00 25.00           C
ATOM      7  CA  GLU     7      58.257  17.055  11.543  1.00 25.00           C
ATOM      8  CA  VAL     8      56.066  14.957   9.266  1.00 25.00           C
ATOM      9  CA  GLY     9      55.001  12.835   6.228  1.00 25.00           C
ATOM     10  CA  LYS    10      57.026   9.580   6.289  1.00 25.00           C
ATOM     11  CA  GLY    11      58.469   9.464   9.767  1.00 25.00           C
ATOM     12  CA  PHE    12      62.205   9.356  10.530  1.00 25.00           C
ATOM     13  CA  LEU    13      61.444  10.093  14.176  1.00 25.00           C
ATOM     14  CA  LEU    14      64.569  11.717  15.672  1.00 25.00           C
ATOM     15  CA  ARG    15      65.724  13.170  18.920  1.00 25.00           C
ATOM     16  CA  LEU    16      67.429  16.188  20.359  1.00 25.00           C
ATOM     17  CA  ASP    17      70.346  18.362  19.305  1.00 25.00           C
ATOM     18  CA  TYR    18      73.675  19.827  20.413  1.00 25.00           C
ATOM     19  CA  GLY    19      75.329  23.250  20.091  1.00 25.00           C
ATOM     20  CA  LYS    20      73.842  25.193  17.200  1.00 25.00           C
ATOM     21  CA  ASP    21      76.813  23.908  15.153  1.00 25.00           C
ATOM     22  CA  LEU    22      75.214  20.434  14.966  1.00 25.00           C
ATOM     23  CA  VAL    23      71.914  21.989  13.800  1.00 25.00           C
ATOM     24  CA  ARG    24      73.775  23.987  11.116  1.00 25.00           C
ATOM     25  CA  GLN    25      75.545  20.801   9.937  1.00 25.00           C
ATOM     26  CA  ILE    26      72.185  18.974   9.753  1.00 25.00           C
ATOM     27  CA  GLU    27      70.698  21.858   7.719  1.00 25.00           C
ATOM     28  CA  GLU    28      73.690  21.749   5.331  1.00 25.00           C
ATOM     29  CA  PHE    29      73.254  17.966   4.918  1.00 25.00           C
ATOM     30  CA  LEU    30      69.528  18.453   4.172  1.00 25.00           C
ATOM     31  CA  GLU    31      70.376  21.131   1.568  1.00 25.00           C
ATOM     32  CA  GLU    32      72.922  18.778  -0.059  1.00 25.00           C
ATOM     33  CA  LYS    33      76.189  16.912   0.492  1.00 25.00           C
ATOM     34  CA  GLY    34      76.503  14.233   3.125  1.00 25.00           C
ATOM     35  CA  ILE    35      74.760  13.097   6.289  1.00 25.00           C
ATOM     36  CA  HIS    36      74.467  11.040   9.440  1.00 25.00           C
ATOM     37  CA  ALA    37      71.207  11.546  11.403  1.00 25.00           C
ATOM     38  CA  ALA    38      68.256  13.689  12.665  1.00 25.00           C
ATOM     39  CA  HIS    39      69.444  13.991  16.307  1.00 25.00           C
ATOM     40  CA  ILE    40      70.475  10.299  16.219  1.00 25.00           C
ATOM     41  CA  SER    41      71.305   6.641  16.698  1.00 25.00           C
ATOM     42  CA  ALA    42      70.049   5.833  13.194  1.00 25.00           C
ATOM     43  CA  ILE    43      66.986   6.585  11.025  1.00 25.00           C
ATOM     44  CA  GLY    44      66.126   4.775   7.798  1.00 25.00           C
ATOM     45  CA  ALA    45      62.947   2.862   8.794  1.00 25.00           C
ATOM     46  CA  VAL    46      59.201   3.487   9.177  1.00 25.00           C
ATOM     47  CA  ARG    47      58.725  -0.174  10.083  1.00 25.00           C
ATOM     48  CA  SER    48      55.412  -0.907  11.693  1.00 25.00           C
ATOM     49  CA  ALA    49      54.826  -2.442  15.082  1.00 25.00           C
ATOM     50  CA  VAL    50      56.042  -2.911  18.658  1.00 25.00           C
ATOM     51  CA  ILE    51      57.153   0.180  20.577  1.00 25.00           C
ATOM     52  CA  GLY    52      56.956   2.697  23.357  1.00 25.00           C
ATOM     53  CA  TYR    53      56.871   3.959  26.990  1.00 25.00           C
