
#######################################################
#                                                     #
#                        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  135 (  135),  selected  135 , name T0385TS168_3-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected  135 , name T0385_D1.pdb
# PARAMETERS: T0385TS168_3-D1.T0385_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      -       -           -
LGA    E      18      -       -           -
LGA    G      19      -       -           -
LGA    S      20      S      17           #
LGA    A      21      E      18           #
LGA    -       -      G      19           -
LGA    -       -      S      20           -
LGA    D      22      A      21          2.519
LGA    N      23      D      22          3.515
LGA    A      24      N      23          2.537
LGA    A      25      A      24          0.702
LGA    L      26      A      25          2.668
LGA    C      27      L      26          2.967
LGA    D      28      C      27          1.325
LGA    A      29      D      28          1.341
LGA    L      30      A      29          2.360
LGA    A      31      L      30          1.633
LGA    V      32      A      31          1.140
LGA    E      33      V      32          1.767
LGA    H      34      E      33          1.260
LGA    A      35      H      34          1.350
LGA    T      36      A      35          2.012
LGA    I      37      T      36          1.532
LGA    Y      38      I      37          1.055
LGA    -       -      Y      38           -
LGA    G      39      G      39          3.558
LGA    Y      40      Y      40          2.534
LGA    G      41      G      41           -
LGA    I      42      I      42           -
LGA    V      43      -       -           -
LGA    S      44      -       -           -
LGA    A      45      -       -           -
LGA    L      46      V      43           #
LGA    -       -      S      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      S      47           -
LGA    S      47      P      48           #
LGA    P      48      -       -           -
LGA    P      49      -       -           -
LGA    G      50      P      49          6.209
LGA    V      51      G      50          3.665
LGA    -       -      V      51           -
LGA    N      52      N      52          2.474
LGA    F      53      F      53          2.961
LGA    L      54      L      54          1.827
LGA    V      55      V      55          1.354
LGA    A      56      A      56          2.040
LGA    D      57      D      57          1.800
LGA    A      58      A      58          1.218
LGA    L      59      L      59          1.192
LGA    K      60      K      60          1.250
LGA    Q      61      Q      61          1.090
LGA    H      62      H      62          1.109
LGA    R      63      R      63          0.774
LGA    H      64      H      64          1.300
LGA    R      65      R      65          1.609
LGA    R      66      R      66          0.968
LGA    D      67      D      67          1.522
LGA    D      68      D      68          2.102
LGA    V      69      V      69          1.699
LGA    I      70      I      70          1.657
LGA    V      71      V      71          2.275
LGA    M      72      M      72          2.110
LGA    L      73      L      73          1.556
LGA    S      74      S      74          2.072
LGA    A      75      A      75          2.510
LGA    R      76      R      76           #
LGA    G      77      G      77           -
LGA    V      78      V      78           -
LGA    T      79      T      79           -
LGA    A      80      A      80           -
LGA    P      81      P      81           -
LGA    I      82      I      82           -
LGA    A      83      A      83           -
LGA    A      84      A      84           -
LGA    A      85      A      85           -
LGA    G      86      G      86           -
LGA    Y      87      Y      87           -
