
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS168_5.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          0.673
LGA    L      12      P       8          1.159
LGA    L      13      A       9          1.161
LGA    F      14      K      10          0.753
LGA    Q      15      R      11          1.211
LGA    M      16      L      12          1.539
LGA    V      17      L      13          1.481
LGA    G      18      F      14          1.543
LGA    N      19      Q      15          2.116
LGA    A      20      M      16          1.924
LGA    I      21      V      17          1.299
LGA    N      22      G      18          2.183
LGA    R      23      N      19          2.742
LGA    N      24      A      20          1.325
LGA    T      25      I      21          2.035
LGA    Q      26      N      22          3.787
LGA    Q      27      R      23          2.432
LGA    L      28      N      24          3.612
LGA    T      29      -       -           -
LGA    Q      30      -       -           -
LGA    D      31      T      25           #
LGA    L      32      -       -           -
LGA    R      33      -       -           -
LGA    A      34      -       -           -
LGA    M      35      -       -           -
LGA    P      36      -       -           -
LGA    N      37      -       -           -
LGA    W      38      -       -           -
LGA    S      39      -       -           -
LGA    L      40      -       -           -
LGA    R      41      -       -           -
LGA    F      42      -       -           -
LGA    V      43      -       -           -
LGA    Y      44      -       -           -
LGA    I      45      -       -           -
LGA    V      46      -       -           -
LGA    D      47      -       -           -
LGA    R      48      -       -           -
LGA    N      49      Q      26          4.705
LGA    N      50      Q      27          4.046
LGA    Q      51      L      28           #
LGA    -       -      T      29           -
LGA    D      52      Q      30          2.096
LGA    L      53      D      31          2.929
LGA    L      54      L      32          2.150
LGA    K      55      R      33          0.899
LGA    R      56      A      34          0.981
LGA    P      57      -       -           -
LGA    L      58      M      35          4.706
LGA    P      59      P      36          4.322
LGA    -       -      N      37           -
LGA    -       -      W      38           -
LGA    P      60      S      39          4.746
LGA    G      61      L      40          4.675
LGA    I      62      R      41           #
LGA    M      63      F      42          3.957
LGA    -       -      V      43           -
LGA    -       -      Y      44           -
LGA    -       -      I      45           -
LGA    -       -      V      46           -
LGA    -       -      D      47           -
LGA    -       -      R      48           -
LGA    -       -      N      49           -
LGA    -       -      N      50           -
LGA    -       -      Q      51           -
LGA    -       -      D      52           -
LGA    -       -      L      53           -
LGA    -       -      L      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    -       -      P      57           -
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    V      64      K      84           #
LGA    L      65      L      85          3.918
LGA    A      66      Y      86          3.656
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      G      87          2.285
LGA    N      93      -       -           -
LGA    D      94      -       -           -
LGA    G      95      -       -           -
LGA    N      96      -       -           -