ATOM     54  CA  TYR    54      54.010   6.299  27.988  1.00 25.00           C
ATOM     55  CA  ASP    55      52.344   7.639  31.187  1.00 25.00           C
ATOM     56  CA  GLN    56      51.880   8.851  34.732  1.00 25.00           C
ATOM     57  CA  GLU    57      48.493   7.394  35.873  1.00 25.00           C
ATOM     58  CA  LYS    58      49.806   4.632  38.188  1.00 25.00           C
ATOM     59  CA  LYS    59      50.150   2.079  35.466  1.00 25.00           C
ATOM     60  CA  GLU    60      48.893   2.008  31.831  1.00 25.00           C
ATOM     61  CA  TYR    61      49.618   2.608  28.146  1.00 25.00           C
ATOM     62  CA  VAL    62      49.746   0.048  25.336  1.00 25.00           C
ATOM     63  CA  LYS    63      51.386   0.175  21.970  1.00 25.00           C
ATOM     64  CA  LYS    64      52.559   0.815  18.428  1.00 25.00           C
ATOM     65  CA  GLU    65      55.297   2.408  16.272  1.00 25.00           C
ATOM     66  CA  LEU    66      58.725   1.094  15.215  1.00 25.00           C
ATOM     67  CA  MET    67      59.801  -2.523  14.398  1.00 25.00           C
ATOM     68  CA  GLU    68      61.011  -5.748  12.767  1.00 25.00           C
ATOM     69  CA  PRO    69      63.429  -4.654  10.039  1.00 25.00           C
ATOM     70  CA  LEU    70      63.547  -2.555   6.893  1.00 25.00           C
ATOM     71  CA  GLU    71      66.596  -0.374   7.621  1.00 25.00           C
ATOM     72  CA  ILE    72      67.946   1.130  10.826  1.00 25.00           C
ATOM     73  CA  LEU    73      65.253   0.587  13.482  1.00 25.00           C
ATOM     74  CA  SER    74      63.679  -0.003  16.948  1.00 25.00           C
ATOM     75  CA  LEU    75      61.915   2.942  18.665  1.00 25.00           C
ATOM     76  CA  SER    76      59.265   5.501  19.656  1.00 25.00           C
ATOM     77  CA  GLY    77      58.664   7.682  22.762  1.00 25.00           C
ATOM     78  CA  ASN    78      55.053   7.483  21.581  1.00 25.00           C
ATOM     79  CA  VAL    79      51.634   7.506  23.264  1.00 25.00           C
ATOM     80  CA  SER    80      48.856   4.950  23.262  1.00 25.00           C
ATOM     81  CA  MET    81      45.167   5.686  23.352  1.00 25.00           C
ATOM     82  CA  LYS    82      41.465   5.645  24.161  1.00 25.00           C
ATOM     83  CA  ASP    83      39.688   7.436  21.359  1.00 25.00           C
ATOM     84  CA  SER    84      42.448  10.095  21.653  1.00 25.00           C
ATOM     85  CA  LYS    85      46.263  10.504  21.751  1.00 25.00           C
ATOM     86  CA  PRO    86      49.825  11.796  21.418  1.00 25.00           C
ATOM     87  CA  PHE    87      52.183  10.523  18.679  1.00 25.00           C
ATOM     88  CA  CYS    88      53.457   9.857  15.150  1.00 25.00           C
ATOM     89  CA  HIS    89      56.637   7.937  14.472  1.00 25.00           C
ATOM     90  CA  ILE    90      59.704   5.757  13.641  1.00 25.00           C
ATOM     91  CA  HIS    91      63.385   5.263  14.432  1.00 25.00           C
ATOM     92  CA  VAL    92      66.245   7.021  16.227  1.00 25.00           C
ATOM     93  CA  LEU    93      67.417   3.444  17.057  1.00 25.00           C
ATOM     94  CA  LEU    94      70.419   1.246  17.880  1.00 25.00           C
ATOM     95  CA  GLY    95      72.725   1.986  14.970  1.00 25.00           C
ATOM     96  CA  LYS    96      75.774   1.752  17.209  1.00 25.00           C
ATOM     97  CA  ASP    97      75.486   0.246  20.677  1.00 25.00           C
ATOM     98  CA  GLY    98      75.537   3.784  22.010  1.00 25.00           C
ATOM     99  CA  GLU    99      72.561   4.807  24.163  1.00 25.00           C
