
#######################################################
#                                                     #
#                        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 T0352TS393_1
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS393_1.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           -
LGA    T       3      T       3           -
LGA    H       4      H       4           -
LGA    D       5      D       5           -
LGA    R       6      R       6           -
LGA    V       7      V       7           -
LGA    R       8      R       8           -
LGA    L       9      L       9           -
LGA    Q      10      Q      10           -
LGA    L      11      L      11           -
LGA    Q      12      Q      12           -
LGA    A      13      A      13           -
LGA    L      14      -       -           -
LGA    E      15      -       -           -
LGA    A      16      -       -           -
LGA    L      17      -       -           -
LGA    L      18      -       -           -
LGA    R      19      -       -           -
LGA    E      20      -       -           -
LGA    H      21      -       -           -
LGA    Q      22      -       -           -
LGA    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    T      37      -       -           -
LGA    Q      38      -       -           -
LGA    P      39      -       -           -
LGA    F      40      -       -           -
LGA    F      41      -       -           -
LGA    M      42      -       -           -
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    M      45      -       -           -
LGA    E      46      -       -           -
LGA    P      47      -       -           -
LGA    L      48      -       -           -
LGA    E      49      -       -           -
LGA    W      50      L      14           #
LGA    -       -      E      15           -
LGA    -       -      A      16           -
LGA    L      51      L      17           #
LGA    Q      52      L      18          4.660
LGA    W      53      -       -           -
LGA    V      54      R      19          4.463
LGA    L      55      E      20           -
LGA    I      56      H      21           -
LGA    -       -      Q      22           -
LGA    -       -      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    P      57      T      37           #
LGA    R      58      Q      38          1.687
LGA    M      59      P      39          3.836
LGA    H      60      F      40          4.243
LGA    D      61      F      41          5.181
LGA    L      62      M      42          4.211
LGA    L      63      D      43           -
LGA    D      64      T      44           -
LGA    N      65      M      45          3.900
LGA    K      66      E      46          1.936
LGA    Q      67      P      47          2.300
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    P      68      W      50          4.300
LGA    L      69      L      51          4.096
LGA    -       -      Q      52           -
LGA    P      70      W      53          2.748
LGA    G      71      V      54          4.892
LGA    -       -      L      55           -
LGA    -       -      I      56           -
LGA    -       -      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    -       -      A      72           -
LGA    A      72      F      73           #
LGA    F      73      -       -           -
LGA    A      74      -       -           -
LGA    V      75      -       -           -
LGA    A      76      A      74          2.682
LGA    P      77      V      75          4.282
LGA    Y      78      A      76          3.958
LGA    Y      79      -       -           -
LGA    E      80      P      77          2.286
LGA    M      81      Y      78          0.646
LGA    A      82      Y      79          1.507