LGA    S      97      -       -           -
LGA    V      98      -       -           -
LGA    K      99      R      88          2.701
LGA    V     100      H      89          4.161
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          2.235
LGA    T     102      V     101          2.499
LGA    I     103      T     102           #
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    2.86    10.81     25.280     1.251

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.907803 * X  +   0.146475 * Y  +  -0.392986 * Z  +  16.542837
  Y_new =  -0.405005 * X  +   0.062816 * Y  +  -0.912154 * Z  +   8.344431
  Z_new =  -0.108922 * X  +   0.987218 * Y  +   0.116347 * Z  +  81.670517 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.453484   -1.688109  [ DEG:    83.2785    -96.7215 ]
  Theta =   0.109139    3.032454  [ DEG:     6.2532    173.7468 ]
  Phi   =  -0.419637    2.721955  [ DEG:   -24.0435    155.9565 ]
 
# 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_5                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS168_5.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   2.86   10.81  25.280
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS168_5
PFRMAT TS
TARGET T0285
MODEL 5
PARENT N/A
ATOM      1  CA  ALA     1      14.600  39.922  96.818  1.00 25.00           C
ATOM      2  CA  TYR     2      17.419  38.789  94.634  1.00 25.00           C
ATOM      3  CA  LEU     3      17.612  35.039  94.059  1.00 25.00           C
ATOM      4  CA  PRO     4      15.786  33.275  91.178  1.00 25.00           C
ATOM      5  CA  ASP     5      17.986  30.187  91.614  1.00 25.00           C
ATOM      6  CA  ASP     6      20.484  28.406  89.370  1.00 25.00           C
ATOM      7  CA  SER     7      18.162  25.470  89.694  1.00 25.00           C
ATOM      8  CA  PRO     8      19.550  22.339  91.264  1.00 25.00           C
ATOM      9  CA  ALA     9      20.438  18.639  91.690  1.00 25.00           C
ATOM     10  CA  LYS    10      17.123  17.631  90.057  1.00 25.00           C
ATOM     11  CA  ARG    11      17.814  20.004  87.132  1.00 25.00           C
ATOM     12  CA  LEU    12      21.316  18.509  86.715  1.00 25.00           C
ATOM     13  CA  LEU    13      19.836  14.977  86.720  1.00 25.00           C
ATOM     14  CA  PHE    14      17.276  16.020  84.069  1.00 25.00           C
ATOM     15  CA  GLN    15      20.073  17.513  81.920  1.00 25.00           C
ATOM     16  CA  MET    16      22.089  14.273  82.251  1.00 25.00           C
ATOM     17  CA  VAL    17      19.020  12.228  81.220  1.00 25.00           C
ATOM     18  CA  GLY    18      18.497  14.499  78.181  1.00 25.00           C
ATOM     19  CA  ASN    19      22.175  14.078  77.202  1.00 25.00           C
ATOM     20  CA  ALA    20      21.848  10.275  77.515  1.00 25.00           C
ATOM     21  CA  ILE    21      18.711  10.339  75.320  1.00 25.00           C
ATOM     22  CA  ASN    22      20.555  12.441  72.703  1.00 25.00           C
ATOM     23  CA  ARG    23      23.479   9.969  72.741  1.00 25.00           C
ATOM     24  CA  ASN    24      21.047   7.047  72.279  1.00 25.00           C
ATOM     25  CA  THR    25      19.395   8.857  69.335  1.00 25.00           C
ATOM     26  CA  GLN    26      22.828   9.472  67.755  1.00 25.00           C
ATOM     27  CA  GLN    27      23.716   5.771  68.181  1.00 25.00           C
ATOM     28  CA  LEU    28      20.401   4.763  66.548  1.00 25.00           C
ATOM     29  CA  THR    29      21.093   7.136  63.623  1.00 25.00           C
ATOM     30  CA  GLN    30      24.594   5.642  63.206  1.00 25.00           C
ATOM     31  CA  ASP    31      23.114   2.110  63.211  1.00 25.00           C