ATOM    100  CA  VAL   100      69.816   5.007  21.576  1.00 25.00           C
ATOM    101  CA  TYR   101      68.744   8.685  21.187  1.00 25.00           C
ATOM    102  CA  GLY   102      65.180   7.398  21.289  1.00 25.00           C
ATOM    103  CA  GLY   103      62.387   9.532  19.739  1.00 25.00           C
ATOM    104  CA  HIS   104      60.710  12.917  19.023  1.00 25.00           C
ATOM    105  CA  LEU   105      57.600  10.796  18.801  1.00 25.00           C
ATOM    106  CA  PHE   106      55.805  13.775  17.194  1.00 25.00           C
ATOM    107  CA  SER   107      52.483  15.406  16.467  1.00 25.00           C
ATOM    108  CA  ALA   108      54.353  18.096  14.569  1.00 25.00           C
ATOM    109  CA  GLU   109      55.497  20.567  17.247  1.00 25.00           C
ATOM    110  CA  VAL   110      54.951  18.000  20.045  1.00 25.00           C
ATOM    111  CA  PHE   111      57.655  17.641  22.732  1.00 25.00           C
ATOM    112  CA  ALA   112      57.908  13.857  23.071  1.00 25.00           C
ATOM    113  CA  CYS   113      61.597  14.350  23.933  1.00 25.00           C
ATOM    114  CA  GLU   114      63.695  11.129  24.302  1.00 25.00           C
ATOM    115  CA  VAL   115      67.006  10.048  25.868  1.00 25.00           C
ATOM    116  CA  PHE   116      66.050   6.360  26.178  1.00 25.00           C
ATOM    117  CA  VAL   117      68.144   3.185  26.152  1.00 25.00           C
ATOM    118  CA  LEU   118      67.412   0.812  23.270  1.00 25.00           C
ATOM    119  CA  PRO   119      69.520  -1.900  24.834  1.00 25.00           C
ATOM    120  CA  LEU   120      67.843  -4.096  22.283  1.00 25.00           C
ATOM    121  CA  SER   121      68.654  -7.675  23.456  1.00 25.00           C
ATOM    122  CA  GLY   122      66.157  -9.072  25.899  1.00 25.00           C
ATOM    123  CA  GLU   123      64.049  -6.033  25.032  1.00 25.00           C
ATOM    124  CA  ALA   124      62.747  -2.466  25.438  1.00 25.00           C
ATOM    125  CA  PRO   125      63.654   0.852  26.896  1.00 25.00           C
ATOM    126  CA  GLU   126      63.514   3.552  29.535  1.00 25.00           C
ATOM    127  CA  ARG   127      61.872   6.939  29.901  1.00 25.00           C
ATOM    128  CA  ALA   128      59.214   8.689  27.761  1.00 25.00           C
ATOM    129  CA  PHE   129      58.995  11.825  29.881  1.00 25.00           C
ATOM    130  CA  ASP   130      60.357  11.786  33.432  1.00 25.00           C
ATOM    131  CA  GLU   131      60.289  12.665  37.077  1.00 25.00           C
ATOM    132  CA  GLN   132      61.535  16.198  37.335  1.00 25.00           C
ATOM    133  CA  THR   133      58.602  18.039  35.767  1.00 25.00           C
ATOM    134  CA  GLY   134      56.629  18.297  32.529  1.00 25.00           C
ATOM    135  CA  LEU   135      54.084  20.074  34.746  1.00 25.00           C
ATOM    136  CA  PHE   136      52.516  22.981  36.515  1.00 25.00           C
ATOM    137  CA  LEU   137      51.075  26.270  35.287  1.00 25.00           C
ATOM    138  CA  TRP   138      48.395  28.921  34.550  1.00 25.00           C
ATOM    139  CA  LEU   139      47.223  31.941  36.625  1.00 25.00           C
ATOM    140  CA  GLU   140      45.339  35.232  36.911  1.00 25.00           C
ATOM    141  CA  HIS   141      46.199  37.704  34.156  1.00 25.00           C
ATOM    142  CA  HIS   142      45.475  34.900  31.736  1.00 25.00           C
ATOM    143  CA  HIS   143      43.125  32.691  29.736  1.00 25.00           C
ATOM    144  CA  HIS   144      44.846  33.800  26.531  1.00 25.00           C
ATOM    145  CA  HIS   145      45.856  37.047  24.859  1.00 25.00           C
ATOM    146  CA  HIS   146      49.222  35.771  23.599  1.00 25.00           C
TER
END
