
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS393_3.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      S       7          4.693
LGA    D       6      P       8          2.365
LGA    S       7      A       9          3.555
LGA    -       -      K      10           -
LGA    -       -      R      11           -
LGA    P       8      L      12          0.636
LGA    A       9      L      13          0.942
LGA    K      10      F      14          1.086
LGA    R      11      Q      15          1.805
LGA    L      12      M      16          2.083
LGA    L      13      V      17          1.548
LGA    F      14      G      18          2.486
LGA    Q      15      N      19          3.372
LGA    M      16      A      20          2.521
LGA    V      17      I      21          1.804
LGA    G      18      N      22          3.333
LGA    N      19      R      23          2.755
LGA    A      20      N      24          2.253
LGA    I      21      -       -           -
LGA    N      22      -       -           -
LGA    R      23      T      25          5.224
LGA    N      24      -       -           -
LGA    T      25      -       -           -
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      Q      26          3.702
LGA    L      40      Q      27          2.229
LGA    R      41      L      28          5.007
LGA    -       -      T      29           -
LGA    F      42      Q      30          4.679
LGA    V      43      D      31          5.364
LGA    Y      44      -       -           -
LGA    I      45      -       -           -
LGA    V      46      -       -           -
LGA    D      47      -       -           -
LGA    R      48      L      32           #
LGA    -       -      R      33           -
LGA    -       -      A      34           -
LGA    -       -      M      35           -
LGA    N      49      P      36          2.910
LGA    N      50      N      37           -
LGA    Q      51      W      38           -
LGA    D      52      S      39           -
LGA    L      53      L      40           -
LGA    L      54      R      41           -
LGA    K      55      F      42           -
LGA    R      56      V      43           -
LGA    P      57      Y      44           -
LGA    L      58      -       -           -
LGA    P      59      -       -           -
LGA    P      60      -       -           -
LGA    G      61      -       -           -
LGA    I      62      -       -           -
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    K      77      -       -           -
LGA    V      78      -       -           -
LGA    Q      79      -       -           -
LGA    D      80      -       -           -
LGA    R      81      -       -           -
LGA    N      82      -       -           -
LGA    R      83      -       -           -
LGA    K      84      -       -           -
LGA    L      85      -       -           -
LGA    Y      86      -       -           -
LGA    G      87      -       -           -
LGA    R      88      -       -           -
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     100      -       -           -
LGA    V     101      -       -           -
LGA    T     102      -       -           -
LGA    I     103      -       -           -
LGA    S     104      I      45           #
LGA    A     105      V      46          1.569
LGA    G     106      D      47          3.571
LGA    -       -      R      48           -
LGA    -       -      N      49           -
LGA    -       -      N      50           -
LGA    R     107      Q      51          3.705
LGA    D     108      D      52           #
LGA    -       -      L      53           -
LGA    -       -      L      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    E     109      P      57          2.112
LGA    G     110      L      58          2.653
LGA    -       -      P      59           -
LGA    P     111      P      60          0.503
LGA    D     112      G      61          1.989
LGA    R     113      I      62          2.231
LGA    D     114      M      63          2.741
