
#######################################################
#                                                     #
#                        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  122 (  122),  selected  122 , name T0342TS393_2-D1
# Molecule2: number of CA atoms  122 (  967),  selected  122 , name T0342_D1.pdb
# PARAMETERS: T0342TS393_2-D1.T0342_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E      14      E      14           -
LGA    E      15      E      15           -
LGA    S      16      S      16           -
LGA    F      17      F      17           -
LGA    L      18      -       -           -
LGA    Y      19      -       -           -
LGA    F      20      L      18           #
LGA    -       -      Y      19           -
LGA    A      21      F      20          1.021
LGA    Y      22      A      21           #
LGA    G      23      -       -           -
LGA    S      24      Y      22          4.148
LGA    N      25      G      23          4.343
LGA    L      26      S      24          4.779
LGA    L      27      N      25           #
LGA    T      28      L      26          3.621
LGA    E      29      L      27           #
LGA    R      30      T      28          4.453
LGA    I      31      E      29           -
LGA    H      32      R      30           -
LGA    -       -      I      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      S      37           -
LGA    -       -      A      38           -
LGA    L      33      A      39           #
LGA    R      34      F      40          0.688
LGA    N      35      F      41           #
LGA    P      36      C      42           -
LGA    S      37      V      43           -
LGA    A      38      A      44           -
LGA    A      39      R      45           -
LGA    F      40      -       -           -
LGA    F      41      -       -           -
LGA    C      42      -       -           -
LGA    V      43      -       -           -
LGA    A      44      -       -           -
LGA    R      45      -       -           -
LGA    L      46      -       -           -
LGA    Q      47      -       -           -
LGA    D      48      -       -           -
LGA    F      49      -       -           -
LGA    K      50      -       -           -
LGA    L      51      -       -           -
LGA    D      52      -       -           -
LGA    F      53      -       -           -
LGA    G      54      -       -           -
LGA    N      55      L      46           #
LGA    S      56      Q      47           -
LGA    -       -      D      48           -
LGA    -       -      F      49           -
LGA    Q      57      K      50          2.498
LGA    -       -      L      51           -
LGA    -       -      D      52           -
LGA    -       -      F      53           -
LGA    -       -      G      54           -
LGA    -       -      N      55           -
LGA    -       -      S      56           -
LGA    -       -      Q      57           -
LGA    -       -      G      58           -
LGA    -       -      K      59           -
LGA    -       -      T      60           -
LGA    -       -      S      61           -
LGA    -       -      Q      62           -
LGA    -       -      T      63           -
LGA    -       -      W      64           -
LGA    -       -      H      65           -
LGA    -       -      G      66           -
LGA    -       -      G      67           -
LGA    -       -      I      68           -
LGA    -       -      A      69           -
LGA    -       -      T      70           -
LGA    -       -      I      71           -
LGA    -       -      F      72           -
LGA    G      58      Q      73           #
LGA    K      59      S      74          3.499
LGA    -       -      P      75           -
LGA    T      60      G      76          5.033
LGA    S      61      D      77          4.624
LGA    Q      62      E      78           #
LGA    T      63      -       -           -
LGA    W      64      V      79          5.135
LGA    H      65      W      80          3.181
LGA    G      66      G      81          3.405
LGA    G      67      V      82          2.641
LGA    I      68      -       -           -
LGA    A      69      -       -           -
LGA    T      70      -       -           -
LGA    I      71      -       -           -
LGA    F      72      -       -           -
LGA    Q      73      -       -           -
LGA    S      74      -       -           -
LGA    P      75      -       -           -
LGA    G      76      -       -           -
LGA    D      77      -       -           -
LGA    E      78      -       -           -
LGA    V      79      -       -           -
