
#######################################################
#                                                     #
#                        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 T0285TS168_4
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS168_4.T0285.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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      S       7          1.839
LGA    L      12      P       8          1.201
LGA    L      13      A       9          1.029
LGA    F      14      K      10          0.788
LGA    Q      15      R      11          0.508
LGA    M      16      L      12          0.115
LGA    V      17      L      13          0.433
LGA    G      18      F      14          0.760
LGA    N      19      Q      15          1.100
LGA    A      20      M      16          1.268
LGA    I      21      V      17          0.767
LGA    N      22      G      18          1.463
LGA    R      23      N      19          2.059
LGA    N      24      A      20          1.362
LGA    T      25      I      21          0.706
LGA    Q      26      N      22          2.127
LGA    Q      27      R      23          1.032
LGA    L      28      N      24          3.435
LGA    T      29      T      25           -
LGA    Q      30      Q      26           -
LGA    D      31      Q      27           #
LGA    L      32      L      28           -
LGA    R      33      T      29           -
LGA    A      34      Q      30           -
LGA    M      35      D      31           -
LGA    P      36      L      32           -
LGA    N      37      R      33           -
LGA    W      38      A      34           -
LGA    S      39      M      35           -
LGA    L      40      P      36           -
LGA    R      41      N      37           -
LGA    F      42      W      38           -
LGA    V      43      S      39           -
LGA    Y      44      L      40           -
LGA    -       -      R      41           -
LGA    -       -      F      42           -
LGA    -       -      V      43           -
LGA    -       -      Y      44           -
LGA    I      45      I      45          4.319
LGA    -       -      V      46           -
LGA    -       -      D      47           -
LGA    -       -      R      48           -
LGA    -       -      N      49           -
LGA    -       -      N      50           -
LGA    V      46      Q      51           #
LGA    D      47      D      52          2.164
LGA    R      48      -       -           -
LGA    N      49      -       -           -
LGA    N      50      -       -           -
LGA    Q      51      -       -           -
LGA    D      52      L      53           #
LGA    L      53      L      54          4.532
LGA    L      54      K      55           -
LGA    K      55      R      56           -
LGA    R      56      P      57           -
LGA    P      57      L      58           -
LGA    L      58      P      59           -
LGA    P      59      P      60           -
LGA    P      60      G      61           -
LGA    G      61      -       -           -
LGA    I      62      -       -           -
LGA    M      63      -       -           -
LGA    V      64      I      62           #
LGA    L      65      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    A      66      Y      75          5.097
LGA    P      67      D      76          2.941
LGA    R      68      K      77          3.920
LGA    L      69      -       -           -
LGA    T      70      -       -           -
LGA    A      71      -       -           -
LGA    K      72      -       -           -
LGA    H      73      -       -           -
LGA    P      74      -       -           -
LGA    Y      75      -       -           -
LGA    D      76      V      78           #
LGA    K      77      Q      79          0.424
LGA    V      78      -       -           -
LGA    Q      79      -       -           -
LGA    D      80      D      80          3.055
LGA    R      81      R      81          3.409
LGA    N      82      N      82          3.657
LGA    R      83      -       -           -
LGA    K      84      -       -           -
LGA    L      85      -       -           -
LGA    Y      86      -       -           -