LGA    Q      88      Q      88           -
LGA    L      89      L      89           -
LGA    -       -      P      90           -
LGA    -       -      M      91           -
LGA    -       -      Q      92           -
LGA    -       -      V      93           -
LGA    -       -      S      94           -
LGA    -       -      S      95           -
LGA    -       -      A      96           -
LGA    -       -      A      97           -
LGA    -       -      D      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      A     103           -
LGA    -       -      V     104           -
LGA    -       -      R     105           -
LGA    -       -      M     106           -
LGA    P      90      E     107           #
LGA    -       -      N     108           -
LGA    M      91      D     109          5.234
LGA    Q      92      G     110          2.524
LGA    V      93      A     111          3.555
LGA    -       -      T     112           -
LGA    -       -      A     113           -
LGA    -       -      W     114           -
LGA    S      94      R     115          2.113
LGA    S      95      A     116          1.389
LGA    A      96      V     117          1.498
LGA    A      97      V     118          3.686
LGA    D      98      E     119           -
LGA    -       -      H     120           -
LGA    -       -      A     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      A     124           -
LGA    -       -      D     125           -
LGA    -       -      D     126           -
LGA    -       -      R     127           -
LGA    -       -      V     128           -
LGA    -       -      F     129           -
LGA    A      99      A     130           #
LGA    A     100      S     131          4.323
LGA    R     101      T     132          3.843
LGA    L     102      A     133          2.714
LGA    A     103      L     134          1.998
LGA    V     104      T     135          0.957
LGA    R     105      E     136          0.820
LGA    M     106      S     137          2.129
LGA    E     107      A     138          3.069
LGA    N     108      V     139          3.817
LGA    D     109      M     140          4.105
LGA    G     110      -       -           -
LGA    A     111      -       -           -
LGA    T     112      -       -           -
LGA    A     113      -       -           -
LGA    W     114      -       -           -
LGA    R     115      -       -           -
LGA    A     116      -       -           -
LGA    V     117      -       -           -
LGA    V     118      -       -           -
LGA    E     119      -       -           -
LGA    H     120      -       -           -
LGA    A     121      -       -           -
LGA    E     122      -       -           -
LGA    T     123      -       -           -
LGA    A     124      -       -           -
LGA    D     125      -       -           -
LGA    D     126      -       -           -
LGA    R     127      -       -           -
LGA    V     128      -       -           -
LGA    F     129      A     141          4.872
LGA    A     130      T     142          3.293
LGA    S     131      R     143           -
LGA    T     132      -       -           -
LGA    A     133      W     144           #
LGA    L     134      N     145           -
LGA    T     135      R     146           -
LGA    E     136      V     147           -
LGA    S     137      L     148           -
LGA    A     138      G     149           -
LGA    V     139      A     150           -
LGA    M     140      W     151           -
LGA    A     141      -       -           -
LGA    T     142      -       -           -
LGA    R     143      -       -           -
LGA    W     144      -       -           -
LGA    N     145      -       -           -
LGA    R     146      -       -           -
LGA    V     147      -       -           -
LGA    L     148      -       -           -
LGA    G     149      -       -           -