LGA    L      83      E      80          2.170
LGA    A      84      M      81          1.820
LGA    T      85      A      82          2.200
LGA    D      86      L      83          5.182
LGA    H      87      A      84          2.315
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    P      88      H      87          1.006
LGA    Q      89      P      88          2.002
LGA    -       -      Q      89           -
LGA    R      90      R      90          2.801
LGA    A      91      A      91          2.819
LGA    L      92      L      92          2.836
LGA    I      93      I      93          2.519
LGA    L      94      L      94          1.948
LGA    A      95      A      95          1.639
LGA    E      96      E      96          1.286
LGA    L      97      L      97          1.079
LGA    E      98      E      98          1.374
LGA    K      99      K      99          1.207
LGA    L     100      L     100          1.065
LGA    D     101      D     101          1.294
LGA    A     102      A     102          3.547
LGA    L     103      L     103          4.938
LGA    F     104      F     104          4.364
LGA    A     105      A     105          4.396
LGA    D     106      D     106           #
LGA    D     107      D     107           -
LGA    A     108      A     108           -
LGA    S     109      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     43    3.17    41.86     24.530     1.314

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.543445 * X  +  -0.608753 * Y  +  -0.578003 * Z  + -15.469593
  Y_new =  -0.671932 * X  +   0.097267 * Y  +  -0.734198 * Z  +   9.717144
  Z_new =   0.503166 * X  +   0.787375 * Y  +  -0.356181 * Z  +  -2.690455 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.995615   -1.145977  [ DEG:   114.3403    -65.6597 ]
  Theta =  -0.527258   -2.614334  [ DEG:   -30.2097   -149.7903 ]
  Phi   =  -0.890725    2.250868  [ DEG:   -51.0348    128.9652 ]
 
# 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: T0352TS393_1                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS393_1.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   43   3.17   41.86  24.530
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS393_1
PFRMAT TS
TARGET T0352
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1     -15.396  11.292  21.553  1.00 25.00           C
ATOM      2  CA  THR     2     -15.059  14.695  19.870  1.00 25.00           C
ATOM      3  CA  THR     3     -15.833  13.403  16.397  1.00 25.00           C
ATOM      4  CA  HIS     4     -19.178  15.052  15.524  1.00 25.00           C
ATOM      5  CA  ASP     5     -17.353  18.243  14.450  1.00 25.00           C
ATOM      6  CA  ARG     6     -14.983  16.180  12.261  1.00 25.00           C
ATOM      7  CA  VAL     7     -17.972  14.399  10.660  1.00 25.00           C
ATOM      8  CA  ARG     8     -19.646  17.774   9.971  1.00 25.00           C
ATOM      9  CA  LEU     9     -16.417  19.077   8.375  1.00 25.00           C
ATOM     10  CA  GLN    10     -16.205  15.943   6.184  1.00 25.00           C
ATOM     11  CA  LEU    11     -19.849  16.422   5.105  1.00 25.00           C
ATOM     12  CA  GLN    12     -19.135  20.083   4.237  1.00 25.00           C
ATOM     13  CA  ALA    13     -16.081  19.027   2.182  1.00 25.00           C
ATOM     14  CA  LEU    14     -18.196  16.426   0.329  1.00 25.00           C
ATOM     15  CA  GLU    15     -20.857  19.080  -0.407  1.00 25.00           C
ATOM     16  CA  ALA    16     -18.158  21.452  -1.734  1.00 25.00           C
ATOM     17  CA  LEU    17     -16.776  18.668  -3.972  1.00 25.00           C
ATOM     18  CA  LEU    18     -20.296  17.957  -5.304  1.00 25.00           C
ATOM     19  CA  ARG    19     -20.797  21.681  -6.038  1.00 25.00           C
ATOM     20  CA  GLU    20     -17.444  21.793  -7.887  1.00 25.00           C
