
#######################################################
#                                                     #
#                        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  141 (  141),  selected  141 , name T0357TS393_2
# Molecule2: number of CA atoms  132 ( 2030),  selected  132 , name T0357.pdb
# PARAMETERS: T0357TS393_2.T0357.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      V       2           -
LGA    V       2      K       3           -
LGA    K       3      F       4           -
LGA    F       4      A       5           -
LGA    A       5      C       6           -
LGA    C       6      R       7           -
LGA    R       7      A       8           -
LGA    A       8      I       9           -
LGA    I       9      T      10           #
LGA    T      10      R      11           #
LGA    R      11      G      12          5.044
LGA    G      12      R      13          2.578
LGA    R      13      A      14          1.935
LGA    A      14      E      15          3.003
LGA    E      15      G      16          3.316
LGA    G      16      E      17           #
LGA    E      17      -       -           -
LGA    A      18      -       -           -
LGA    L      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      -       -           -
LGA    K      22      -       -           -
LGA    E      23      -       -           -
LGA    Y      24      -       -           -
LGA    I      25      -       -           -
LGA    S      26      -       -           -
LGA    F      27      -       -           -
LGA    L      28      -       -           -
LGA    G      29      -       -           -
LGA    G      30      -       -           -
LGA    I      31      -       -           -
LGA    D      32      -       -           -
LGA    K      33      -       -           -
LGA    E      34      -       -           -
LGA    T      35      -       -           -
LGA    G      36      -       -           -
LGA    I      37      -       -           -
LGA    V      38      -       -           -
LGA    K      39      A      18          4.249
LGA    E      40      L      19          3.319
LGA    D      41      V      20           -
LGA    -       -      T      21           -
LGA    -       -      K      22           -
LGA    -       -      E      23           -
LGA    -       -      Y      24           -
LGA    -       -      I      25           -
LGA    -       -      S      26           -
LGA    -       -      F      27           -
LGA    -       -      L      28           -
LGA    -       -      G      29           -
LGA    -       -      G      30           -
LGA    -       -      I      31           -
LGA    -       -      D      32           -
LGA    -       -      K      33           -
LGA    -       -      E      34           -
LGA    -       -      T      35           -
LGA    -       -      G      36           -
LGA    -       -      I      37           -
LGA    -       -      V      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      D      41           -
LGA    -       -      C      42           -
LGA    -       -      E      43           -
LGA    -       -      I      44           -
LGA    -       -      K      45           -
LGA    -       -      G      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      V      49           -
LGA    -       -      A      50           -
LGA    C      42      G      51           #
LGA    E      43      -       -           -
LGA    I      44      -       -           -
LGA    K      45      -       -           -
LGA    G      46      -       -           -
LGA    E      47      -       -           -
LGA    S      48      -       -           -
LGA    V      49      -       -           -
LGA    A      50      -       -           -
LGA    G      51      R      52           #
LGA    R      52      I      53          3.284
LGA    I      53      L      54          2.345
LGA    L      54      V      55          3.264
LGA    V      55      F      56          1.975
LGA    F      56      P      57          2.540
LGA    P      57      G      58          3.054
LGA    G      58      G      59          5.704