LGA    G      87      -       -           -
LGA    R      88      -       -           -
LGA    H      89      R      83          2.119
LGA    I      90      K      84          3.242
LGA    T      91      L      85          3.099
LGA    L      92      Y      86          4.085
LGA    N      93      G      87          3.673
LGA    D      94      -       -           -
LGA    G      95      -       -           -
LGA    N      96      -       -           -
LGA    S      97      -       -           -
LGA    V      98      -       -           -
LGA    K      99      -       -           -
LGA    V     100      R      88          2.468
LGA    -       -      H      89           -
LGA    -       -      I      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      N      93           -
LGA    -       -      D      94           -
LGA    -       -      G      95           -
LGA    -       -      N      96           -
LGA    -       -      S      97           -
LGA    -       -      V      98           -
LGA    -       -      K      99           -
LGA    V     101      V     100          1.117
LGA    T     102      V     101          2.819
LGA    I     103      T     102          5.198
LGA    S     104      I     103           -
LGA    A     105      S     104           -
LGA    G     106      A     105           -
LGA    R     107      -       -           -
LGA    D     108      -       -           -
LGA    E     109      -       -           -
LGA    G     110      -       -           -
LGA    P     111      -       -           -
LGA    D     112      -       -           -
LGA    R     113      -       -           -
LGA    D     114      -       -           -
LGA    I     115      -       -           -
LGA    I     116      -       -           -
LGA    W     117      -       -           -
LGA    E     118      -       -           -
LGA    M     119      -       -           -
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     37    2.66    18.92     24.778     1.339

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.581679 * X  +   0.658707 * Y  +  -0.477236 * Z  +  16.368029
  Y_new =   0.598056 * X  +  -0.051344 * Y  +  -0.799808 * Z  +   9.034927
  Z_new =  -0.551343 * X  +  -0.750645 * Y  +  -0.364078 * Z  +  81.151169 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.022389    1.119204  [ DEG:  -115.8743     64.1257 ]
  Theta =   0.583973    2.557620  [ DEG:    33.4592    146.5408 ]
  Phi   =   2.342313   -0.799280  [ DEG:   134.2046    -45.7954 ]
 
# 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: T0285TS168_4                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS168_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   37   2.66   18.92  24.778
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS168_4
PFRMAT TS
TARGET T0285
MODEL 4
PARENT N/A
ATOM      1  CA  ALA     1       3.919  32.841  86.987  1.00 25.00           C
ATOM      2  CA  TYR     2       7.216  32.611  88.915  1.00 25.00           C
ATOM      3  CA  LEU     3      10.369  34.310  90.157  1.00 25.00           C
ATOM      4  CA  PRO     4      13.301  33.087  88.082  1.00 25.00           C
ATOM      5  CA  ASP     5      17.067  33.239  88.183  1.00 25.00           C
ATOM      6  CA  ASP     6      20.280  31.404  89.017  1.00 25.00           C
ATOM      7  CA  SER     7      21.240  27.670  89.094  1.00 25.00           C
ATOM      8  CA  PRO     8      19.837  24.107  89.273  1.00 25.00           C
ATOM      9  CA  ALA     9      20.718  20.462  90.055  1.00 25.00           C
ATOM     10  CA  LYS    10      17.294  19.332  88.763  1.00 25.00           C
ATOM     11  CA  ARG    11      17.813  21.353  85.550  1.00 25.00           C
ATOM     12  CA  LEU    12      21.265  19.764  85.080  1.00 25.00           C
ATOM     13  CA  LEU    13      19.757  16.280  85.576  1.00 25.00           C
ATOM     14  CA  PHE    14      17.037  17.062  82.996  1.00 25.00           C
ATOM     15  CA  GLN    15      19.699  18.259  80.516  1.00 25.00           C
ATOM     16  CA  MET    16      21.704  15.045  81.079  1.00 25.00           C
ATOM     17  CA  VAL    17      18.554  12.948  80.484  1.00 25.00           C
ATOM     18  CA  GLY    18      17.853  14.873  77.250  1.00 25.00           C