ATOM     21  CA  HIS    21     -18.449  18.723  -9.944  1.00 25.00           C
ATOM     22  CA  GLN    22     -21.794  20.371 -10.816  1.00 25.00           C
ATOM     23  CA  HIS    23     -19.969  23.562 -11.891  1.00 25.00           C
ATOM     24  CA  TRP    24     -17.599  21.499 -14.080  1.00 25.00           C
ATOM     25  CA  ARG    25     -20.587  19.719 -15.681  1.00 25.00           C
ATOM     26  CA  ASN    26     -22.201  22.910 -17.054  1.00 25.00           C
ATOM     27  CA  ASP    27     -19.699  25.726 -16.411  1.00 25.00           C
ATOM     28  CA  GLU    28     -21.622  27.956 -18.909  1.00 25.00           C
ATOM     29  CA  PRO    29     -19.137  26.548 -21.435  1.00 25.00           C
ATOM     30  CA  GLN    30     -20.214  23.316 -23.133  1.00 25.00           C
ATOM     31  CA  PRO    31     -18.019  20.247 -23.395  1.00 25.00           C
ATOM     32  CA  HIS    32     -14.607  21.761 -22.541  1.00 25.00           C
ATOM     33  CA  GLN    33     -14.262  19.372 -19.570  1.00 25.00           C
ATOM     34  CA  PHE    34     -15.141  16.402 -21.823  1.00 25.00           C
ATOM     35  CA  ASN    35     -12.526  17.538 -24.380  1.00 25.00           C
ATOM     36  CA  SER    36      -9.938  15.239 -22.772  1.00 25.00           C
ATOM     37  CA  THR    37      -8.374  12.882 -25.293  1.00 25.00           C
ATOM     38  CA  GLN    38     -11.740  11.090 -25.048  1.00 25.00           C
ATOM     39  CA  PRO    39     -14.201   8.144 -24.728  1.00 25.00           C
ATOM     40  CA  PHE    40     -15.101   6.924 -21.201  1.00 25.00           C
ATOM     41  CA  PHE    41     -18.235   4.809 -20.696  1.00 25.00           C
ATOM     42  CA  MET    42     -21.502   6.726 -21.338  1.00 25.00           C
ATOM     43  CA  ASP    43     -25.019   5.333 -21.738  1.00 25.00           C
ATOM     44  CA  THR    44     -27.407   7.907 -20.253  1.00 25.00           C
ATOM     45  CA  MET    45     -26.179  10.645 -17.962  1.00 25.00           C
ATOM     46  CA  GLU    46     -27.302   8.336 -15.213  1.00 25.00           C
ATOM     47  CA  PRO    47     -25.096   8.704 -12.152  1.00 25.00           C
ATOM     48  CA  LEU    48     -25.765   8.663  -8.381  1.00 25.00           C
ATOM     49  CA  GLU    49     -23.031   6.026  -7.900  1.00 25.00           C
ATOM     50  CA  TRP    50     -20.585   8.153  -9.941  1.00 25.00           C
ATOM     51  CA  LEU    51     -21.444  11.222  -7.817  1.00 25.00           C
ATOM     52  CA  GLN    52     -20.865   9.199  -4.617  1.00 25.00           C
ATOM     53  CA  TRP    53     -17.481   8.004  -5.956  1.00 25.00           C
ATOM     54  CA  VAL    54     -16.510  11.612  -6.794  1.00 25.00           C
ATOM     55  CA  LEU    55     -17.504  12.725  -3.267  1.00 25.00           C
ATOM     56  CA  ILE    56     -15.405   9.900  -1.757  1.00 25.00           C
ATOM     57  CA  PRO    57     -12.414  10.938  -3.911  1.00 25.00           C
ATOM     58  CA  ARG    58     -12.826  14.573  -2.777  1.00 25.00           C
ATOM     59  CA  MET    59     -12.949  13.443   0.880  1.00 25.00           C
ATOM     60  CA  HIS    60      -9.768  11.371   0.372  1.00 25.00           C
ATOM     61  CA  ASP    61      -8.025  14.390  -1.211  1.00 25.00           C
ATOM     62  CA  LEU    62      -9.085  16.584   1.743  1.00 25.00           C
ATOM     63  CA  LEU    63      -7.734  13.973   4.197  1.00 25.00           C
ATOM     64  CA  ASP    64      -4.417  13.857   2.287  1.00 25.00           C
ATOM     65  CA  ASN    65      -3.929  17.514   1.510  1.00 25.00           C
ATOM     66  CA  LYS    66      -3.712  20.892   3.332  1.00 25.00           C
ATOM     67  CA  GLN    67      -3.066  19.933   6.991  1.00 25.00           C
ATOM     68  CA  PRO    68      -1.956  16.310   6.658  1.00 25.00           C
ATOM     69  CA  LEU    69      -4.756  14.555   8.598  1.00 25.00           C