LGA    G      59      K      60           #
LGA    K      60      G      61          5.103
LGA    G      61      S      62          1.461
LGA    S      62      T      63          3.623
LGA    T      63      V      64          4.697
LGA    V      64      G      65           #
LGA    G      65      -       -           -
LGA    S      66      -       -           -
LGA    Y      67      S      66           #
LGA    V      68      Y      67           #
LGA    L      69      V      68          3.870
LGA    L      70      L      69          1.783
LGA    N      71      L      70          3.054
LGA    L      72      N      71          2.409
LGA    R      73      L      72          3.822
LGA    K      74      R      73           #
LGA    N      75      K      74          3.617
LGA    G      76      -       -           -
LGA    V      77      N      75          3.862
LGA    A      78      G      76          2.441
LGA    P      79      V      77          2.842
LGA    K      80      A      78          0.767
LGA    A      81      P      79          3.624
LGA    -       -      K      80           -
LGA    I      82      A      81           #
LGA    I      83      I      82          3.607
LGA    N      84      I      83          3.705
LGA    K      85      N      84          4.334
LGA    -       -      K      85           -
LGA    K      86      K      86          5.288
LGA    T      87      T      87           #
LGA    E      88      E      88          4.855
LGA    T      89      T      89          2.767
LGA    I      90      I      90          2.197
LGA    I      91      I      91          2.514
LGA    A      92      A      92          2.835
LGA    V      93      V      93          2.416
LGA    G      94      G      94          2.094
LGA    A      95      A      95          2.079
LGA    A      96      A      96          2.226
LGA    M      97      M      97          2.208
LGA    A      98      A      98          1.616
LGA    E      99      E      99          4.193
LGA    I     100      I     100          2.207
LGA    P     101      P     101          4.073
LGA    L     102      -       -           -
LGA    V     103      -       -           -
LGA    E     104      L     102           #
LGA    V     105      V     103           #
LGA    R     106      -       -           -
LGA    D     107      -       -           -
LGA    E     108      -       -           -
LGA    K     109      -       -           -
LGA    F     110      -       -           -
LGA    F     111      E     104          3.153
LGA    E     112      V     105          2.688
LGA    A     113      R     106          5.485
LGA    V     114      D     107           #
LGA    K     115      -       -           -
LGA    T     116      E     108          3.036
LGA    G     117      K     109           -
LGA    -       -      F     110           -
LGA    -       -      F     111           -
LGA    -       -      E     112           -
LGA    -       -      A     113           -
LGA    D     118      V     114           #
LGA    R     119      -       -           -
LGA    V     120      K     115           #
LGA    V     121      T     116           -
LGA    -       -      G     117           -
LGA    -       -      D     118           -
LGA    -       -      R     119           -
LGA    V     122      V     120          3.980
LGA    N     123      V     121          2.798
LGA    -       -      V     122           -
LGA    A     124      N     123          2.894
LGA    -       -      A     124           -
LGA    D     125      D     125          3.567
LGA    E     126      E     126          3.425
LGA    G     127      G     127          3.875
LGA    Y     128      Y     128           -
LGA    V     129      V     129           -
LGA    E     130      E     130           -
LGA    L     131      L     131           -
LGA    I     132      I     132           -
LGA    E     133      E     133           -
LGA    L     134      -       -           -
LGA    E     135      -       -           -
LGA    H     136      -       -           -
LGA    H     137      -       -           -