ATOM     32  CA  LEU    32      20.555   3.153  60.560  1.00 25.00           C
ATOM     33  CA  ARG    33      23.351   4.645  58.410  1.00 25.00           C
ATOM     34  CA  ALA    34      22.096   8.222  58.742  1.00 25.00           C
ATOM     35  CA  MET    35      18.979   9.877  60.167  1.00 25.00           C
ATOM     36  CA  PRO    36      17.123  12.391  62.249  1.00 25.00           C
ATOM     37  CA  ASN    37      17.320  15.453  64.569  1.00 25.00           C
ATOM     38  CA  TRP    38      14.053  15.253  66.560  1.00 25.00           C
ATOM     39  CA  SER    39      13.275  17.959  69.181  1.00 25.00           C
ATOM     40  CA  LEU    40      14.268  15.263  71.630  1.00 25.00           C
ATOM     41  CA  ARG    41      13.888  11.697  73.059  1.00 25.00           C
ATOM     42  CA  PHE    42      15.085   8.061  72.815  1.00 25.00           C
ATOM     43  CA  VAL    43      16.526   5.928  75.539  1.00 25.00           C
ATOM     44  CA  TYR    44      18.324   3.227  77.605  1.00 25.00           C
ATOM     45  CA  ILE    45      21.319   5.358  78.579  1.00 25.00           C
ATOM     46  CA  VAL    46      23.076   2.003  78.946  1.00 25.00           C
ATOM     47  CA  ASP    47      23.351  -1.644  79.756  1.00 25.00           C
ATOM     48  CA  ARG    48      21.816  -2.641  76.442  1.00 25.00           C
ATOM     49  CA  ASN    49      24.402  -3.894  73.910  1.00 25.00           C
ATOM     50  CA  ASN    50      24.430  -1.326  71.080  1.00 25.00           C
ATOM     51  CA  GLN    51      28.180  -2.244  71.031  1.00 25.00           C
ATOM     52  CA  ASP    52      30.883   0.266  72.060  1.00 25.00           C
ATOM     53  CA  LEU    53      28.508   3.173  71.303  1.00 25.00           C
ATOM     54  CA  LEU    54      27.838   3.674  75.022  1.00 25.00           C
ATOM     55  CA  LYS    55      30.921   2.455  76.893  1.00 25.00           C
ATOM     56  CA  ARG    56      32.075   6.033  76.474  1.00 25.00           C
ATOM     57  CA  PRO    57      32.453   8.828  73.900  1.00 25.00           C
ATOM     58  CA  LEU    58      29.575  10.602  75.612  1.00 25.00           C
ATOM     59  CA  PRO    59      31.489  10.849  78.911  1.00 25.00           C
ATOM     60  CA  PRO    60      28.481  12.528  80.635  1.00 25.00           C
ATOM     61  CA  GLY    61      26.931   9.021  80.438  1.00 25.00           C
ATOM     62  CA  ILE    62      23.478   8.888  82.049  1.00 25.00           C
ATOM     63  CA  MET    63      20.845   8.666  84.841  1.00 25.00           C
ATOM     64  CA  VAL    64      17.133   8.788  85.665  1.00 25.00           C
ATOM     65  CA  LEU    65      14.288  11.267  85.133  1.00 25.00           C
ATOM     66  CA  ALA    66      10.634  12.158  85.459  1.00 25.00           C
ATOM     67  CA  PRO    67       7.196  10.749  84.860  1.00 25.00           C
ATOM     68  CA  ARG    68       5.351  13.565  83.119  1.00 25.00           C
ATOM     69  CA  LEU    69       2.240  15.195  84.491  1.00 25.00           C
ATOM     70  CA  THR    70      -0.211  18.061  85.235  1.00 25.00           C
ATOM     71  CA  ALA    71      -0.304  15.806  88.340  1.00 25.00           C
ATOM     72  CA  LYS    72       1.534  14.936  91.554  1.00 25.00           C
ATOM     73  CA  HIS    73       3.999  12.464  89.971  1.00 25.00           C
ATOM     74  CA  PRO    74       3.596  10.558  93.247  1.00 25.00           C
ATOM     75  CA  TYR    75       3.400   6.794  93.016  1.00 25.00           C
ATOM     76  CA  ASP    76       3.569   5.643  96.691  1.00 25.00           C
ATOM     77  CA  LYS    77       7.133   4.568  95.792  1.00 25.00           C
ATOM     78  CA  VAL    78       8.149   8.231  95.331  1.00 25.00           C
