
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0352TS599_4
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS599_4.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    T       2      T       2          5.001
LGA    T       3      T       3          1.633
LGA    H       4      H       4          0.441
LGA    D       5      D       5          0.511
LGA    R       6      R       6          0.318
LGA    V       7      V       7          0.781
LGA    R       8      R       8          0.854
LGA    L       9      L       9          0.431
LGA    Q      10      Q      10          0.599
LGA    L      11      L      11          1.772
LGA    Q      12      Q      12          1.920
LGA    A      13      A      13          1.055
LGA    L      14      L      14          1.818
LGA    E      15      E      15          2.381
LGA    A      16      A      16          1.641
LGA    L      17      L      17          1.955
LGA    L      18      L      18          2.617
LGA    R      19      R      19          2.463
LGA    E      20      E      20          2.740
LGA    H      21      H      21          3.071
LGA    Q      22      Q      22          3.425
LGA    H      23      H      23           #
LGA    -       -      W      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      E      28           -
LGA    -       -      P      29           -
LGA    -       -      Q      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      Q      33           -
LGA    -       -      F      34           -
LGA    -       -      N      35           -
LGA    -       -      S      36           -
LGA    W      24      T      37          5.585
LGA    R      25      Q      38           #
LGA    N      26      P      39           -
LGA    D      27      F      40           #
LGA    E      28      -       -           -
LGA    P      29      -       -           -
LGA    Q      30      -       -           -
LGA    P      31      -       -           -
LGA    H      32      -       -           -
LGA    Q      33      -       -           -
LGA    F      34      -       -           -
LGA    N      35      -       -           -
LGA    S      36      -       -           -
LGA    T      37      -       -           -
LGA    Q      38      -       -           -
LGA    P      39      -       -           -
LGA    F      40      -       -           -
LGA    F      41      F      41          0.870
LGA    M      42      M      42          3.702
LGA    D      43      D      43          3.754
LGA    T      44      T      44           -
LGA    M      45      M      45           -
LGA    E      46      E      46           -
LGA    -       -      P      47           -
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    -       -      W      50           -
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    -       -      W      53           -
LGA    P      47      V      54           #
LGA    L      48      L      55          4.714
LGA    E      49      I      56          1.254
LGA    W      50      P      57           #
LGA    -       -      R      58           -
LGA    -       -      M      59           -
LGA    -       -      H      60           -
LGA    -       -      D      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    -       -      N      65           -
LGA    -       -      K      66           -
LGA    -       -      Q      67           -
LGA    -       -      P      68           -
LGA    -       -      L      69           -
LGA    -       -      P      70           -
LGA    -       -      G      71           -
LGA    L      51      A      72           #
LGA    Q      52      -       -           -
LGA    W      53      -       -           -
LGA    V      54      F      73          5.201
LGA    L      55      A      74          1.965
LGA    I      56      -       -           -
LGA    P      57      -       -           -
LGA    R      58      -       -           -
LGA    M      59      V      75          3.416
LGA    H      60      A      76          4.307
LGA    D      61      P      77          3.033
LGA    L      62      Y      78          2.100
LGA    L      63      Y      79          3.230
LGA    D      64      E      80          2.422
LGA    N      65      M      81          0.180