LGA    H     138      -       -           -
LGA    H     139      -       -           -
LGA    H     140      -       -           -
LGA    H     141      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  141  132    5.0     57    3.37    38.60     24.164     1.641

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.948347 * X  +  -0.292089 * Y  +  -0.123785 * Z  +   2.608355
  Y_new =  -0.012551 * X  +  -0.355347 * Y  +   0.934650 * Z  +  -2.789101
  Z_new =  -0.316988 * X  +   0.887926 * Y  +   0.333326 * Z  +  -1.381964 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.211676   -1.929917  [ DEG:    69.4239   -110.5761 ]
  Theta =   0.322552    2.819041  [ DEG:    18.4809    161.5191 ]
  Phi   =  -3.128359    0.013234  [ DEG:  -179.2418      0.7582 ]
 
# 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: T0357TS393_2                                  
REMARK     2: T0357.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0357TS393_2.T0357.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  141  132   5.0   57   3.37   38.60  24.164
REMARK  ---------------------------------------------------------- 
MOLECULE T0357TS393_2
PFRMAT TS
TARGET T0357
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      19.090 -11.067 -13.005  1.00 25.00           C
ATOM      2  CA  VAL     2      16.244 -10.032 -10.734  1.00 25.00           C
ATOM      3  CA  LYS     3      15.876  -7.328  -8.114  1.00 25.00           C
ATOM      4  CA  PHE     4      13.065  -6.451  -5.696  1.00 25.00           C
ATOM      5  CA  ALA     5       9.393  -6.979  -6.638  1.00 25.00           C
ATOM      6  CA  CYS     6       5.672  -6.212  -6.657  1.00 25.00           C
ATOM      7  CA  ARG     7       3.661  -3.046  -5.830  1.00 25.00           C
ATOM      8  CA  ALA     8       3.568  -1.124  -2.532  1.00 25.00           C
ATOM      9  CA  ILE     9       6.434   1.368  -2.662  1.00 25.00           C
ATOM     10  CA  THR    10       8.760   4.280  -2.185  1.00 25.00           C
ATOM     11  CA  ARG    11      11.329   2.634  -4.393  1.00 25.00           C
ATOM     12  CA  GLY    12      13.970   1.024  -6.610  1.00 25.00           C
ATOM     13  CA  ARG    13      11.096  -0.835  -8.273  1.00 25.00           C
ATOM     14  CA  ALA    14       7.626  -2.083  -8.988  1.00 25.00           C
ATOM     15  CA  GLU    15       4.607  -3.616 -10.812  1.00 25.00           C
ATOM     16  CA  GLY    16       0.915  -3.838  -9.818  1.00 25.00           C
ATOM     17  CA  GLU    17      -2.770  -4.926  -9.617  1.00 25.00           C
ATOM     18  CA  ALA    18      -5.791  -4.533  -7.387  1.00 25.00           C
ATOM     19  CA  LEU    19      -7.008  -4.507  -3.724  1.00 25.00           C
ATOM     20  CA  VAL    20      -7.035  -1.630  -1.187  1.00 25.00           C
ATOM     21  CA  THR    21      -8.847  -0.778   1.981  1.00 25.00           C
ATOM     22  CA  LYS    22     -12.054   0.724   0.479  1.00 25.00           C
ATOM     23  CA  GLU    23     -15.535  -0.798   0.656  1.00 25.00           C
ATOM     24  CA  TYR    24     -14.878  -3.121  -2.285  1.00 25.00           C
ATOM     25  CA  ILE    25     -12.399  -5.197  -0.392  1.00 25.00           C
ATOM     26  CA  SER    26     -13.334  -7.780   2.213  1.00 25.00           C
ATOM     27  CA  PHE    27     -11.231 -10.357   0.314  1.00 25.00           C
ATOM     28  CA  LEU    28     -11.535 -12.716  -2.677  1.00 25.00           C
ATOM     29  CA  GLY    29     -14.839 -11.137  -3.899  1.00 25.00           C
ATOM     30  CA  GLY    30     -16.330  -7.872  -5.184  1.00 25.00           C
ATOM     31  CA  ILE    31     -12.678  -6.799  -5.204  1.00 25.00           C
ATOM     32  CA  ASP    32     -10.469  -9.326  -6.950  1.00 25.00           C
ATOM     33  CA  LYS    33      -8.199 -12.305  -7.693  1.00 25.00           C
ATOM     34  CA  GLU    34      -5.073 -11.402  -5.752  1.00 25.00           C
ATOM     35  CA  THR    35      -2.861  -8.287  -5.769  1.00 25.00           C
ATOM     36  CA  GLY    36      -1.046  -4.931  -5.239  1.00 25.00           C
ATOM     37  CA  ILE    37      -3.279  -2.187  -3.749  1.00 25.00           C