LGA    I     115      V      64          2.419
LGA    I     116      L      65          1.077
LGA    W     117      A      66          1.258
LGA    E     118      P      67          1.775
LGA    M     119      R      68          2.123
LGA    F     120      L      69          2.383
LGA    L     121      T      70          1.978
LGA    -       -      A      71           -
LGA    -       -      K      72           -
LGA    E     122      H      73          3.569
LGA    -       -      P      74           -
LGA    N     123      Y      75          4.159
LGA    L     124      D      76          3.879
LGA    E     125      K      77           -
LGA    -       -      V      78           -
LGA    -       -      Q      79           -
LGA    -       -      D      80           -
LGA    -       -      R      81           -
LGA    -       -      N      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      L      85           -
LGA    -       -      Y      86           -
LGA    -       -      G      87           -
LGA    -       -      R      88           -
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     100           -
LGA    -       -      V     101           -
LGA    -       -      T     102           -
LGA    -       -      I     103           -
LGA    -       -      S     104           -
LGA    -       -      A     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  125   99    5.0     42    2.94     2.38     27.154     1.384

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.497487 * X  +  -0.428478 * Y  +   0.754263 * Z  +  22.254032
  Y_new =  -0.115573 * X  +  -0.894483 * Y  +  -0.431906 * Z  +   7.592018
  Z_new =   0.859738 * X  +   0.127695 * Y  +  -0.494514 * Z  +  69.757164 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.888889   -0.252704  [ DEG:   165.5211    -14.4789 ]
  Theta =  -1.034757   -2.106836  [ DEG:   -59.2872   -120.7128 ]
  Phi   =  -0.228264    2.913328  [ DEG:   -13.0786    166.9214 ]
 
# 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_3                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS393_3.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   42   2.94    2.38  27.154
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS393_3
PFRMAT TS
TARGET T0285
MODEL 3
PARENT N/A
ATOM      1  CA  ALA     1      15.874  30.746  82.104  1.00 25.00           C
ATOM      2  CA  TYR     2      13.732  28.751  84.468  1.00 25.00           C
ATOM      3  CA  LEU     3      13.586  25.009  83.680  1.00 25.00           C
ATOM      4  CA  PRO     4      16.065  23.972  86.283  1.00 25.00           C
ATOM      5  CA  ASP     5      19.759  24.295  86.870  1.00 25.00           C
ATOM      6  CA  ASP     6      20.325  20.571  86.476  1.00 25.00           C
ATOM      7  CA  SER     7      20.890  18.149  83.600  1.00 25.00           C
ATOM      8  CA  PRO     8      21.751  15.016  81.601  1.00 25.00           C
ATOM      9  CA  ALA     9      18.594  12.933  81.000  1.00 25.00           C
ATOM     10  CA  LYS    10      18.115  14.600  77.585  1.00 25.00           C
ATOM     11  CA  ARG    11      21.761  13.854  76.682  1.00 25.00           C
ATOM     12  CA  LEU    12      21.297  10.198  77.722  1.00 25.00           C
ATOM     13  CA  LEU    13      18.135   9.963  75.574  1.00 25.00           C
ATOM     14  CA  PHE    14      20.021  11.452  72.591  1.00 25.00           C
ATOM     15  CA  GLN    15      22.851   8.920  73.085  1.00 25.00           C
ATOM     16  CA  MET    16      20.306   6.061  73.207  1.00 25.00           C
ATOM     17  CA  VAL    17      18.682   7.336  69.981  1.00 25.00           C
ATOM     18  CA  GLY    18      22.115   7.503  68.290  1.00 25.00           C
ATOM     19  CA  ASN    19      22.869   3.920  69.415  1.00 25.00           C
ATOM     20  CA  ALA    20      19.498   2.749  68.026  1.00 25.00           C
ATOM     21  CA  ILE    21      20.237   4.488  64.695  1.00 25.00           C
ATOM     22  CA  ASN    22      23.675   2.807  64.551  1.00 25.00           C
