
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS393_2.T0285.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      S       7           -
LGA    Y       2      P       8           -
LGA    L       3      A       9           -
LGA    P       4      K      10           -
LGA    D       5      R      11           -
LGA    D       6      L      12           -
LGA    S       7      L      13           -
LGA    P       8      F      14           -
LGA    A       9      Q      15           -
LGA    K      10      M      16           -
LGA    R      11      V      17           -
LGA    -       -      G      18           -
LGA    -       -      N      19           -
LGA    -       -      A      20           -
LGA    -       -      I      21           -
LGA    -       -      N      22           -
LGA    -       -      R      23           -
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           -
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    L      12      N      49          4.585
LGA    L      13      N      50          3.464
LGA    F      14      Q      51          1.924
LGA    Q      15      -       -           -
LGA    M      16      -       -           -
LGA    V      17      -       -           -
LGA    G      18      D      52          2.309
LGA    N      19      L      53          2.415
LGA    A      20      L      54           #
LGA    I      21      -       -           -
LGA    N      22      -       -           -
LGA    R      23      -       -           -
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      -       -           -
LGA    L      40      -       -           -
LGA    R      41      -       -           -
LGA    F      42      K      55          2.162
LGA    V      43      R      56          1.765
LGA    Y      44      P      57          4.316
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      L      58           #
LGA    L      65      P      59           -
LGA    A      66      P      60           -
LGA    -       -      G      61           -
LGA    P      67      I      62          3.196
LGA    R      68      M      63          2.969
LGA    -       -      V      64           -
LGA    -       -      L      65           -
LGA    L      69      A      66          2.552
LGA    T      70      P      67          3.657
LGA    A      71      R      68          3.966
LGA    K      72      L      69          4.056
LGA    -       -      T      70           -
LGA    -       -      A      71           -
LGA    -       -      K      72           -
LGA    H      73      H      73           #
LGA    P      74      P      74          4.853
LGA    Y      75      Y      75          5.289
LGA    D      76      D      76          3.956
LGA    K      77      K      77          4.945
LGA    V      78      V      78          1.779
LGA    Q      79      -       -           -
LGA    D      80      Q      79          3.726
LGA    R      81      D      80          3.041
LGA    N      82      R      81          4.508
LGA    R      83      N      82          3.880
LGA    K      84      R      83          1.952
LGA    L      85      K      84          4.165
LGA    Y      86      L      85          3.202
LGA    G      87      Y      86          1.916
LGA    R      88      G      87          4.465
LGA    H      89      R      88          4.211
LGA    I      90      H      89          4.807
LGA    T      91      I      90          5.033
LGA    L      92      -       -           -
LGA    N      93      -       -           -
LGA    D      94      -       -           -
LGA    G      95      T      91           #
LGA    N      96      L      92           #
LGA    S      97      N      93           #
LGA    -       -      D      94           -
LGA    -       -      G      95           -