ATOM     38  CA  VAL    38      -5.046   0.670  -5.555  1.00 25.00           C
ATOM     39  CA  LYS    39      -3.460   0.105  -9.010  1.00 25.00           C
ATOM     40  CA  GLU    40      -5.293   0.445 -12.325  1.00 25.00           C
ATOM     41  CA  ASP    41      -4.614  -1.747 -15.369  1.00 25.00           C
ATOM     42  CA  CYS    42      -0.959  -1.881 -14.430  1.00 25.00           C
ATOM     43  CA  GLU    43       0.286   0.265 -17.258  1.00 25.00           C
ATOM     44  CA  ILE    44      -0.071   3.753 -15.818  1.00 25.00           C
ATOM     45  CA  LYS    45       0.302   6.042 -18.792  1.00 25.00           C
ATOM     46  CA  GLY    46       4.127   5.796 -19.083  1.00 25.00           C
ATOM     47  CA  GLU    47       4.517   8.519 -16.405  1.00 25.00           C
ATOM     48  CA  SER    48       2.681   9.533 -13.232  1.00 25.00           C
ATOM     49  CA  VAL    49       2.845   7.740  -9.850  1.00 25.00           C
ATOM     50  CA  ALA    50       4.694   5.142 -11.938  1.00 25.00           C
ATOM     51  CA  GLY    51       4.383   1.387 -11.686  1.00 25.00           C
ATOM     52  CA  ARG    52       1.262   2.224  -9.587  1.00 25.00           C
ATOM     53  CA  ILE    53       0.570   1.008  -6.056  1.00 25.00           C
ATOM     54  CA  LEU    54       0.167   1.942  -2.386  1.00 25.00           C
ATOM     55  CA  VAL    55      -3.388   1.949  -0.895  1.00 25.00           C
ATOM     56  CA  PHE    56      -5.941   3.374   1.548  1.00 25.00           C
ATOM     57  CA  PRO    57      -4.463   5.437   4.358  1.00 25.00           C
ATOM     58  CA  GLY    58      -4.226   3.360   7.519  1.00 25.00           C
ATOM     59  CA  GLY    59      -4.552   0.110   5.593  1.00 25.00           C
ATOM     60  CA  LYS    60      -5.981  -1.851   8.492  1.00 25.00           C
ATOM     61  CA  GLY    61      -6.763  -4.984  10.521  1.00 25.00           C
ATOM     62  CA  SER    62      -5.691  -8.390   9.292  1.00 25.00           C
ATOM     63  CA  THR    63      -5.506  -7.188   5.636  1.00 25.00           C
ATOM     64  CA  VAL    64      -5.060  -4.444   3.060  1.00 25.00           C
ATOM     65  CA  GLY    65      -5.761  -7.152   0.444  1.00 25.00           C
ATOM     66  CA  SER    66      -2.232  -6.723  -0.982  1.00 25.00           C
ATOM     67  CA  TYR    67      -0.749  -7.028   2.536  1.00 25.00           C
ATOM     68  CA  VAL    68      -2.784 -10.213   3.146  1.00 25.00           C
ATOM     69  CA  LEU    69      -1.553 -11.666  -0.178  1.00 25.00           C
ATOM     70  CA  LEU    70       2.064 -10.838   0.774  1.00 25.00           C
ATOM     71  CA  ASN    71       1.584 -12.536   4.173  1.00 25.00           C
ATOM     72  CA  LEU    72       0.142 -15.637   2.447  1.00 25.00           C
ATOM     73  CA  ARG    73       3.131 -15.726   0.055  1.00 25.00           C
ATOM     74  CA  LYS    74       5.543 -15.458   3.017  1.00 25.00           C
ATOM     75  CA  ASN    75       8.034 -16.760   0.398  1.00 25.00           C
ATOM     76  CA  GLY    76       6.927 -16.535  -3.278  1.00 25.00           C
ATOM     77  CA  VAL    77       5.243 -13.247  -4.036  1.00 25.00           C
ATOM     78  CA  ALA    78       5.548 -11.229  -7.280  1.00 25.00           C
ATOM     79  CA  PRO    79       2.157  -9.656  -7.782  1.00 25.00           C
ATOM     80  CA  LYS    80       1.940  -9.257  -4.023  1.00 25.00           C
ATOM     81  CA  ALA    81       2.712  -6.137  -1.957  1.00 25.00           C
ATOM     82  CA  ILE    82       0.429  -3.371  -0.599  1.00 25.00           C
ATOM     83  CA  ILE    83       0.513  -0.349   1.753  1.00 25.00           C
ATOM     84  CA  ASN    84       1.992   3.027   2.705  1.00 25.00           C
ATOM     85  CA  LYS    85       0.522   4.347   5.975  1.00 25.00           C
ATOM     86  CA  LYS    86       0.566   3.336   9.701  1.00 25.00           C
ATOM     87  CA  THR    87       3.660   1.106   9.917  1.00 25.00           C
ATOM     88  CA  GLU    88       2.442  -1.394  12.538  1.00 25.00           C
ATOM     89  CA  THR    89      -1.142  -1.384  11.262  1.00 25.00           C