ATOM     23  CA  ARG    23      22.065  -0.599  65.242  1.00 25.00           C
ATOM     24  CA  ASN    24      19.510   0.016  62.457  1.00 25.00           C
ATOM     25  CA  THR    25      22.330   0.958  60.044  1.00 25.00           C
ATOM     26  CA  GLN    26      24.229  -2.234  60.978  1.00 25.00           C
ATOM     27  CA  GLN    27      21.072  -4.317  60.377  1.00 25.00           C
ATOM     28  CA  LEU    28      20.593  -2.651  56.962  1.00 25.00           C
ATOM     29  CA  THR    29      24.240  -3.396  56.060  1.00 25.00           C
ATOM     30  CA  GLN    30      23.775  -7.052  57.099  1.00 25.00           C
ATOM     31  CA  ASP    31      20.613  -7.287  54.951  1.00 25.00           C
ATOM     32  CA  LEU    32      22.498  -5.798  51.969  1.00 25.00           C
ATOM     33  CA  ARG    33      25.329  -8.331  52.463  1.00 25.00           C
ATOM     34  CA  ALA    34      28.213  -7.160  54.619  1.00 25.00           C
ATOM     35  CA  MET    35      29.167  -7.414  58.293  1.00 25.00           C
ATOM     36  CA  PRO    36      27.389  -9.837  60.567  1.00 25.00           C
ATOM     37  CA  ASN    37      26.545  -9.014  64.166  1.00 25.00           C
ATOM     38  CA  TRP    38      24.338  -6.025  64.836  1.00 25.00           C
ATOM     39  CA  SER    39      26.555  -3.582  66.799  1.00 25.00           C
ATOM     40  CA  LEU    40      25.645  -0.429  68.829  1.00 25.00           C
ATOM     41  CA  ARG    41      27.722   2.785  68.476  1.00 25.00           C
ATOM     42  CA  PHE    42      27.454   5.284  71.369  1.00 25.00           C
ATOM     43  CA  VAL    43      27.998   8.513  69.477  1.00 25.00           C
ATOM     44  CA  TYR    44      27.367  11.934  71.033  1.00 25.00           C
ATOM     45  CA  ILE    45      30.850  11.436  72.543  1.00 25.00           C
ATOM     46  CA  VAL    46      28.964  11.983  75.794  1.00 25.00           C
ATOM     47  CA  ASP    47      32.295  12.067  77.705  1.00 25.00           C
ATOM     48  CA  ARG    48      31.545   8.506  78.859  1.00 25.00           C
ATOM     49  CA  ASN    49      35.279   8.369  79.556  1.00 25.00           C
ATOM     50  CA  ASN    50      35.287   5.780  76.834  1.00 25.00           C
ATOM     51  CA  GLN    51      36.897   6.782  73.507  1.00 25.00           C
ATOM     52  CA  ASP    52      39.998   4.700  74.352  1.00 25.00           C
ATOM     53  CA  LEU    53      37.779   1.697  75.205  1.00 25.00           C
ATOM     54  CA  LEU    54      35.916   2.099  71.881  1.00 25.00           C
ATOM     55  CA  LYS    55      34.570  -1.370  72.463  1.00 25.00           C
ATOM     56  CA  ARG    56      35.621  -4.545  70.645  1.00 25.00           C
ATOM     57  CA  PRO    57      37.267  -2.590  67.825  1.00 25.00           C
ATOM     58  CA  LEU    58      34.186  -0.505  67.309  1.00 25.00           C
ATOM     59  CA  PRO    59      35.726   0.118  63.839  1.00 25.00           C
ATOM     60  CA  PRO    60      33.287   0.635  60.933  1.00 25.00           C
ATOM     61  CA  GLY    61      30.928   2.352  63.441  1.00 25.00           C
ATOM     62  CA  ILE    62      30.723   5.706  65.161  1.00 25.00           C
ATOM     63  CA  MET    63      27.017   6.715  64.778  1.00 25.00           C
ATOM     64  CA  VAL    64      25.221  10.064  65.294  1.00 25.00           C
ATOM     65  CA  LEU    65      21.952  11.861  65.663  1.00 25.00           C
ATOM     66  CA  ALA    66      22.387  14.154  68.721  1.00 25.00           C
ATOM     67  CA  PRO    67      25.165  16.699  68.210  1.00 25.00           C
ATOM     68  CA  ARG    68      24.661  20.470  68.175  1.00 25.00           C
ATOM     69  CA  LEU    69      21.632  20.122  65.998  1.00 25.00           C
ATOM     70  CA  THR    70      19.036  22.342  64.368  1.00 25.00           C
ATOM     71  CA  ALA    71      18.107  21.287  60.805  1.00 25.00           C
ATOM     72  CA  LYS    72      18.557  20.915  57.028  1.00 25.00           C
ATOM     73  CA  HIS    73      21.276  19.126  54.949  1.00 25.00           C
ATOM     74  CA  PRO    74      23.620  19.638  57.912  1.00 25.00           C