LGA    A     150      -       -           -
LGA    W     151      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  135  135    5.0     64    2.53    42.19     33.179     2.433

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.772434 * X  +  -0.013675 * Y  +  -0.634948 * Z  +  24.296274
  Y_new =   0.625520 * X  +  -0.156575 * Y  +   0.764336 * Z  +  13.717513
  Z_new =  -0.109870 * X  +  -0.987571 * Y  +  -0.112390 * Z  +  25.588577 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.684113    1.457479  [ DEG:   -96.4926     83.5074 ]
  Theta =   0.110092    3.031501  [ DEG:     6.3078    173.6922 ]
  Phi   =   0.680690   -2.460902  [ DEG:    39.0007   -140.9993 ]
 
# 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: T0385TS168_3-D1                               
REMARK     2: T0385_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS168_3-D1.T0385_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  135  135   5.0   64   2.53   42.19  33.179
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS168_3-D1
PFRMAT TS
TARGET T0385
MODEL 3
PARENT N/A
ATOM     17  CA  SER    17      17.440   5.767  49.904  1.00 25.00           C
ATOM     18  CA  GLU    18      21.154   6.006  50.700  1.00 25.00           C
ATOM     19  CA  GLY    19      20.969   9.803  50.562  1.00 25.00           C
ATOM     20  CA  SER    20      23.731   9.375  48.053  1.00 25.00           C
ATOM     21  CA  ALA    21      25.109  11.435  45.113  1.00 25.00           C
ATOM     22  CA  ASP    22      24.557  14.610  43.044  1.00 25.00           C
ATOM     23  CA  ASN    23      28.069  14.280  41.553  1.00 25.00           C
ATOM     24  CA  ALA    24      27.376  10.618  40.670  1.00 25.00           C
ATOM     25  CA  ALA    25      24.078  11.620  38.999  1.00 25.00           C
ATOM     26  CA  LEU    26      25.891  14.333  36.993  1.00 25.00           C
ATOM     27  CA  CYS    27      28.533  11.788  35.892  1.00 25.00           C
ATOM     28  CA  ASP    28      25.777   9.357  34.811  1.00 25.00           C
ATOM     29  CA  ALA    29      24.066  12.146  32.819  1.00 25.00           C
ATOM     30  CA  LEU    30      27.390  13.006  31.122  1.00 25.00           C
ATOM     31  CA  ALA    31      27.920   9.318  30.235  1.00 25.00           C
ATOM     32  CA  VAL    32      24.386   9.138  28.770  1.00 25.00           C
ATOM     33  CA  GLU    33      25.058  12.288  26.697  1.00 25.00           C
ATOM     34  CA  HIS    34      28.333  10.773  25.412  1.00 25.00           C
ATOM     35  CA  ALA    35      26.498   7.549  24.462  1.00 25.00           C
ATOM     36  CA  THR    36      23.835   9.582  22.607  1.00 25.00           C
ATOM     37  CA  ILE    37      26.568  11.500  20.732  1.00 25.00           C
ATOM     38  CA  TYR    38      28.257   8.200  19.769  1.00 25.00           C
ATOM     39  CA  GLY    39      27.357   9.387  16.241  1.00 25.00           C
ATOM     40  CA  TYR    40      25.380  11.901  14.101  1.00 25.00           C
ATOM     41  CA  GLY    41      24.750  14.286  16.960  1.00 25.00           C
ATOM     42  CA  ILE    42      27.335  16.725  18.466  1.00 25.00           C
ATOM     43  CA  VAL    43      26.038  19.348  15.985  1.00 25.00           C
ATOM     44  CA  SER    44      24.522  22.488  14.612  1.00 25.00           C
ATOM     45  CA  ALA    45      22.017  20.227  12.764  1.00 25.00           C
ATOM     46  CA  LEU    46      23.428  17.139  11.051  1.00 25.00           C
ATOM     47  CA  SER    47      25.485  18.435   8.125  1.00 25.00           C
ATOM     48  CA  PRO    48      28.316  20.751   7.316  1.00 25.00           C
ATOM     49  CA  PRO    49      30.741  20.696   4.409  1.00 25.00           C
ATOM     50  CA  GLY    50      31.870  17.217   3.267  1.00 25.00           C
ATOM     51  CA  VAL    51      28.851  15.732   5.096  1.00 25.00           C
ATOM     52  CA  ASN    52      30.965  12.735   6.201  1.00 25.00           C
