
#######################################################
#                                                     #
#                        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  125 (  125),  selected  125 , name T0285TS393_4
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS393_4.T0285.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      -       -           -
LGA    Y       2      -       -           -
LGA    L       3      -       -           -
LGA    P       4      -       -           -
LGA    D       5      -       -           -
LGA    D       6      -       -           -
LGA    S       7      -       -           -
LGA    P       8      -       -           -
LGA    A       9      -       -           -
LGA    K      10      -       -           -
LGA    R      11      -       -           -
LGA    L      12      -       -           -
LGA    L      13      -       -           -
LGA    F      14      -       -           -
LGA    Q      15      -       -           -
LGA    M      16      -       -           -
LGA    V      17      -       -           -
LGA    G      18      -       -           -
LGA    N      19      -       -           -
LGA    A      20      -       -           -
LGA    I      21      -       -           -
LGA    N      22      S       7          4.405
LGA    R      23      P       8          2.528
LGA    -       -      A       9           -
LGA    N      24      K      10           #
LGA    T      25      R      11           -
LGA    Q      26      -       -           -
LGA    Q      27      -       -           -
LGA    L      28      -       -           -
LGA    T      29      -       -           -
LGA    Q      30      -       -           -
LGA    D      31      -       -           -
LGA    L      32      -       -           -
LGA    R      33      -       -           -
LGA    A      34      -       -           -
LGA    M      35      -       -           -
LGA    P      36      -       -           -
LGA    N      37      -       -           -
LGA    W      38      -       -           -
LGA    S      39      L      12           #
LGA    L      40      L      13           #
LGA    R      41      F      14           #
LGA    -       -      Q      15           -
LGA    -       -      M      16           -
LGA    F      42      V      17          4.367
LGA    V      43      G      18           #
LGA    Y      44      N      19           -
LGA    I      45      A      20          4.044
LGA    V      46      I      21          3.931
LGA    D      47      N      22          4.110
LGA    R      48      R      23          3.673
LGA    -       -      N      24           -
LGA    -       -      T      25           -
LGA    -       -      Q      26           -
LGA    N      49      Q      27          2.769
LGA    -       -      L      28           -
LGA    -       -      T      29           -
LGA    -       -      Q      30           -
LGA    N      50      D      31          1.867
LGA    -       -      L      32           -
LGA    Q      51      R      33          4.350
LGA    D      52      A      34          4.554
LGA    L      53      -       -           -
LGA    L      54      -       -           -
LGA    K      55      -       -           -
LGA    R      56      M      35           #
LGA    P      57      P      36          2.357
LGA    L      58      N      37          4.292
LGA    P      59      W      38          2.546
LGA    -       -      S      39           -
LGA    -       -      L      40           -
LGA    P      60      R      41          2.172
LGA    G      61      F      42          3.198
LGA    I      62      V      43          2.169
LGA    M      63      Y      44          3.438
LGA    V      64      I      45          5.216
LGA    L      65      V      46          2.487
LGA    A      66      -       -           -
LGA    P      67      D      47          3.114
LGA    R      68      R      48          2.756
LGA    L      69      -       -           -
LGA    T      70      -       -           -
LGA    A      71      -       -           -
LGA    K      72      -       -           -
LGA    H      73      -       -           -
LGA    P      74      -       -           -
LGA    Y      75      -       -           -
LGA    D      76      N      49          3.482
LGA    K      77      N      50          3.688
LGA    V      78      Q      51           #
LGA    Q      79      D      52           -
LGA    D      80      L      53           -