LGA    K      66      A      82          2.055
LGA    Q      67      L      83           #
LGA    -       -      A      84           -
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    -       -      H      87           -
LGA    -       -      P      88           -
LGA    P      68      Q      89           #
LGA    L      69      R      90          1.656
LGA    P      70      A      91           -
LGA    G      71      -       -           -
LGA    A      72      -       -           -
LGA    F      73      -       -           -
LGA    A      74      L      92          1.873
LGA    V      75      I      93          1.515
LGA    A      76      L      94          2.128
LGA    P      77      A      95          1.273
LGA    Y      78      E      96          1.147
LGA    Y      79      L      97          2.564
LGA    E      80      E      98          2.420
LGA    M      81      K      99          1.655
LGA    A      82      L     100          2.267
LGA    L      83      D     101          2.722
LGA    A      84      A     102          2.151
LGA    T      85      L     103          1.944
LGA    D      86      F     104          2.126
LGA    H      87      A     105          2.759
LGA    P      88      D     106           -
LGA    Q      89      D     107           -
LGA    R      90      A     108           -
LGA    A      91      S     109           -
LGA    L      92      -       -           -
LGA    I      93      -       -           -
LGA    L      94      -       -           -
LGA    A      95      -       -           -
LGA    E      96      -       -           -
LGA    L      97      -       -           -
LGA    E      98      -       -           -
LGA    K      99      -       -           -
LGA    L     100      -       -           -
LGA    D     101      -       -           -
LGA    A     102      -       -           -
LGA    L     103      -       -           -
LGA    F     104      -       -           -
LGA    A     105      -       -           -
LGA    D     106      -       -           -
LGA    D     107      -       -           -
LGA    A     108      -       -           -
LGA    S     109      -       -           -
LGA    L     110      -       -           -
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117  109    5.0     52    2.55    51.92     32.385     1.962

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.173755 * X  +  -0.372516 * Y  +   0.911614 * Z  + -12.646272
  Y_new =  -0.662076 * X  +  -0.641083 * Y  +  -0.388160 * Z  +   8.097960
  Z_new =   0.729016 * X  +  -0.671003 * Y  +  -0.135243 * Z  +   4.363931 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.769685    1.371908  [ DEG:  -101.3955     78.6045 ]
  Theta =  -0.816884   -2.324709  [ DEG:   -46.8040   -133.1960 ]
  Phi   =  -1.827448    1.314144  [ DEG:  -104.7051     75.2949 ]
 
# 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: T0352TS599_4                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS599_4.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   52   2.55   51.92  32.385
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS599_4
PFRMAT TS                                                                       
TARGET T0352                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       1.019   0.329  -5.740  1.00  0.00              
ATOM      2  CA  THR     2      -0.376  -3.268  -5.478  1.00  0.00              
ATOM      3  CA  THR     3      -3.216  -5.329  -4.713  1.00  0.00              
ATOM      4  CA  HIS     4      -1.393  -1.890  -6.335  1.00  0.00              
ATOM      5  CA  ASP     5      -2.930  -2.235  -9.822  1.00  0.00              
ATOM      6  CA  ARG     6      -6.286  -2.906  -8.216  1.00  0.00              
ATOM      7  CA  VAL     7      -5.986   0.136  -5.982  1.00  0.00              
ATOM      8  CA  ARG     8      -5.037   2.333  -8.932  1.00  0.00              
ATOM      9  CA  LEU     9      -8.049   1.085 -10.929  1.00  0.00              
ATOM     10  CA  GLN    10     -10.375   1.766  -8.007  1.00  0.00              
ATOM     11  CA  LEU    11      -8.995   5.291  -7.686  1.00  0.00              
ATOM     12  CA  GLN    12      -9.445   5.891 -11.411  1.00  0.00              
ATOM     13  CA  ALA    13     -13.065   4.759 -11.214  1.00  0.00              