LGA    W      80      -       -           -
LGA    G      81      -       -           -
LGA    V      82      -       -           -
LGA    V      83      V      83          1.287
LGA    W      84      W      84          0.856
LGA    K      85      K      85          2.355
LGA    M      86      M      86          1.400
LGA    N      87      N      87          3.122
LGA    K      88      K      88          2.265
LGA    S      89      S      89          1.970
LGA    N      90      N      90          0.945
LGA    L      91      L      91          1.000
LGA    N      92      N      92          1.008
LGA    S      93      S      93          0.944
LGA    L      94      L      94          1.286
LGA    D      95      D      95          1.882
LGA    E      96      E      96          2.415
LGA    Q      97      Q      97          2.579
LGA    E      98      E      98           #
LGA    G      99      -       -           -
LGA    V     100      G      99          2.068
LGA    K     101      V     100          0.775
LGA    S     102      K     101          4.637
LGA    -       -      S     102           -
LGA    -       -      G     103           -
LGA    -       -      M     104           -
LGA    G     103      Y     105           #
LGA    M     104      V     106          1.701
LGA    Y     105      V     107          2.587
LGA    V     106      I     108          2.414
LGA    V     107      E     109          2.617
LGA    I     108      V     110          3.976
LGA    E     109      K     111           -
LGA    -       -      V     112           -
LGA    -       -      A     113           -
LGA    -       -      T     114           -
LGA    -       -      Q     115           -
LGA    -       -      E     116           -
LGA    -       -      G     117           -
LGA    -       -      K     118           -
LGA    -       -      E     119           -
LGA    V     110      I     120          4.975
LGA    K     111      T     121          3.465
LGA    V     112      -       -           -
LGA    A     113      -       -           -
LGA    T     114      -       -           -
LGA    Q     115      -       -           -
LGA    E     116      -       -           -
LGA    G     117      -       -           -
LGA    K     118      -       -           -
LGA    E     119      -       -           -
LGA    I     120      -       -           -
LGA    T     121      -       -           -
LGA    C     122      -       -           -
LGA    R     123      -       -           -
LGA    S     124      C     122          3.694
LGA    Y     125      R     123          2.030
LGA    L     126      S     124          3.161
LGA    M     127      Y     125          3.936
LGA    T     128      L     126          1.515
LGA    N     129      M     127          3.029
LGA    Y     130      T     128           #
LGA    E     131      -       -           -
LGA    S     132      N     129          4.912
LGA    A     133      -       -           -
LGA    P     134      -       -           -
LGA    P     135      Y     130          1.780
LGA    -       -      E     131           -
LGA    -       -      S     132           -
LGA    -       -      A     133           -
LGA    -       -      P     134           -
LGA    -       -      P     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  122    5.0     48    3.05    33.33     23.864     1.523

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.694020 * X  +  -0.369583 * Y  +  -0.617855 * Z  +  -0.646806
  Y_new =   0.549519 * X  +   0.282530 * Y  +  -0.786261 * Z  +  84.732712
  Z_new =   0.465151 * X  +  -0.885204 * Y  +   0.007011 * Z  +   1.323016 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.562876    1.578717  [ DEG:   -89.5462     90.4538 ]
  Theta =  -0.483805   -2.657788  [ DEG:   -27.7200   -152.2800 ]
  Phi   =   2.471877   -0.669716  [ DEG:   141.6281    -38.3719 ]
 
# 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: T0342TS393_2-D1                               
REMARK     2: T0342_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0342TS393_2-D1.T0342_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  122  122   5.0   48   3.05   33.33  23.864
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS393_2-D1
PFRMAT TS
TARGET T0342
MODEL 2
PARENT N/A
ATOM     14  CA  GLU    14       2.970  73.572   5.170  1.00 25.00           C
ATOM     15  CA  GLU    15       2.184  76.120   2.397  1.00 25.00           C
ATOM     16  CA  SER    16      -0.968  76.907   0.421  1.00 25.00           C
ATOM     17  CA  PHE    17      -2.435  80.352  -0.254  1.00 25.00           C
ATOM     18  CA  LEU    18      -1.523  83.796  -1.413  1.00 25.00           C