ATOM     70  CA  PRO    70      -4.502  10.786   9.102  1.00 25.00           C
ATOM     71  CA  GLY    71      -7.219   8.583   7.680  1.00 25.00           C
ATOM     72  CA  ALA    72     -10.086   7.030   5.626  1.00 25.00           C
ATOM     73  CA  PHE    73     -12.022   7.251   8.923  1.00 25.00           C
ATOM     74  CA  ALA    74     -13.837  10.384   7.675  1.00 25.00           C
ATOM     75  CA  VAL    75     -14.736   8.592   4.412  1.00 25.00           C
ATOM     76  CA  ALA    76     -16.072   5.600   6.392  1.00 25.00           C
ATOM     77  CA  PRO    77     -18.175   7.949   8.568  1.00 25.00           C
ATOM     78  CA  TYR    78     -19.573   9.644   5.432  1.00 25.00           C
ATOM     79  CA  TYR    79     -20.450   6.225   3.945  1.00 25.00           C
ATOM     80  CA  GLU    80     -22.212   5.236   7.199  1.00 25.00           C
ATOM     81  CA  MET    81     -24.187   8.516   7.155  1.00 25.00           C
ATOM     82  CA  ALA    82     -25.204   7.884   3.517  1.00 25.00           C
ATOM     83  CA  LEU    83     -26.340   4.341   4.425  1.00 25.00           C
ATOM     84  CA  ALA    84     -28.394   5.721   7.348  1.00 25.00           C
ATOM     85  CA  THR    85     -31.628   7.195   6.009  1.00 25.00           C
ATOM     86  CA  ASP    86     -31.203   7.536   2.241  1.00 25.00           C
ATOM     87  CA  HIS    87     -32.420   4.165   0.821  1.00 25.00           C
ATOM     88  CA  PRO    88     -31.470   2.774  -2.597  1.00 25.00           C
ATOM     89  CA  GLN    89     -28.863   5.276  -3.864  1.00 25.00           C
ATOM     90  CA  ARG    90     -27.340   5.501  -0.357  1.00 25.00           C
ATOM     91  CA  ALA    91     -27.185   1.680  -0.152  1.00 25.00           C
ATOM     92  CA  LEU    92     -25.470   1.542  -3.574  1.00 25.00           C
ATOM     93  CA  ILE    93     -22.929   4.171  -2.433  1.00 25.00           C
ATOM     94  CA  LEU    94     -22.235   2.156   0.748  1.00 25.00           C
ATOM     95  CA  ALA    95     -21.725  -1.013  -1.341  1.00 25.00           C
ATOM     96  CA  GLU    96     -19.305   0.863  -3.641  1.00 25.00           C
ATOM     97  CA  LEU    97     -17.363   2.140  -0.597  1.00 25.00           C
ATOM     98  CA  GLU    98     -17.166  -1.418   0.803  1.00 25.00           C
ATOM     99  CA  LYS    99     -15.884  -2.701  -2.570  1.00 25.00           C
ATOM    100  CA  LEU   100     -13.235   0.064  -2.642  1.00 25.00           C
ATOM    101  CA  ASP   101     -12.145  -0.855   0.913  1.00 25.00           C
ATOM    102  CA  ALA   102     -11.881  -4.540  -0.094  1.00 25.00           C
ATOM    103  CA  LEU   103      -9.771  -3.582  -3.143  1.00 25.00           C
ATOM    104  CA  PHE   104      -7.476  -1.468  -0.921  1.00 25.00           C
ATOM    105  CA  ALA   105      -7.092  -4.401   1.512  1.00 25.00           C
ATOM    106  CA  ASP   106      -6.229  -6.735  -1.398  1.00 25.00           C
ATOM    107  CA  ASP   107      -3.621  -4.232  -2.664  1.00 25.00           C
ATOM    108  CA  ALA   108      -2.099  -4.008   0.842  1.00 25.00           C
ATOM    109  CA  SER   109      -1.943  -7.829   1.047  1.00 25.00           C
ATOM    110  CA  LEU   110      -1.525  -9.994   4.126  1.00 25.00           C
ATOM    111  CA  GLU   111       0.398  -6.982   5.387  1.00 25.00           C
ATOM    112  CA  HIS   112       3.603  -8.415   3.953  1.00 25.00           C
ATOM    113  CA  HIS   113       5.256  -8.857   0.582  1.00 25.00           C
ATOM    114  CA  HIS   114       6.712  -5.332   0.494  1.00 25.00           C
ATOM    115  CA  HIS   115       7.983  -2.124   2.027  1.00 25.00           C
ATOM    116  CA  HIS   116       6.497   0.785   4.070  1.00 25.00           C
ATOM    117  CA  HIS   117       3.316  -1.173   4.900  1.00 25.00           C
TER
END