LGA    -       -      N      96           -
LGA    -       -      S      97           -
LGA    V      98      V      98          3.865
LGA    K      99      K      99           #
LGA    V     100      V     100           -
LGA    V     101      V     101           -
LGA    T     102      T     102           -
LGA    I     103      I     103           -
LGA    S     104      S     104           -
LGA    A     105      A     105           -
LGA    G     106      -       -           -
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     32    3.69    18.75     17.203     0.845

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.839208 * X  +   0.532826 * Y  +   0.108747 * Z  +  20.828991
  Y_new =   0.543358 * X  +  -0.829723 * Y  +  -0.127755 * Z  +  -2.883472
  Z_new =   0.022159 * X  +   0.166301 * Y  +  -0.985826 * Z  +  80.270927 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.974474   -0.167119  [ DEG:   170.4248     -9.5752 ]
  Theta =  -0.022161   -3.119432  [ DEG:    -1.2697   -178.7303 ]
  Phi   =   0.574591   -2.567002  [ DEG:    32.9216   -147.0784 ]
 
# 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_2                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS393_2.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   32   3.69   18.75  17.203
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS393_2
PFRMAT TS
TARGET T0285
MODEL 2
PARENT N/A
ATOM      1  CA  ALA     1      12.695 -26.357  95.175  1.00 25.00           C
ATOM      2  CA  TYR     2       9.566 -24.508  96.325  1.00 25.00           C
ATOM      3  CA  LEU     3       6.472 -23.036  94.756  1.00 25.00           C
ATOM      4  CA  PRO     4       7.345 -19.358  94.460  1.00 25.00           C
ATOM      5  CA  ASP     5       6.544 -18.045  90.923  1.00 25.00           C
ATOM      6  CA  ASP     6       9.552 -15.687  91.221  1.00 25.00           C
ATOM      7  CA  SER     7      12.865 -15.199  89.492  1.00 25.00           C
ATOM      8  CA  PRO     8      15.260 -13.663  86.952  1.00 25.00           C
ATOM      9  CA  ALA     9      13.173 -12.595  83.924  1.00 25.00           C
ATOM     10  CA  LYS    10      13.054  -9.001  85.241  1.00 25.00           C
ATOM     11  CA  ARG    11      16.853  -9.027  85.725  1.00 25.00           C
ATOM     12  CA  LEU    12      17.323 -10.321  82.152  1.00 25.00           C
ATOM     13  CA  LEU    13      15.031  -7.556  80.821  1.00 25.00           C
ATOM     14  CA  PHE    14      17.028  -4.931  82.769  1.00 25.00           C
ATOM     15  CA  GLN    15      20.297  -6.318  81.335  1.00 25.00           C
ATOM     16  CA  MET    16      18.836  -6.170  77.797  1.00 25.00           C
ATOM     17  CA  VAL    17      17.745  -2.545  78.372  1.00 25.00           C
ATOM     18  CA  GLY    18      21.257  -1.660  79.622  1.00 25.00           C
ATOM     19  CA  ASN    19      22.799  -3.303  76.526  1.00 25.00           C
ATOM     20  CA  ALA    20      20.423  -1.325  74.264  1.00 25.00           C
ATOM     21  CA  ILE    21      21.376   1.920  76.058  1.00 25.00           C
ATOM     22  CA  ASN    22      25.092   1.106  75.609  1.00 25.00           C
ATOM     23  CA  ARG    23      24.519   0.433  71.883  1.00 25.00           C
ATOM     24  CA  ASN    24      22.674   3.772  71.539  1.00 25.00           C
ATOM     25  CA  THR    25      25.558   5.576  73.297  1.00 25.00           C
ATOM     26  CA  GLN    26      28.073   3.901  70.943  1.00 25.00           C
ATOM     27  CA  GLN    27      25.986   4.970  67.914  1.00 25.00           C
ATOM     28  CA  LEU    28      25.867   8.563  69.232  1.00 25.00           C
ATOM     29  CA  THR    29      29.666   8.537  69.715  1.00 25.00           C
ATOM     30  CA  GLN    30      30.136   7.243  66.142  1.00 25.00           C