ATOM     19  CA  TYR    19      -0.482  85.250   1.923  1.00 25.00           C
ATOM     20  CA  PHE    20       3.146  85.587   0.740  1.00 25.00           C
ATOM     21  CA  ALA    21       5.870  88.258   0.954  1.00 25.00           C
ATOM     22  CA  TYR    22       6.787  91.995   0.640  1.00 25.00           C
ATOM     23  CA  GLY    23      10.381  92.772   1.647  1.00 25.00           C
ATOM     24  CA  SER    24       9.412  90.475   4.523  1.00 25.00           C
ATOM     25  CA  ASN    25       6.009  90.460   6.175  1.00 25.00           C
ATOM     26  CA  LEU    26       3.815  89.922   9.254  1.00 25.00           C
ATOM     27  CA  LEU    27       5.982  86.863   9.812  1.00 25.00           C
ATOM     28  CA  THR    28       8.501  84.585   8.060  1.00 25.00           C
ATOM     29  CA  GLU    29       9.852  81.045   8.616  1.00 25.00           C
ATOM     30  CA  ARG    30       6.735  79.569   6.951  1.00 25.00           C
ATOM     31  CA  ILE    31       7.179  81.930   3.969  1.00 25.00           C
ATOM     32  CA  HIS    32      10.854  80.895   3.666  1.00 25.00           C
ATOM     33  CA  LEU    33       9.846  77.201   3.748  1.00 25.00           C
ATOM     34  CA  ARG    34       7.234  77.827   1.018  1.00 25.00           C
ATOM     35  CA  ASN    35       6.731  74.024   1.357  1.00 25.00           C
ATOM     36  CA  PRO    36       3.773  71.979   0.012  1.00 25.00           C
ATOM     37  CA  SER    37       0.260  71.575   1.440  1.00 25.00           C
ATOM     38  CA  ALA    38      -2.232  73.253   3.835  1.00 25.00           C
ATOM     39  CA  ALA    39      -2.036  76.656   5.524  1.00 25.00           C
ATOM     40  CA  PHE    40      -0.382  79.920   4.454  1.00 25.00           C
ATOM     41  CA  PHE    41       2.000  82.779   5.085  1.00 25.00           C
ATOM     42  CA  CYS    42       3.992  85.966   5.275  1.00 25.00           C
ATOM     43  CA  VAL    43       1.695  88.905   4.601  1.00 25.00           C
ATOM     44  CA  ALA    44       1.555  89.814   0.944  1.00 25.00           C
ATOM     45  CA  ARG    45      -0.151  88.535  -2.256  1.00 25.00           C
ATOM     46  CA  LEU    46      -0.867  89.858  -5.787  1.00 25.00           C
ATOM     47  CA  GLN    47      -2.036  88.590  -9.177  1.00 25.00           C
ATOM     48  CA  ASP    48      -1.544  91.236 -11.904  1.00 25.00           C
ATOM     49  CA  PHE    49      -2.450  93.575  -9.036  1.00 25.00           C
ATOM     50  CA  LYS    50      -4.325  92.600  -5.908  1.00 25.00           C
ATOM     51  CA  LEU    51      -4.056  91.701  -2.170  1.00 25.00           C
ATOM     52  CA  ASP    52      -1.586  93.056   0.376  1.00 25.00           C
ATOM     53  CA  PHE    53      -0.492  93.509   3.995  1.00 25.00           C
ATOM     54  CA  GLY    54       3.315  94.117   3.975  1.00 25.00           C
ATOM     55  CA  ASN    55       6.601  95.391   5.426  1.00 25.00           C
ATOM     56  CA  SER    56       8.968  94.392   8.207  1.00 25.00           C
ATOM     57  CA  GLN    57      11.022  97.301   9.503  1.00 25.00           C
ATOM     58  CA  GLY    58      11.693  98.190   5.879  1.00 25.00           C
ATOM     59  CA  LYS    59      13.833 101.128   6.921  1.00 25.00           C
ATOM     60  CA  THR    60      15.912  98.507   8.750  1.00 25.00           C
ATOM     61  CA  SER    61      15.918  94.963   7.447  1.00 25.00           C
ATOM     62  CA  GLN    62      18.365  93.774  10.175  1.00 25.00           C
ATOM     63  CA  THR    63      15.491  94.712  12.461  1.00 25.00           C
ATOM     64  CA  TRP    64      12.465  92.582  11.424  1.00 25.00           C
ATOM     65  CA  HIS    65      11.561  89.658   9.098  1.00 25.00           C
ATOM     66  CA  GLY    66      12.660  87.109   6.546  1.00 25.00           C
ATOM     67  CA  GLY    67      10.710  85.689   3.569  1.00 25.00           C
ATOM     68  CA  ILE    68      11.267  87.897   0.563  1.00 25.00           C
ATOM     69  CA  ALA    69      14.002  89.325  -1.633  1.00 25.00           C
ATOM     70  CA  THR    70      14.275  92.840  -3.102  1.00 25.00           C
ATOM     71  CA  ILE    71      12.746  91.730  -6.441  1.00 25.00           C
ATOM     72  CA  PHE    72      10.431  94.281  -8.114  1.00 25.00           C
ATOM     73  CA  GLN    73       9.925  97.588  -9.933  1.00 25.00           C
ATOM     74  CA  SER    74       9.702 100.408 -12.500  1.00 25.00           C
ATOM     75  CA  PRO    75      12.756 102.732 -12.918  1.00 25.00           C
ATOM     76  CA  GLY    76      14.967 100.691 -10.564  1.00 25.00           C