LGA    R      81      -       -           -
LGA    N      82      -       -           -
LGA    R      83      -       -           -
LGA    K      84      L      54           #
LGA    L      85      K      55          2.827
LGA    Y      86      R      56          4.360
LGA    -       -      P      57           -
LGA    G      87      L      58          2.597
LGA    R      88      P      59          4.473
LGA    H      89      P      60           -
LGA    I      90      G      61           #
LGA    T      91      I      62          4.963
LGA    -       -      M      63           -
LGA    -       -      V      64           -
LGA    -       -      L      65           -
LGA    -       -      A      66           -
LGA    -       -      P      67           -
LGA    -       -      R      68           -
LGA    -       -      L      69           -
LGA    -       -      T      70           -
LGA    -       -      A      71           -
LGA    -       -      K      72           -
LGA    -       -      H      73           -
LGA    -       -      P      74           -
LGA    -       -      Y      75           -
LGA    -       -      D      76           -
LGA    L      92      K      77          3.718
LGA    N      93      V      78          1.468
LGA    D      94      Q      79          5.227
LGA    G      95      D      80           -
LGA    N      96      R      81           -
LGA    S      97      N      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    V      98      L      85           #
LGA    K      99      -       -           -
LGA    V     100      Y      86          4.616
LGA    V     101      G      87          3.016
LGA    T     102      R      88           #
LGA    I     103      H      89           -
LGA    S     104      I      90           -
LGA    A     105      T      91           -
LGA    G     106      L      92           -
LGA    R     107      N      93           -
LGA    D     108      D      94           -
LGA    E     109      G      95           -
LGA    G     110      N      96           -
LGA    P     111      S      97           -
LGA    D     112      V      98           -
LGA    R     113      K      99           -
LGA    D     114      V     100           -
LGA    I     115      V     101           -
LGA    I     116      T     102           -
LGA    W     117      I     103           -
LGA    E     118      S     104           -
LGA    M     119      A     105           -
LGA    F     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    N     123      -       -           -
LGA    L     124      -       -           -
LGA    E     125      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  125   99    5.0     34    3.63     8.82     18.598     0.911

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.715089 * X  +  -0.429125 * Y  +  -0.551815 * Z  +  16.134560
  Y_new =   0.246998 * X  +   0.893587 * Y  +  -0.374827 * Z  +  10.455503
  Z_new =   0.653942 * X  +   0.131737 * Y  +   0.744987 * Z  +  79.382416 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.175022   -2.966570  [ DEG:    10.0280   -169.9720 ]
  Theta =  -0.712783   -2.428810  [ DEG:   -40.8394   -139.1606 ]
  Phi   =   0.332579   -2.809014  [ DEG:    19.0553   -160.9447 ]
 
# 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: T0285TS393_4                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS393_4.T0285.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  125   99   5.0   34   3.63    8.82  18.598
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS393_4
PFRMAT TS
TARGET T0285
MODEL 4
PARENT N/A
ATOM      1  CA  ALA     1      -4.093   5.397  60.259  1.00 25.00           C
ATOM      2  CA  TYR     2      -2.147   2.524  61.728  1.00 25.00           C
ATOM      3  CA  LEU     3       0.453   3.731  64.204  1.00 25.00           C
ATOM      4  CA  PRO     4       2.718   4.806  61.383  1.00 25.00           C
ATOM      5  CA  ASP     5       5.061   7.129  59.419  1.00 25.00           C
ATOM      6  CA  ASP     6       8.089   5.336  61.000  1.00 25.00           C
ATOM      7  CA  SER     7       9.956   7.533  63.542  1.00 25.00           C
ATOM      8  CA  PRO     8      12.256   7.889  66.587  1.00 25.00           C
ATOM      9  CA  ALA     9      14.884  10.658  66.277  1.00 25.00           C
ATOM     10  CA  LYS    10      12.469  13.162  67.880  1.00 25.00           C
ATOM     11  CA  ARG    11      11.801  10.717  70.751  1.00 25.00           C
ATOM     12  CA  LEU    12      15.568  10.256  71.268  1.00 25.00           C