ATOM     14  CA  LEU    14     -13.696   7.070  -8.311  1.00  0.00              
ATOM     15  CA  GLU    15     -12.083  10.026 -10.166  1.00  0.00              
ATOM     16  CA  ALA    16     -14.220   9.557 -13.262  1.00  0.00              
ATOM     17  CA  LEU    17     -17.417   9.359 -11.240  1.00  0.00              
ATOM     18  CA  LEU    18     -16.594  12.369  -9.133  1.00  0.00              
ATOM     19  CA  ARG    19     -15.759  14.463 -12.176  1.00  0.00              
ATOM     20  CA  GLU    20     -18.904  13.651 -14.088  1.00  0.00              
ATOM     21  CA  HIS    21     -20.857  14.565 -10.891  1.00  0.00              
ATOM     22  CA  GLN    22     -19.086  17.900 -10.208  1.00  0.00              
ATOM     23  CA  HIS    23     -17.809  16.893  -6.746  1.00  0.00              
ATOM     24  CA  TRP    24     -14.097  17.658  -7.148  1.00  0.00              
ATOM     25  CA  ARG    25     -14.413  21.374  -7.943  1.00  0.00              
ATOM     26  CA  ASN    26     -16.448  21.824  -4.747  1.00  0.00              
ATOM     27  CA  ASP    27     -14.647  19.788  -2.068  1.00  0.00              
ATOM     28  CA  GLU    28     -13.033  21.862   0.613  1.00  0.00              
ATOM     29  CA  PRO    29     -13.567  20.497   4.058  1.00  0.00              
ATOM     30  CA  GLN    30     -14.777  23.226   6.292  1.00  0.00              
ATOM     31  CA  PRO    31     -12.178  24.964   8.509  1.00  0.00              
ATOM     32  CA  HIS    32     -14.008  23.880  11.637  1.00  0.00              
ATOM     33  CA  GLN    33     -13.862  20.194  10.595  1.00  0.00              
ATOM     34  CA  PHE    34     -10.139  20.416   9.867  1.00  0.00              
ATOM     35  CA  ASN    35      -9.356  22.067  13.242  1.00  0.00              
ATOM     36  CA  SER    36     -11.308  19.542  15.317  1.00  0.00              
ATOM     37  CA  THR    37      -9.903  16.315  13.955  1.00  0.00              
ATOM     38  CA  GLN    38     -12.865  14.996  12.014  1.00  0.00              
ATOM     39  CA  PRO    39     -12.296  14.282   8.367  1.00  0.00              
ATOM     40  CA  PHE    40     -12.004  16.855   5.626  1.00  0.00              
ATOM     41  CA  PHE    41     -12.603  16.165   1.978  1.00  0.00              
ATOM     42  CA  MET    42     -10.235  17.705  -0.508  1.00  0.00              
ATOM     43  CA  ASP    43     -11.339  18.178  -4.055  1.00  0.00              
ATOM     44  CA  THR    44      -8.924  15.938  -5.860  1.00  0.00              
ATOM     45  CA  MET    45      -9.066  13.160  -3.275  1.00  0.00              
ATOM     46  CA  GLU    46      -6.296  10.567  -3.659  1.00  0.00              
ATOM     47  CA  PRO    47      -7.128   6.895  -3.594  1.00  0.00              
ATOM     48  CA  LEU    48      -5.341   6.290  -0.253  1.00  0.00              
ATOM     49  CA  GLU    49      -7.273   9.141   1.350  1.00  0.00              
ATOM     50  CA  TRP    50     -10.561   7.771   0.031  1.00  0.00              
ATOM     51  CA  LEU    51      -9.878   4.301   1.400  1.00  0.00              
ATOM     52  CA  GLN    52      -9.013   5.752   4.811  1.00  0.00              
ATOM     53  CA  TRP    53     -12.237   7.764   4.658  1.00  0.00              
ATOM     54  CA  VAL    54     -14.422   4.832   3.791  1.00  0.00              
ATOM     55  CA  LEU    55     -13.239   2.904   6.785  1.00  0.00              
ATOM     56  CA  ILE    56     -13.039   5.703   9.371  1.00  0.00              
ATOM     57  CA  PRO    57     -15.444   5.114  12.256  1.00  0.00              
ATOM     58  CA  ARG    58     -17.705   8.193  11.654  1.00  0.00              
ATOM     59  CA  MET    59     -17.930   7.326   7.897  1.00  0.00              
ATOM     60  CA  HIS    60     -18.849   3.711   8.693  1.00  0.00              
ATOM     61  CA  ASP    61     -21.756   4.892  10.910  1.00  0.00              
ATOM     62  CA  LEU    62     -23.054   7.191   8.164  1.00  0.00              
ATOM     63  CA  LEU    63     -22.884   4.379   5.549  1.00  0.00              
ATOM     64  CA  ASP    64     -24.721   1.976   7.885  1.00  0.00              
ATOM     65  CA  ASN    65     -27.356   4.724   8.474  1.00  0.00              