ATOM     31  CA  ASP    31      27.845  10.009  64.812  1.00 25.00           C
ATOM     32  CA  LEU    32      29.842  12.633  66.760  1.00 25.00           C
ATOM     33  CA  ARG    33      33.111  11.247  65.325  1.00 25.00           C
ATOM     34  CA  ALA    34      34.572   8.970  67.989  1.00 25.00           C
ATOM     35  CA  MET    35      36.426   9.066  71.335  1.00 25.00           C
ATOM     36  CA  PRO    36      36.104   5.554  72.584  1.00 25.00           C
ATOM     37  CA  ASN    37      37.457   2.119  71.906  1.00 25.00           C
ATOM     38  CA  TRP    38      34.387   1.115  73.883  1.00 25.00           C
ATOM     39  CA  SER    39      31.407  -1.117  74.652  1.00 25.00           C
ATOM     40  CA  LEU    40      30.120   0.616  77.798  1.00 25.00           C
ATOM     41  CA  ARG    41      27.738  -0.380  80.568  1.00 25.00           C
ATOM     42  CA  PHE    42      26.104  -3.519  81.964  1.00 25.00           C
ATOM     43  CA  VAL    43      24.967  -1.382  84.852  1.00 25.00           C
ATOM     44  CA  TYR    44      21.254  -1.227  85.581  1.00 25.00           C
ATOM     45  CA  ILE    45      20.775  -4.762  86.817  1.00 25.00           C
ATOM     46  CA  VAL    46      23.450  -6.651  88.820  1.00 25.00           C
ATOM     47  CA  ASP    47      23.585  -9.508  91.411  1.00 25.00           C
ATOM     48  CA  ARG    48      23.703  -6.660  93.991  1.00 25.00           C
ATOM     49  CA  ASN    49      26.665  -4.490  95.092  1.00 25.00           C
ATOM     50  CA  ASN    50      29.320  -4.255  92.410  1.00 25.00           C
ATOM     51  CA  GLN    51      30.025  -0.530  91.861  1.00 25.00           C
ATOM     52  CA  ASP    52      33.777  -1.254  91.601  1.00 25.00           C
ATOM     53  CA  LEU    53      33.092  -4.029  89.052  1.00 25.00           C
ATOM     54  CA  LEU    54      30.900  -1.643  87.009  1.00 25.00           C
ATOM     55  CA  LYS    55      33.899   0.377  85.810  1.00 25.00           C
ATOM     56  CA  ARG    56      37.296  -0.725  84.429  1.00 25.00           C
ATOM     57  CA  PRO    57      39.135   2.399  83.292  1.00 25.00           C
ATOM     58  CA  LEU    58      35.732   3.069  81.642  1.00 25.00           C
ATOM     59  CA  PRO    59      35.167   6.504  83.207  1.00 25.00           C
ATOM     60  CA  PRO    60      31.720   7.895  82.414  1.00 25.00           C
ATOM     61  CA  GLY    61      29.668   4.921  81.386  1.00 25.00           C
ATOM     62  CA  ILE    62      26.136   5.081  82.687  1.00 25.00           C
ATOM     63  CA  MET    63      24.033   3.215  80.122  1.00 25.00           C
ATOM     64  CA  VAL    64      21.080   3.340  82.519  1.00 25.00           C
ATOM     65  CA  LEU    65      17.729   1.752  81.919  1.00 25.00           C
ATOM     66  CA  ALA    66      15.114  -0.386  83.756  1.00 25.00           C
ATOM     67  CA  PRO    67      14.465   0.288  87.471  1.00 25.00           C
ATOM     68  CA  ARG    68      12.343   3.143  88.936  1.00 25.00           C
ATOM     69  CA  LEU    69       9.399   2.603  86.634  1.00 25.00           C
ATOM     70  CA  THR    70       5.547   2.834  86.679  1.00 25.00           C
ATOM     71  CA  ALA    71       2.614   1.814  84.427  1.00 25.00           C
ATOM     72  CA  LYS    72       3.881   4.536  82.183  1.00 25.00           C
ATOM     73  CA  HIS    73       6.703   6.942  83.206  1.00 25.00           C
ATOM     74  CA  PRO    74       8.523  10.033  81.946  1.00 25.00           C
ATOM     75  CA  TYR    75       9.770  11.251  85.328  1.00 25.00           C
ATOM     76  CA  ASP    76       7.049  10.011  87.723  1.00 25.00           C
ATOM     77  CA  LYS    77       9.681   8.152  89.791  1.00 25.00           C