ATOM     13  CA  LEU    13      16.048  14.055  71.334  1.00 25.00           C
ATOM     14  CA  PHE    14      13.236  14.390  73.911  1.00 25.00           C
ATOM     15  CA  GLN    15      14.853  11.669  76.067  1.00 25.00           C
ATOM     16  CA  MET    16      18.225  13.473  75.858  1.00 25.00           C
ATOM     17  CA  VAL    17      16.557  16.762  76.891  1.00 25.00           C
ATOM     18  CA  GLY    18      14.886  15.009  79.859  1.00 25.00           C
ATOM     19  CA  ASN    19      18.254  13.523  80.911  1.00 25.00           C
ATOM     20  CA  ALA    20      19.877  16.985  80.696  1.00 25.00           C
ATOM     21  CA  ILE    21      17.065  18.463  82.835  1.00 25.00           C
ATOM     22  CA  ASN    22      17.540  15.682  85.425  1.00 25.00           C
ATOM     23  CA  ARG    23      21.308  16.364  85.503  1.00 25.00           C
ATOM     24  CA  ASN    24      20.645  20.103  86.003  1.00 25.00           C
ATOM     25  CA  THR    25      18.228  19.316  88.868  1.00 25.00           C
ATOM     26  CA  GLN    26      20.851  17.044  90.489  1.00 25.00           C
ATOM     27  CA  GLN    27      23.477  19.814  90.178  1.00 25.00           C
ATOM     28  CA  LEU    28      21.064  22.318  91.782  1.00 25.00           C
ATOM     29  CA  THR    29      20.396  19.873  94.653  1.00 25.00           C
ATOM     30  CA  GLN    30      24.163  19.412  95.170  1.00 25.00           C
ATOM     31  CA  ASP    31      24.643  23.211  95.235  1.00 25.00           C
ATOM     32  CA  LEU    32      21.831  23.546  97.813  1.00 25.00           C
ATOM     33  CA  ARG    33      23.448  20.825  99.969  1.00 25.00           C
ATOM     34  CA  ALA    34      26.070  18.118  99.648  1.00 25.00           C
ATOM     35  CA  MET    35      27.829  16.308  96.794  1.00 25.00           C
ATOM     36  CA  PRO    36      29.984  16.254  93.630  1.00 25.00           C
ATOM     37  CA  ASN    37      30.447  16.936  89.922  1.00 25.00           C
ATOM     38  CA  TRP    38      26.846  15.960  89.011  1.00 25.00           C
ATOM     39  CA  SER    39      26.094  14.256  85.678  1.00 25.00           C
ATOM     40  CA  LEU    40      23.551  12.288  83.653  1.00 25.00           C
ATOM     41  CA  ARG    41      22.457  10.388  80.602  1.00 25.00           C
ATOM     42  CA  PHE    42      20.358   9.236  77.694  1.00 25.00           C
ATOM     43  CA  VAL    43      17.473   6.770  77.983  1.00 25.00           C
ATOM     44  CA  TYR    44      18.809   3.453  76.679  1.00 25.00           C
ATOM     45  CA  ILE    45      21.224   5.232  74.417  1.00 25.00           C
ATOM     46  CA  VAL    46      18.191   5.890  72.147  1.00 25.00           C
ATOM     47  CA  ASP    47      20.607   5.606  69.189  1.00 25.00           C
ATOM     48  CA  ARG    48      24.187   4.305  69.736  1.00 25.00           C
ATOM     49  CA  ASN    49      27.685   3.916  68.368  1.00 25.00           C
ATOM     50  CA  ASN    50      28.601   5.591  71.723  1.00 25.00           C
ATOM     51  CA  GLN    51      31.256   5.309  74.467  1.00 25.00           C
ATOM     52  CA  ASP    52      33.266   8.137  72.848  1.00 25.00           C
ATOM     53  CA  LEU    53      30.120  10.314  72.686  1.00 25.00           C
ATOM     54  CA  LEU    54      29.410   9.605  76.382  1.00 25.00           C
ATOM     55  CA  LYS    55      32.812  10.598  77.849  1.00 25.00           C
ATOM     56  CA  ARG    56      33.521  13.403  80.231  1.00 25.00           C
ATOM     57  CA  PRO    57      34.988  10.591  82.406  1.00 25.00           C
ATOM     58  CA  LEU    58      31.371  10.276  83.536  1.00 25.00           C
ATOM     59  CA  PRO    59      32.013   7.440  85.990  1.00 25.00           C
ATOM     60  CA  PRO    60      29.222   6.613  88.348  1.00 25.00           C
ATOM     61  CA  GLY    61      27.148   8.603  85.885  1.00 25.00           C
ATOM     62  CA  ILE    62      23.411   7.763  85.817  1.00 25.00           C
ATOM     63  CA  MET    63      20.023   7.045  84.200  1.00 25.00           C
ATOM     64  CA  VAL    64      16.675   5.665  82.863  1.00 25.00           C
ATOM     65  CA  LEU    65      17.479   2.178  81.548  1.00 25.00           C
ATOM     66  CA  ALA    66      14.555   2.431  79.124  1.00 25.00           C
ATOM     67  CA  PRO    67      14.904  -0.249  76.477  1.00 25.00           C
ATOM     68  CA  ARG    68      13.646  -2.654  79.163  1.00 25.00           C