ATOM     66  CA  LYS    66     -28.369   4.904   4.883  1.00  0.00              
ATOM     67  CA  GLN    67     -27.162   8.318   3.849  1.00  0.00              
ATOM     68  CA  PRO    68     -27.664   8.220   0.159  1.00  0.00              
ATOM     69  CA  LEU    69     -24.626   8.236  -2.044  1.00  0.00              
ATOM     70  CA  PRO    70     -24.241  11.112  -4.481  1.00  0.00              
ATOM     71  CA  GLY    71     -26.286  10.989  -7.627  1.00  0.00              
ATOM     72  CA  ALA    72     -23.690   9.891 -10.169  1.00  0.00              
ATOM     73  CA  PHE    73     -21.984   7.325  -7.858  1.00  0.00              
ATOM     74  CA  ALA    74     -24.029   5.209  -5.490  1.00  0.00              
ATOM     75  CA  VAL    75     -21.872   5.097  -2.426  1.00  0.00              
ATOM     76  CA  ALA    76     -23.423   2.282  -0.358  1.00  0.00              
ATOM     77  CA  PRO    77     -22.460  -0.505  -2.772  1.00  0.00              
ATOM     78  CA  TYR    78     -18.926   0.812  -3.241  1.00  0.00              
ATOM     79  CA  TYR    79     -18.169   1.179   0.501  1.00  0.00              
ATOM     80  CA  GLU    80     -19.425  -2.351   1.219  1.00  0.00              
ATOM     81  CA  MET    81     -17.333  -3.809  -1.594  1.00  0.00              
ATOM     82  CA  ALA    82     -14.157  -2.075  -0.549  1.00  0.00              
ATOM     83  CA  LEU    83     -14.467  -3.205   3.038  1.00  0.00              
ATOM     84  CA  ALA    84     -15.042  -6.846   2.166  1.00  0.00              
ATOM     85  CA  THR    85     -12.044  -7.116  -0.210  1.00  0.00              
ATOM     86  CA  ASP    86      -9.561  -5.266   1.883  1.00  0.00              
ATOM     87  CA  HIS    87      -9.935  -6.880   5.248  1.00  0.00              
ATOM     88  CA  PRO    88      -6.654  -5.700   6.816  1.00  0.00              
ATOM     89  CA  GLN    89      -6.580  -1.951   6.135  1.00  0.00              
ATOM     90  CA  ARG    90     -10.210  -1.613   7.297  1.00  0.00              
ATOM     91  CA  ALA    91      -9.541  -3.441  10.554  1.00  0.00              
ATOM     92  CA  LEU    92      -6.477  -1.268  11.360  1.00  0.00              
ATOM     93  CA  ILE    93      -8.423   1.887  10.737  1.00  0.00              
ATOM     94  CA  LEU    94     -11.292   0.799  13.001  1.00  0.00              
ATOM     95  CA  ALA    95      -8.776  -0.135  15.707  1.00  0.00              
ATOM     96  CA  GLU    96      -7.090   3.276  15.463  1.00  0.00              
ATOM     97  CA  LEU    97     -10.440   5.056  15.664  1.00  0.00              
ATOM     98  CA  GLU    98     -11.404   3.059  18.735  1.00  0.00              
ATOM     99  CA  LYS    99      -8.131   3.869  20.401  1.00  0.00              
ATOM    100  CA  LEU   100      -8.515   7.574  19.709  1.00  0.00              
ATOM    101  CA  ASP   101     -12.072   7.563  21.158  1.00  0.00              
ATOM    102  CA  ALA   102     -10.722   6.026  24.356  1.00  0.00              
ATOM    103  CA  LEU   103      -7.998   8.694  24.527  1.00  0.00              
ATOM    104  CA  PHE   104     -10.559  11.471  23.986  1.00  0.00              
ATOM    105  CA  ALA   105     -12.820  10.095  26.731  1.00  0.00              
ATOM    106  CA  ASP   106     -10.017   9.807  29.255  1.00  0.00              
ATOM    107  CA  ASP   107      -8.690  13.332  28.582  1.00  0.00              
ATOM    108  CA  ALA   108      -5.293  12.278  27.355  1.00  0.00              
ATOM    109  CA  SER   109      -4.602  14.064  24.023  1.00  0.00              
ATOM    110  CA  LEU   110      -3.281  11.353  21.748  1.00  0.00              
ATOM    111  CA  GLU   111      -4.148  12.757  18.366  1.00  0.00              
ATOM    112  CA  HIS   112      -1.094  12.867  16.197  1.00  0.00              
ATOM    113  CA  HIS   113      -1.934  15.943  14.095  1.00  0.00              
ATOM    114  CA  HIS   114      -0.765  16.789  17.591  1.00  0.00              
ATOM    115  CA  HIS   115      -4.496  18.280  18.814  1.00  0.00              
ATOM    116  CA  HIS   116      -4.704  19.507  22.514  1.00  0.00              
ATOM    117  CA  HIS   117      -8.267  17.579  23.621  1.00  0.00              
TER                                                                             
END