ATOM     19  CA  ASN    19      21.455  14.285  76.089  1.00 25.00           C
ATOM     20  CA  ALA    20      21.114  10.547  76.848  1.00 25.00           C
ATOM     21  CA  ILE    21      17.840  10.418  74.866  1.00 25.00           C
ATOM     22  CA  ASN    22      19.526  12.184  71.916  1.00 25.00           C
ATOM     23  CA  ARG    23      22.425   9.684  72.044  1.00 25.00           C
ATOM     24  CA  ASN    24      19.941   6.769  72.071  1.00 25.00           C
ATOM     25  CA  THR    25      18.115   8.265  69.055  1.00 25.00           C
ATOM     26  CA  GLN    26      21.442   8.645  67.197  1.00 25.00           C
ATOM     27  CA  GLN    27      22.322   5.000  67.979  1.00 25.00           C
ATOM     28  CA  LEU    28      18.898   3.871  66.687  1.00 25.00           C
ATOM     29  CA  THR    29      19.417   5.891  63.475  1.00 25.00           C
ATOM     30  CA  GLN    30      22.869   4.302  63.003  1.00 25.00           C
ATOM     31  CA  ASP    31      21.361   0.817  63.500  1.00 25.00           C
ATOM     32  CA  LEU    32      18.641   1.601  60.920  1.00 25.00           C
ATOM     33  CA  ARG    33      21.304   2.797  58.440  1.00 25.00           C
ATOM     34  CA  ALA    34      21.909   6.516  58.437  1.00 25.00           C
ATOM     35  CA  MET    35      22.046   9.361  60.973  1.00 25.00           C
ATOM     36  CA  PRO    36      19.486  12.044  60.157  1.00 25.00           C
ATOM     37  CA  ASN    37      17.960  15.121  61.840  1.00 25.00           C
ATOM     38  CA  TRP    38      17.629  15.635  65.531  1.00 25.00           C
ATOM     39  CA  SER    39      15.375  18.012  67.364  1.00 25.00           C
ATOM     40  CA  LEU    40      16.714  16.387  70.512  1.00 25.00           C
ATOM     41  CA  ARG    41      14.316  13.542  71.290  1.00 25.00           C
ATOM     42  CA  PHE    42      12.838  10.428  72.924  1.00 25.00           C
ATOM     43  CA  VAL    43      13.777   7.026  74.299  1.00 25.00           C
ATOM     44  CA  TYR    44      15.240   3.519  74.151  1.00 25.00           C
ATOM     45  CA  ILE    45      18.625   3.646  75.803  1.00 25.00           C
ATOM     46  CA  VAL    46      20.458   1.336  78.178  1.00 25.00           C
ATOM     47  CA  ASP    47      21.597  -1.885  79.783  1.00 25.00           C
ATOM     48  CA  ARG    48      23.808  -1.940  76.645  1.00 25.00           C
ATOM     49  CA  ASN    49      23.018  -3.631  73.267  1.00 25.00           C
ATOM     50  CA  ASN    50      24.177  -0.308  71.724  1.00 25.00           C
ATOM     51  CA  GLN    51      27.772  -1.365  72.532  1.00 25.00           C
ATOM     52  CA  ASP    52      30.212  -3.167  74.870  1.00 25.00           C
ATOM     53  CA  LEU    53      29.468  -0.631  77.642  1.00 25.00           C
ATOM     54  CA  LEU    54      28.460   2.529  75.824  1.00 25.00           C
ATOM     55  CA  LYS    55      31.514   2.300  73.557  1.00 25.00           C
ATOM     56  CA  ARG    56      33.231   3.941  76.561  1.00 25.00           C
ATOM     57  CA  PRO    57      33.341   7.360  74.910  1.00 25.00           C
ATOM     58  CA  LEU    58      29.919   8.106  76.488  1.00 25.00           C
ATOM     59  CA  PRO    59      31.429  11.024  78.433  1.00 25.00           C
ATOM     60  CA  PRO    60      29.164  13.460  76.594  1.00 25.00           C
ATOM     61  CA  GLY    61      25.918  11.884  77.642  1.00 25.00           C
ATOM     62  CA  ILE    62      24.722   9.782  80.528  1.00 25.00           C
ATOM     63  CA  MET    63      22.229  10.549  83.300  1.00 25.00           C
ATOM     64  CA  VAL    64      18.687   9.811  84.479  1.00 25.00           C
ATOM     65  CA  LEU    65      15.508  11.773  84.086  1.00 25.00           C
ATOM     66  CA  ALA    66      12.035  12.967  82.947  1.00 25.00           C
ATOM     67  CA  PRO    67       8.676  13.697  84.636  1.00 25.00           C
ATOM     68  CA  ARG    68       6.982  14.302  88.037  1.00 25.00           C
ATOM     69  CA  LEU    69       4.963  11.995  90.243  1.00 25.00           C
ATOM     70  CA  THR    70       1.183  11.582  90.901  1.00 25.00           C
ATOM     71  CA  ALA    71       0.795   7.781  91.242  1.00 25.00           C
ATOM     72  CA  LYS    72       1.424   7.331  94.909  1.00 25.00           C