ATOM     53  CA  PHE    53      33.694  15.100   7.477  1.00 25.00           C
ATOM     54  CA  LEU    54      31.079  17.114   9.417  1.00 25.00           C
ATOM     55  CA  VAL    55      29.702  13.888  10.957  1.00 25.00           C
ATOM     56  CA  ALA    56      33.242  12.833  11.971  1.00 25.00           C
ATOM     57  CA  ASP    57      33.834  16.263  13.567  1.00 25.00           C
ATOM     58  CA  ALA    58      30.534  15.965  15.489  1.00 25.00           C
ATOM     59  CA  LEU    59      31.533  12.477  16.714  1.00 25.00           C
ATOM     60  CA  LYS    60      34.931  13.824  17.855  1.00 25.00           C
ATOM     61  CA  GLN    61      33.198  16.683  19.724  1.00 25.00           C
ATOM     62  CA  HIS    62      30.847  14.181  21.421  1.00 25.00           C
ATOM     63  CA  ARG    63      33.843  12.029  22.452  1.00 25.00           C
ATOM     64  CA  HIS    64      35.599  15.117  23.886  1.00 25.00           C
ATOM     65  CA  ARG    65      32.438  16.034  25.846  1.00 25.00           C
ATOM     66  CA  ARG    66      32.226  12.466  27.220  1.00 25.00           C
ATOM     67  CA  ASP    67      35.906  12.626  28.272  1.00 25.00           C
ATOM     68  CA  ASP    68      35.286  15.977  30.021  1.00 25.00           C
ATOM     69  CA  VAL    69      32.267  14.492  31.850  1.00 25.00           C
ATOM     70  CA  ILE    70      34.381  11.495  32.955  1.00 25.00           C
ATOM     71  CA  VAL    71      37.110  13.859  34.231  1.00 25.00           C
ATOM     72  CA  MET    72      34.494  15.873  36.172  1.00 25.00           C
ATOM     73  CA  LEU    73      33.118  12.647  37.711  1.00 25.00           C
ATOM     74  CA  SER    74      36.658  11.592  38.725  1.00 25.00           C
ATOM     75  CA  ALA    75      37.249  15.023  40.322  1.00 25.00           C
ATOM     76  CA  ARG    76      37.275  18.803  39.766  1.00 25.00           C
ATOM     77  CA  GLY    77      37.085  22.155  37.859  1.00 25.00           C
ATOM     78  CA  VAL    78      36.708  22.647  34.097  1.00 25.00           C
ATOM     79  CA  THR    79      35.626  26.144  35.140  1.00 25.00           C
ATOM     80  CA  ALA    80      33.933  27.759  32.167  1.00 25.00           C
ATOM     81  CA  PRO    81      31.528  24.780  32.053  1.00 25.00           C
ATOM     82  CA  ILE    82      28.727  27.058  30.777  1.00 25.00           C
ATOM     83  CA  ALA    83      31.054  28.445  28.070  1.00 25.00           C
ATOM     84  CA  ALA    84      31.998  24.885  27.022  1.00 25.00           C
ATOM     85  CA  ALA    85      35.413  26.399  26.230  1.00 25.00           C
ATOM     86  CA  GLY    86      37.754  23.512  25.489  1.00 25.00           C
ATOM     87  CA  TYR    87      36.732  23.931  21.832  1.00 25.00           C
ATOM     88  CA  GLN    88      34.373  20.986  22.606  1.00 25.00           C
ATOM     89  CA  LEU    89      30.990  19.170  22.624  1.00 25.00           C
ATOM     90  CA  PRO    90      27.802  17.099  22.926  1.00 25.00           C
ATOM     91  CA  MET    91      24.281  16.848  24.445  1.00 25.00           C
ATOM     92  CA  GLN    92      21.743  18.600  26.670  1.00 25.00           C
ATOM     93  CA  VAL    93      19.700  21.280  28.451  1.00 25.00           C
ATOM     94  CA  SER    94      20.097  23.694  31.326  1.00 25.00           C
ATOM     95  CA  SER    95      21.307  21.261  33.930  1.00 25.00           C
ATOM     96  CA  ALA    96      23.704  18.573  35.112  1.00 25.00           C
ATOM     97  CA  ALA    97      27.000  20.475  34.687  1.00 25.00           C
ATOM     98  CA  ASP    98      28.040  18.094  31.872  1.00 25.00           C
ATOM     99  CA  ALA    99      24.660  18.616  30.149  1.00 25.00           C
ATOM    100  CA  ALA   100      25.071  22.413  30.437  1.00 25.00           C
ATOM    101  CA  ARG   101      28.586  22.169  28.935  1.00 25.00           C