ATOM     78  CA  VAL    78      11.834  11.317  89.941  1.00 25.00           C
ATOM     79  CA  GLN    79       8.799  13.356  91.082  1.00 25.00           C
ATOM     80  CA  ASP    80       8.047  10.762  93.798  1.00 25.00           C
ATOM     81  CA  ARG    81      10.217   8.783  96.123  1.00 25.00           C
ATOM     82  CA  ASN    82      13.037  11.308  96.197  1.00 25.00           C
ATOM     83  CA  ARG    83      14.725  14.741  95.991  1.00 25.00           C
ATOM     84  CA  LYS    84      16.544  12.936  93.156  1.00 25.00           C
ATOM     85  CA  LEU    85      18.243  10.185  91.047  1.00 25.00           C
ATOM     86  CA  TYR    86      17.859  11.591  87.525  1.00 25.00           C
ATOM     87  CA  GLY    87      15.659  10.396  84.657  1.00 25.00           C
ATOM     88  CA  ARG    88      16.877  10.823  81.102  1.00 25.00           C
ATOM     89  CA  HIS    89      15.954   7.139  80.705  1.00 25.00           C
ATOM     90  CA  ILE    90      15.960   5.263  77.412  1.00 25.00           C
ATOM     91  CA  THR    91      17.370   5.040  73.868  1.00 25.00           C
ATOM     92  CA  LEU    92      17.108   4.077  70.147  1.00 25.00           C
ATOM     93  CA  ASN    93      14.065   4.595  67.865  1.00 25.00           C
ATOM     94  CA  ASP    94      12.894   3.908  64.301  1.00 25.00           C
ATOM     95  CA  GLY    95      11.117   0.543  64.834  1.00 25.00           C
ATOM     96  CA  ASN    96       9.141  -0.236  67.990  1.00 25.00           C
ATOM     97  CA  SER    97       9.626   2.374  70.725  1.00 25.00           C
ATOM     98  CA  VAL    98      12.573   2.262  73.082  1.00 25.00           C
ATOM     99  CA  LYS    99      15.191   0.655  75.254  1.00 25.00           C
ATOM    100  CA  VAL   100      15.074  -2.783  73.662  1.00 25.00           C
ATOM    101  CA  VAL   101      16.851  -2.333  70.367  1.00 25.00           C
ATOM    102  CA  THR   102      20.333  -3.809  69.675  1.00 25.00           C
ATOM    103  CA  ILE   103      21.726  -6.390  72.150  1.00 25.00           C
ATOM    104  CA  SER   104      22.322 -10.077  71.427  1.00 25.00           C
ATOM    105  CA  ALA   105      24.472 -11.710  74.145  1.00 25.00           C
ATOM    106  CA  GLY   106      27.669 -13.009  72.529  1.00 25.00           C
ATOM    107  CA  ARG   107      31.058 -14.385  73.465  1.00 25.00           C
ATOM    108  CA  ASP   108      34.672 -15.723  73.494  1.00 25.00           C
ATOM    109  CA  GLU   109      36.220 -18.379  75.724  1.00 25.00           C
ATOM    110  CA  GLY   110      35.739 -17.130  79.289  1.00 25.00           C
ATOM    111  CA  PRO   111      34.490 -20.353  80.996  1.00 25.00           C
ATOM    112  CA  ASP   112      31.794 -21.747  78.691  1.00 25.00           C
ATOM    113  CA  ARG   113      28.145 -20.856  79.173  1.00 25.00           C
ATOM    114  CA  ASP   114      27.606 -23.339  76.308  1.00 25.00           C
ATOM    115  CA  ILE   115      24.678 -24.925  78.200  1.00 25.00           C
ATOM    116  CA  ILE   116      23.144 -21.463  78.775  1.00 25.00           C
ATOM    117  CA  TRP   117      23.515 -20.653  75.051  1.00 25.00           C
ATOM    118  CA  GLU   118      21.831 -23.969  74.137  1.00 25.00           C
ATOM    119  CA  MET   119      18.954 -23.200  76.546  1.00 25.00           C
ATOM    120  CA  PHE   120      18.548 -19.725  74.991  1.00 25.00           C
ATOM    121  CA  LEU   121      18.475 -21.273  71.489  1.00 25.00           C
ATOM    122  CA  GLU   122      15.817 -23.784  72.627  1.00 25.00           C
ATOM    123  CA  ASN   123      13.723 -20.936  74.101  1.00 25.00           C
ATOM    124  CA  LEU   124      10.264 -20.520  75.594  1.00 25.00           C
ATOM    125  CA  GLU   125       7.782 -22.524  73.506  1.00 25.00           C
TER
END