ATOM     90  CA  ILE    90      -1.674  -5.000  10.115  1.00 25.00           C
ATOM     91  CA  ILE    91      -1.628  -3.872   6.455  1.00 25.00           C
ATOM     92  CA  ALA    92       1.621  -1.938   7.066  1.00 25.00           C
ATOM     93  CA  VAL    93       3.180  -5.028   8.707  1.00 25.00           C
ATOM     94  CA  GLY    94       2.122  -7.178   5.719  1.00 25.00           C
ATOM     95  CA  ALA    95       3.663  -4.632   3.309  1.00 25.00           C
ATOM     96  CA  ALA    96       6.918  -4.656   5.326  1.00 25.00           C
ATOM     97  CA  MET    97       6.979  -8.484   5.229  1.00 25.00           C
ATOM     98  CA  ALA    98       6.436  -8.421   1.439  1.00 25.00           C
ATOM     99  CA  GLU    99       7.282  -8.236  -2.264  1.00 25.00           C
ATOM    100  CA  ILE   100       7.465  -4.474  -2.492  1.00 25.00           C
ATOM    101  CA  PRO   101      10.314  -2.114  -3.163  1.00 25.00           C
ATOM    102  CA  LEU   102      10.899   0.491  -0.387  1.00 25.00           C
ATOM    103  CA  VAL   103      11.042   0.469   3.372  1.00 25.00           C
ATOM    104  CA  GLU   104       9.626   1.660   6.690  1.00 25.00           C
ATOM    105  CA  VAL   105       7.922   4.262   8.906  1.00 25.00           C
ATOM    106  CA  ARG   106       4.725   6.169   8.589  1.00 25.00           C
ATOM    107  CA  ASP   107       3.059   8.477  11.075  1.00 25.00           C
ATOM    108  CA  GLU   108       1.497   9.986   7.980  1.00 25.00           C
ATOM    109  CA  LYS   109       4.242  11.613   5.854  1.00 25.00           C
ATOM    110  CA  PHE   110       4.160   8.599   3.494  1.00 25.00           C
ATOM    111  CA  PHE   111       0.350   8.880   3.229  1.00 25.00           C
ATOM    112  CA  GLU   112       0.656  12.615   2.436  1.00 25.00           C
ATOM    113  CA  ALA   113       3.261  11.854  -0.266  1.00 25.00           C
ATOM    114  CA  VAL   114       0.950   9.201  -1.779  1.00 25.00           C
ATOM    115  CA  LYS   115      -1.951  11.700  -1.794  1.00 25.00           C
ATOM    116  CA  THR   116      -5.681  11.990  -1.174  1.00 25.00           C
ATOM    117  CA  GLY   117      -5.791   8.212  -1.603  1.00 25.00           C
ATOM    118  CA  ASP   118      -5.660   5.511  -4.200  1.00 25.00           C
ATOM    119  CA  ARG   119      -4.362   4.967  -7.683  1.00 25.00           C
ATOM    120  CA  VAL   120      -0.980   5.397  -5.999  1.00 25.00           C
ATOM    121  CA  VAL   121       2.483   5.464  -4.436  1.00 25.00           C
ATOM    122  CA  VAL   122       5.356   4.169  -6.586  1.00 25.00           C
ATOM    123  CA  ASN   123       8.743   5.769  -6.488  1.00 25.00           C
ATOM    124  CA  ALA   124      11.760   7.404  -4.868  1.00 25.00           C
ATOM    125  CA  ASP   125      13.672   6.761  -1.598  1.00 25.00           C
ATOM    126  CA  GLU   126      12.910   5.399   1.918  1.00 25.00           C
ATOM    127  CA  GLY   127       9.222   5.000   2.755  1.00 25.00           C
ATOM    128  CA  TYR   128       7.080   1.894   2.302  1.00 25.00           C
ATOM    129  CA  VAL   129       7.717  -1.780   1.720  1.00 25.00           C
ATOM    130  CA  GLU   130      10.608  -4.236   1.838  1.00 25.00           C
ATOM    131  CA  LEU   131      11.770  -7.165  -0.291  1.00 25.00           C
ATOM    132  CA  ILE   132      11.242 -10.167   1.963  1.00 25.00           C
ATOM    133  CA  GLU   133      14.343 -11.857   3.348  1.00 25.00           C
ATOM    134  CA  LEU   134      17.267 -13.494   5.239  1.00 25.00           C
ATOM    135  CA  GLU   135      20.165 -15.494   6.674  1.00 25.00           C
ATOM    136  CA  HIS   136      23.653 -14.079   7.291  1.00 25.00           C
ATOM    137  CA  HIS   137      26.155 -16.763   6.365  1.00 25.00           C
ATOM    138  CA  HIS   138      28.109 -15.235   3.445  1.00 25.00           C
ATOM    139  CA  HIS   139      27.938 -17.665   0.523  1.00 25.00           C
ATOM    140  CA  HIS   140      30.502 -20.461   0.508  1.00 25.00           C
ATOM    141  CA  HIS   141      31.774 -23.968   1.417  1.00 25.00           C
TER
END