ATOM     75  CA  TYR    75      25.532  22.073  55.699  1.00 25.00           C
ATOM     76  CA  ASP    76      29.339  22.475  55.812  1.00 25.00           C
ATOM     77  CA  LYS    77      29.702  18.899  57.137  1.00 25.00           C
ATOM     78  CA  VAL    78      27.449  17.603  54.324  1.00 25.00           C
ATOM     79  CA  GLN    79      29.547  19.493  51.738  1.00 25.00           C
ATOM     80  CA  ASP    80      32.751  17.996  53.208  1.00 25.00           C
ATOM     81  CA  ARG    81      34.883  20.711  54.758  1.00 25.00           C
ATOM     82  CA  ASN    82      37.639  19.695  57.197  1.00 25.00           C
ATOM     83  CA  ARG    83      37.113  22.432  59.763  1.00 25.00           C
ATOM     84  CA  LYS    84      36.814  20.124  62.793  1.00 25.00           C
ATOM     85  CA  LEU    85      33.292  20.549  64.293  1.00 25.00           C
ATOM     86  CA  TYR    86      30.306  18.980  62.459  1.00 25.00           C
ATOM     87  CA  GLY    87      27.400  16.838  61.231  1.00 25.00           C
ATOM     88  CA  ARG    88      25.025  13.818  61.240  1.00 25.00           C
ATOM     89  CA  HIS    89      21.394  12.779  60.777  1.00 25.00           C
ATOM     90  CA  ILE    90      22.095   9.084  61.396  1.00 25.00           C
ATOM     91  CA  THR    91      19.721   6.680  59.712  1.00 25.00           C
ATOM     92  CA  LEU    92      15.962   6.585  59.862  1.00 25.00           C
ATOM     93  CA  ASN    93      12.896   8.474  58.680  1.00 25.00           C
ATOM     94  CA  ASP    94       9.765   7.145  57.053  1.00 25.00           C
ATOM     95  CA  GLY    95       7.557   6.023  59.991  1.00 25.00           C
ATOM     96  CA  ASN    96       7.104   7.933  63.289  1.00 25.00           C
ATOM     97  CA  SER    97      10.302   9.920  62.743  1.00 25.00           C
ATOM     98  CA  VAL    98      14.055  10.068  63.501  1.00 25.00           C
ATOM     99  CA  LYS    99      15.608   6.861  64.852  1.00 25.00           C
ATOM    100  CA  VAL   100      15.346   3.118  64.426  1.00 25.00           C
ATOM    101  CA  VAL   101      14.512   1.871  67.974  1.00 25.00           C
ATOM    102  CA  THR   102      16.412  -0.911  69.727  1.00 25.00           C
ATOM    103  CA  ILE   103      18.740   0.461  72.410  1.00 25.00           C
ATOM    104  CA  SER   104      17.008  -0.775  75.624  1.00 25.00           C
ATOM    105  CA  ALA   105      18.177  -0.127  79.193  1.00 25.00           C
ATOM    106  CA  GLY   106      17.269  -3.135  81.305  1.00 25.00           C
ATOM    107  CA  ARG   107      19.423  -1.781  84.114  1.00 25.00           C
ATOM    108  CA  ASP   108      20.887  -4.648  86.116  1.00 25.00           C
ATOM    109  CA  GLU   109      21.243  -3.771  89.778  1.00 25.00           C
ATOM    110  CA  GLY   110      18.765  -1.162  91.037  1.00 25.00           C
ATOM    111  CA  PRO   111      16.722   0.843  93.500  1.00 25.00           C
ATOM    112  CA  ASP   112      13.798   2.269  91.438  1.00 25.00           C
ATOM    113  CA  ARG   113      14.832   1.030  88.007  1.00 25.00           C
ATOM    114  CA  ASP   114      11.809  -1.009  86.832  1.00 25.00           C
ATOM    115  CA  ILE   115       9.446   1.429  88.603  1.00 25.00           C
ATOM    116  CA  ILE   116      11.212   4.391  86.936  1.00 25.00           C
ATOM    117  CA  TRP   117      10.886   2.693  83.519  1.00 25.00           C
ATOM    118  CA  GLU   118       7.157   2.091  84.146  1.00 25.00           C
ATOM    119  CA  MET   119       6.701   5.767  85.120  1.00 25.00           C
ATOM    120  CA  PHE   120       8.513   6.862  81.928  1.00 25.00           C
ATOM    121  CA  LEU   121       6.263   4.575  79.837  1.00 25.00           C
ATOM    122  CA  GLU   122       3.157   6.044  81.529  1.00 25.00           C
ATOM    123  CA  ASN   123       4.409   9.590  80.807  1.00 25.00           C
ATOM    124  CA  LEU   124       4.494  11.647  84.050  1.00 25.00           C
ATOM    125  CA  GLU   125       0.723  12.291  84.122  1.00 25.00           C
TER
END