ATOM     79  CA  GLN    79       6.629   9.107  98.735  1.00 25.00           C
ATOM     80  CA  ASP    80       8.537   6.210 100.359  1.00 25.00           C
ATOM     81  CA  ARG    81      11.791   7.412  98.736  1.00 25.00           C
ATOM     82  CA  ASN    82      11.150  10.963 100.022  1.00 25.00           C
ATOM     83  CA  ARG    83      10.516   9.600 103.544  1.00 25.00           C
ATOM     84  CA  LYS    84      13.775   7.595 103.381  1.00 25.00           C
ATOM     85  CA  LEU    85      17.054   7.890 101.488  1.00 25.00           C
ATOM     86  CA  TYR    86      20.071   7.172  99.280  1.00 25.00           C
ATOM     87  CA  GLY    87      17.435   7.569  96.496  1.00 25.00           C
ATOM     88  CA  ARG    88      16.914   3.809  96.156  1.00 25.00           C
ATOM     89  CA  HIS    89      17.062   3.856  92.372  1.00 25.00           C
ATOM     90  CA  ILE    90      16.716   4.004  88.601  1.00 25.00           C
ATOM     91  CA  THR    91      13.531   5.721  87.468  1.00 25.00           C
ATOM     92  CA  LEU    92      12.751   7.046  84.012  1.00 25.00           C
ATOM     93  CA  ASN    93       9.166   6.630  82.786  1.00 25.00           C
ATOM     94  CA  ASP    94       5.427   6.115  82.924  1.00 25.00           C
ATOM     95  CA  GLY    95       3.808   6.037  79.429  1.00 25.00           C
ATOM     96  CA  ASN    96       6.446   8.593  78.495  1.00 25.00           C
ATOM     97  CA  SER    97       7.121   9.787  74.907  1.00 25.00           C
ATOM     98  CA  VAL    98      10.461  11.234  76.142  1.00 25.00           C
ATOM     99  CA  LYS    99      11.664  11.099  79.714  1.00 25.00           C
ATOM    100  CA  VAL   100      13.970   8.379  78.315  1.00 25.00           C
ATOM    101  CA  VAL   101      17.021   8.198  80.525  1.00 25.00           C
ATOM    102  CA  THR   102      17.675   4.867  82.203  1.00 25.00           C
ATOM    103  CA  ILE   103      21.021   3.614  83.555  1.00 25.00           C
ATOM    104  CA  SER   104      23.505   3.059  86.424  1.00 25.00           C
ATOM    105  CA  ALA   105      23.266  -0.445  87.951  1.00 25.00           C
ATOM    106  CA  GLY   106      23.785  -4.179  88.484  1.00 25.00           C
ATOM    107  CA  ARG   107      22.940  -3.899  92.198  1.00 25.00           C
ATOM    108  CA  ASP   108      19.251  -4.516  91.237  1.00 25.00           C
ATOM    109  CA  GLU   109      16.646  -5.944  93.639  1.00 25.00           C
ATOM    110  CA  GLY   110      15.888  -8.397  90.806  1.00 25.00           C
ATOM    111  CA  PRO   111      15.353  -8.270  87.042  1.00 25.00           C
ATOM    112  CA  ASP   112      17.040  -5.094  85.804  1.00 25.00           C
ATOM    113  CA  ARG   113      16.375  -1.540  84.724  1.00 25.00           C
ATOM    114  CA  ASP   114      12.605  -2.008  85.209  1.00 25.00           C
ATOM    115  CA  ILE   115      11.982   1.579  84.018  1.00 25.00           C
ATOM    116  CA  ILE   116      14.161   0.957  80.929  1.00 25.00           C
ATOM    117  CA  TRP   117      12.219  -2.257  80.176  1.00 25.00           C
ATOM    118  CA  GLU   118       8.907  -0.363  80.508  1.00 25.00           C
ATOM    119  CA  MET   119      10.191   2.350  78.129  1.00 25.00           C
ATOM    120  CA  PHE   120      11.249  -0.330  75.606  1.00 25.00           C
ATOM    121  CA  LEU   121       7.790  -1.955  75.844  1.00 25.00           C
ATOM    122  CA  GLU   122       6.125   1.445  75.268  1.00 25.00           C
ATOM    123  CA  ASN   123       8.354   2.047  72.213  1.00 25.00           C
ATOM    124  CA  LEU   124       6.250  -0.488  70.399  1.00 25.00           C
ATOM    125  CA  GLU   125       3.155  -0.340  68.101  1.00 25.00           C
TER
END