ATOM     69  CA  LEU    69       9.964  -2.521  80.049  1.00 25.00           C
ATOM     70  CA  THR    70       7.185  -5.132  80.292  1.00 25.00           C
ATOM     71  CA  ALA    71       4.542  -3.940  82.828  1.00 25.00           C
ATOM     72  CA  LYS    72       5.212  -7.025  85.013  1.00 25.00           C
ATOM     73  CA  HIS    73       7.342  -4.518  86.943  1.00 25.00           C
ATOM     74  CA  PRO    74      10.269  -5.776  84.794  1.00 25.00           C
ATOM     75  CA  TYR    75      10.631  -8.638  82.315  1.00 25.00           C
ATOM     76  CA  ASP    76      13.392 -10.527  80.449  1.00 25.00           C
ATOM     77  CA  LYS    77      16.007  -8.060  81.769  1.00 25.00           C
ATOM     78  CA  VAL    78      14.683  -8.526  85.333  1.00 25.00           C
ATOM     79  CA  GLN    79      14.873 -12.331  84.932  1.00 25.00           C
ATOM     80  CA  ASP    80      18.477 -12.042  83.664  1.00 25.00           C
ATOM     81  CA  ARG    81      18.937 -15.825  83.690  1.00 25.00           C
ATOM     82  CA  ASN    82      21.025 -15.379  80.576  1.00 25.00           C
ATOM     83  CA  ARG    83      22.483 -12.216  79.153  1.00 25.00           C
ATOM     84  CA  LYS    84      25.116 -10.591  81.343  1.00 25.00           C
ATOM     85  CA  LEU    85      23.242  -7.424  82.171  1.00 25.00           C
ATOM     86  CA  TYR    86      21.987  -5.720  85.379  1.00 25.00           C
ATOM     87  CA  GLY    87      19.912  -3.017  87.145  1.00 25.00           C
ATOM     88  CA  ARG    88      19.585   0.759  87.469  1.00 25.00           C
ATOM     89  CA  HIS    89      15.961   1.682  86.637  1.00 25.00           C
ATOM     90  CA  ILE    90      17.122   5.101  87.853  1.00 25.00           C
ATOM     91  CA  THR    91      14.690   7.919  88.493  1.00 25.00           C
ATOM     92  CA  LEU    92      13.030  11.319  89.225  1.00 25.00           C
ATOM     93  CA  ASN    93       9.988  11.868  91.430  1.00 25.00           C
ATOM     94  CA  ASP    94       7.248  14.239  92.599  1.00 25.00           C
ATOM     95  CA  GLY    95       4.128  14.249  90.336  1.00 25.00           C
ATOM     96  CA  ASN    96       2.896  11.228  88.366  1.00 25.00           C
ATOM     97  CA  SER    97       6.264   9.500  88.367  1.00 25.00           C
ATOM     98  CA  VAL    98       9.182   8.417  86.203  1.00 25.00           C
ATOM     99  CA  LYS    99       9.227  10.512  83.042  1.00 25.00           C
ATOM    100  CA  VAL   100      12.498   9.127  81.747  1.00 25.00           C
ATOM    101  CA  VAL   101      14.991  10.984  83.957  1.00 25.00           C
ATOM    102  CA  THR   102      12.800  14.060  84.032  1.00 25.00           C
ATOM    103  CA  ILE   103      12.164  17.431  82.280  1.00 25.00           C
ATOM    104  CA  SER   104      13.226  19.710  79.444  1.00 25.00           C
ATOM    105  CA  ALA   105      14.356  21.517  76.247  1.00 25.00           C
ATOM    106  CA  GLY   106      16.069  23.772  73.647  1.00 25.00           C
ATOM    107  CA  ARG   107      16.783  27.457  74.012  1.00 25.00           C
ATOM    108  CA  ASP   108      15.877  30.959  72.747  1.00 25.00           C
ATOM    109  CA  GLU   109      18.712  31.903  70.446  1.00 25.00           C
ATOM    110  CA  GLY   110      16.849  31.858  67.150  1.00 25.00           C
ATOM    111  CA  PRO   111      14.003  31.372  64.649  1.00 25.00           C
ATOM    112  CA  ASP   112      11.068  28.901  64.640  1.00 25.00           C
ATOM    113  CA  ARG   113      11.722  26.610  67.638  1.00 25.00           C
ATOM    114  CA  ASP   114       9.058  28.845  69.244  1.00 25.00           C
ATOM    115  CA  ILE   115       6.547  27.841  66.532  1.00 25.00           C
ATOM    116  CA  ILE   116       7.342  24.143  67.130  1.00 25.00           C
ATOM    117  CA  TRP   117       6.834  24.619  70.896  1.00 25.00           C
ATOM    118  CA  GLU   118       3.474  26.340  70.252  1.00 25.00           C
ATOM    119  CA  MET   119       2.406  23.454  67.971  1.00 25.00           C
ATOM    120  CA  PHE   120       3.395  20.923  70.670  1.00 25.00           C
ATOM    121  CA  LEU   121       1.377  22.875  73.274  1.00 25.00           C
ATOM    122  CA  GLU   122      -1.653  22.915  70.932  1.00 25.00           C
ATOM    123  CA  ASN   123      -1.325  19.137  70.403  1.00 25.00           C
ATOM    124  CA  LEU   124      -2.657  17.848  73.730  1.00 25.00           C
ATOM    125  CA  GLU   125      -5.822  19.767  73.125  1.00 25.00           C
TER
END