ATOM     77  CA  ASP    77      16.945  97.838  -8.965  1.00 25.00           C
ATOM     78  CA  GLU    78      13.922  97.594  -6.668  1.00 25.00           C
ATOM     79  CA  VAL    79      11.604  97.269  -3.671  1.00 25.00           C
ATOM     80  CA  TRP    80       9.559  94.149  -3.105  1.00 25.00           C
ATOM     81  CA  GLY    81       9.272  90.402  -2.979  1.00 25.00           C
ATOM     82  CA  VAL    82       9.734  86.761  -4.148  1.00 25.00           C
ATOM     83  CA  VAL    83       7.769  84.806  -1.605  1.00 25.00           C
ATOM     84  CA  TRP    84       5.448  81.799  -1.676  1.00 25.00           C
ATOM     85  CA  LYS    85       2.219  80.132  -2.848  1.00 25.00           C
ATOM     86  CA  MET    86       0.179  81.611  -5.607  1.00 25.00           C
ATOM     87  CA  ASN    87      -2.317  82.856  -8.156  1.00 25.00           C
ATOM     88  CA  LYS    88      -5.479  83.791 -10.007  1.00 25.00           C
ATOM     89  CA  SER    89      -8.138  81.950  -7.953  1.00 25.00           C
ATOM     90  CA  ASN    90      -5.931  82.193  -4.833  1.00 25.00           C
ATOM     91  CA  LEU    91      -5.449  85.944  -5.435  1.00 25.00           C
ATOM     92  CA  ASN    92      -9.234  86.394  -5.811  1.00 25.00           C
ATOM     93  CA  SER    93      -9.811  84.482  -2.544  1.00 25.00           C
ATOM     94  CA  LEU    94      -7.236  86.691  -0.767  1.00 25.00           C
ATOM     95  CA  ASP    95      -8.963  89.832  -2.117  1.00 25.00           C
ATOM     96  CA  GLU    96     -12.348  88.528  -0.890  1.00 25.00           C
ATOM     97  CA  GLN    97     -10.856  87.836   2.569  1.00 25.00           C
ATOM     98  CA  GLU    98     -12.406  90.775   4.484  1.00 25.00           C
ATOM     99  CA  GLY    99     -11.350  94.414   4.349  1.00 25.00           C
ATOM    100  CA  VAL   100      -7.733  94.710   3.208  1.00 25.00           C
ATOM    101  CA  LYS   101      -9.099  95.387  -0.218  1.00 25.00           C
ATOM    102  CA  SER   102      -8.675  95.600  -3.943  1.00 25.00           C
ATOM    103  CA  GLY   103      -7.137  98.980  -3.127  1.00 25.00           C
ATOM    104  CA  MET   104      -4.309  96.924  -1.637  1.00 25.00           C
ATOM    105  CA  TYR   105      -1.014  98.012  -3.222  1.00 25.00           C
ATOM    106  CA  VAL   106       0.058  94.669  -4.532  1.00 25.00           C
ATOM    107  CA  VAL   107       2.624  96.727  -6.422  1.00 25.00           C
ATOM    108  CA  ILE   108       5.105  93.902  -7.206  1.00 25.00           C
ATOM    109  CA  GLU   109       3.925  90.525  -8.624  1.00 25.00           C
ATOM    110  CA  VAL   110       7.464  89.486  -7.699  1.00 25.00           C
ATOM    111  CA  LYS   111       9.988  87.060  -9.179  1.00 25.00           C
ATOM    112  CA  VAL   112       7.525  84.622 -10.676  1.00 25.00           C
ATOM    113  CA  ALA   113      10.598  82.510 -11.377  1.00 25.00           C
ATOM    114  CA  THR   114      13.499  80.067 -11.657  1.00 25.00           C
ATOM    115  CA  GLN   115      13.883  80.925 -15.329  1.00 25.00           C
ATOM    116  CA  GLU   116      16.548  78.293 -15.931  1.00 25.00           C
ATOM    117  CA  GLY   117      19.446  80.525 -14.740  1.00 25.00           C
ATOM    118  CA  LYS   118      18.156  82.669 -11.876  1.00 25.00           C
ATOM    119  CA  GLU   119      16.524  85.192  -9.526  1.00 25.00           C
ATOM    120  CA  ILE   120      13.641  84.170  -7.297  1.00 25.00           C
ATOM    121  CA  THR   121      12.047  82.208  -4.419  1.00 25.00           C
ATOM    122  CA  CYS   122       8.538  82.320  -5.882  1.00 25.00           C
ATOM    123  CA  ARG   123       5.196  84.090  -6.190  1.00 25.00           C
ATOM    124  CA  SER   124       4.003  86.967  -4.119  1.00 25.00           C
ATOM    125  CA  TYR   125       4.225  90.691  -3.446  1.00 25.00           C
ATOM    126  CA  LEU   126       4.335  94.255  -2.232  1.00 25.00           C
ATOM    127  CA  MET   127       2.808  97.064  -0.058  1.00 25.00           C
ATOM    128  CA  THR   128      -0.173  98.218   1.945  1.00 25.00           C
ATOM    129  CA  ASN   129      -3.590  99.656   2.491  1.00 25.00           C
ATOM    130  CA  TYR   130      -7.423  99.744   2.826  1.00 25.00           C
ATOM    131  CA  GLU   131     -10.026 102.407   3.667  1.00 25.00           C
ATOM    132  CA  SER   132      -9.143 105.185   6.177  1.00 25.00           C
ATOM    133  CA  ALA   133     -10.158 105.566   9.778  1.00 25.00           C
ATOM    134  CA  PRO   134      -8.782 102.090  10.151  1.00 25.00           C
ATOM    135  CA  PRO   135      -5.060 102.742   9.447  1.00 25.00           C
TER
END