ATOM    102  CA  LEU   102      27.231  20.055  26.044  1.00 25.00           C
ATOM    103  CA  ALA   103      24.464  22.630  25.424  1.00 25.00           C
ATOM    104  CA  VAL   104      27.058  25.448  25.405  1.00 25.00           C
ATOM    105  CA  ARG   105      29.201  23.491  22.906  1.00 25.00           C
ATOM    106  CA  MET   106      26.141  22.951  20.668  1.00 25.00           C
ATOM    107  CA  GLU   107      25.339  26.692  20.819  1.00 25.00           C
ATOM    108  CA  ASN   108      28.955  27.531  19.879  1.00 25.00           C
ATOM    109  CA  ASP   109      28.779  25.095  16.928  1.00 25.00           C
ATOM    110  CA  GLY   110      25.502  26.700  15.767  1.00 25.00           C
ATOM    111  CA  ALA   111      27.093  30.176  15.995  1.00 25.00           C
ATOM    112  CA  THR   112      30.096  28.962  13.952  1.00 25.00           C
ATOM    113  CA  ALA   113      27.739  27.504  11.308  1.00 25.00           C
ATOM    114  CA  TRP   114      25.832  30.823  11.145  1.00 25.00           C
ATOM    115  CA  ARG   115      29.129  32.724  10.720  1.00 25.00           C
ATOM    116  CA  ALA   116      30.169  30.344   7.905  1.00 25.00           C
ATOM    117  CA  VAL   117      26.788  30.866   6.182  1.00 25.00           C
ATOM    118  CA  VAL   118      27.201  34.662   6.470  1.00 25.00           C
ATOM    119  CA  GLU   119      30.716  34.418   4.967  1.00 25.00           C
ATOM    120  CA  HIS   120      29.360  32.304   2.077  1.00 25.00           C
ATOM    121  CA  ALA   121      26.594  34.879   1.457  1.00 25.00           C
ATOM    122  CA  GLU   122      23.824  33.932   3.835  1.00 25.00           C
ATOM    123  CA  THR   123      22.047  32.896   7.081  1.00 25.00           C
ATOM    124  CA  ALA   124      20.249  31.960  10.340  1.00 25.00           C
ATOM    125  CA  ASP   125      18.088  31.145  13.363  1.00 25.00           C
ATOM    126  CA  ASP   126      21.475  29.606  14.276  1.00 25.00           C
ATOM    127  CA  ARG   127      20.569  29.758  17.995  1.00 25.00           C
ATOM    128  CA  VAL   128      17.212  28.063  17.272  1.00 25.00           C
ATOM    129  CA  PHE   129      18.998  25.319  15.287  1.00 25.00           C
ATOM    130  CA  ALA   130      21.449  24.786  18.180  1.00 25.00           C
ATOM    131  CA  SER   131      18.527  24.534  20.642  1.00 25.00           C
ATOM    132  CA  THR   132      16.805  21.973  18.375  1.00 25.00           C
ATOM    133  CA  ALA   133      20.040  19.932  18.182  1.00 25.00           C
ATOM    134  CA  LEU   134      20.353  20.022  21.998  1.00 25.00           C
ATOM    135  CA  THR   135      16.724  18.849  22.347  1.00 25.00           C
ATOM    136  CA  GLU   136      17.387  15.987  19.892  1.00 25.00           C
ATOM    137  CA  SER   137      20.500  14.972  21.877  1.00 25.00           C
ATOM    138  CA  ALA   138      18.471  15.006  25.125  1.00 25.00           C
ATOM    139  CA  VAL   139      15.777  12.828  23.493  1.00 25.00           C
ATOM    140  CA  MET   140      18.457  10.368  22.294  1.00 25.00           C
ATOM    141  CA  ALA   141      19.935  10.219  25.824  1.00 25.00           C
ATOM    142  CA  THR   142      16.456   9.549  27.278  1.00 25.00           C
ATOM    143  CA  ARG   143      15.900   6.750  24.726  1.00 25.00           C
ATOM    144  CA  TRP   144      19.287   5.211  25.639  1.00 25.00           C
ATOM    145  CA  ASN   145      18.382   5.364  29.356  1.00 25.00           C
ATOM    146  CA  ARG   146      15.176   3.693  30.629  1.00 25.00           C
ATOM    147  CA  VAL   147      12.051   5.702  31.474  1.00 25.00           C
ATOM    148  CA  LEU   148      11.422   8.538  33.886  1.00 25.00           C
ATOM    149  CA  GLY   149       9.185   5.950  35.659  1.00 25.00           C
ATOM    150  CA  ALA   150       6.936   2.908  36.000  1.00 25.00           C
ATOM    151  CA  TRP   151       9.256  -0.038  36.665  1.00 25.00           C
TER
END