ATOM     73  CA  HIS    73       4.681   5.483  94.027  1.00 25.00           C
ATOM     74  CA  PRO    74       7.828   7.410  93.105  1.00 25.00           C
ATOM     75  CA  TYR    75       8.274   8.177  96.805  1.00 25.00           C
ATOM     76  CA  ASP    76       7.901  11.736  95.701  1.00 25.00           C
ATOM     77  CA  LYS    77      11.451  11.849  94.270  1.00 25.00           C
ATOM     78  CA  VAL    78      12.341  14.725  96.637  1.00 25.00           C
ATOM     79  CA  GLN    79      10.947  12.747  99.605  1.00 25.00           C
ATOM     80  CA  ASP    80      13.007   9.690  98.566  1.00 25.00           C
ATOM     81  CA  ARG    81      16.150  11.861  98.318  1.00 25.00           C
ATOM     82  CA  ASN    82      15.464  13.296 101.802  1.00 25.00           C
ATOM     83  CA  ARG    83      15.024   9.758 103.200  1.00 25.00           C
ATOM     84  CA  LYS    84      18.329   8.684 101.589  1.00 25.00           C
ATOM     85  CA  LEU    85      21.088   9.118  99.034  1.00 25.00           C
ATOM     86  CA  TYR    86      21.833   5.829  97.220  1.00 25.00           C
ATOM     87  CA  GLY    87      18.133   4.892  97.396  1.00 25.00           C
ATOM     88  CA  ARG    88      17.739   6.974  94.169  1.00 25.00           C
ATOM     89  CA  HIS    89      17.424  10.617  93.091  1.00 25.00           C
ATOM     90  CA  ILE    90      15.480  10.422  89.825  1.00 25.00           C
ATOM     91  CA  THR    91      12.306  11.164  87.906  1.00 25.00           C
ATOM     92  CA  LEU    92      12.088   8.020  85.750  1.00 25.00           C
ATOM     93  CA  ASN    93       9.595   8.206  82.904  1.00 25.00           C
ATOM     94  CA  ASP    94       5.812   8.492  82.439  1.00 25.00           C
ATOM     95  CA  GLY    95       2.854   9.434  80.161  1.00 25.00           C
ATOM     96  CA  ASN    96       4.248  12.037  77.708  1.00 25.00           C
ATOM     97  CA  SER    97       7.469  13.908  76.890  1.00 25.00           C
ATOM     98  CA  VAL    98       9.989  11.388  78.327  1.00 25.00           C
ATOM     99  CA  LYS    99      13.738  11.800  77.835  1.00 25.00           C
ATOM    100  CA  VAL   100      14.822   8.372  79.099  1.00 25.00           C
ATOM    101  CA  VAL   101      17.336   5.987  80.596  1.00 25.00           C
ATOM    102  CA  THR   102      18.108   4.555  83.990  1.00 25.00           C
ATOM    103  CA  ILE   103      21.666   5.537  83.129  1.00 25.00           C
ATOM    104  CA  SER   104      22.451   1.971  84.066  1.00 25.00           C
ATOM    105  CA  ALA   105      22.436  -0.883  86.641  1.00 25.00           C
ATOM    106  CA  GLY   106      21.651  -2.869  89.830  1.00 25.00           C
ATOM    107  CA  ARG   107      19.636  -5.943  88.846  1.00 25.00           C
ATOM    108  CA  ASP   108      17.135  -8.800  88.332  1.00 25.00           C
ATOM    109  CA  GLU   109      14.330  -8.933  90.907  1.00 25.00           C
ATOM    110  CA  GLY   110      11.787  -7.719  88.394  1.00 25.00           C
ATOM    111  CA  PRO   111      12.660  -6.278  84.927  1.00 25.00           C
ATOM    112  CA  ASP   112      15.173  -4.108  83.085  1.00 25.00           C
ATOM    113  CA  ARG   113      15.764  -0.532  81.919  1.00 25.00           C
ATOM    114  CA  ASP   114      12.265   0.003  83.380  1.00 25.00           C
ATOM    115  CA  ILE   115      12.448   3.731  82.517  1.00 25.00           C
ATOM    116  CA  ILE   116      13.515   2.875  78.939  1.00 25.00           C
ATOM    117  CA  TRP   117      10.593   0.419  78.630  1.00 25.00           C
ATOM    118  CA  GLU   118       8.171   3.102  79.899  1.00 25.00           C
ATOM    119  CA  MET   119       9.565   5.600  77.352  1.00 25.00           C
ATOM    120  CA  PHE   120       9.133   3.023  74.551  1.00 25.00           C
ATOM    121  CA  LEU   121       5.520   2.395  75.655  1.00 25.00           C
ATOM    122  CA  GLU   122       4.838   6.163  75.657  1.00 25.00           C
ATOM    123  CA  ASN   123       6.319   6.457  72.138  1.00 25.00           C
ATOM    124  CA  LEU   124       3.055   8.425  71.554  1.00 25.00           C
ATOM    125  CA  GLU   125      -0.751   8.175  71.394  1.00 25.00           C
TER
END
