
#######################################################
#                                                     #
#                        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  108 (  108),  selected  108 , name T0291TS168_2-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS168_2-D1.T0291_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       1      T       1           #
LGA    Y       2      Y       2           #
LGA    V       3      V       3          3.755
LGA    D       4      D       4          5.167
LGA    P       5      P       5          4.544
LGA    H       6      H       6          5.440
LGA    T       7      -       -           -
LGA    Y       8      -       -           -
LGA    E       9      -       -           -
LGA    D      10      -       -           -
LGA    P      11      -       -           -
LGA    T      12      -       -           -
LGA    Q      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      V      15          2.309
LGA    H      16      H      16          1.586
LGA    E      17      E      17          3.683
LGA    F      18      F      18          1.823
LGA    A      19      A      19          1.307
LGA    K      20      K      20          2.835
LGA    E      21      E      21          2.288
LGA    L      22      L      22          1.116
LGA    D      23      D      23          2.207
LGA    A      24      A      24          3.283
LGA    T      25      -       -           -
LGA    N      26      T      25          2.356
LGA    I      27      N      26          3.163
LGA    S      28      I      27          3.051
LGA    I      29      S      28          2.769
LGA    D      30      I      29          3.093
LGA    K      31      D      30          1.922
LGA    V      32      K      31          1.407
LGA    V      33      V      32          3.999
LGA    G      34      V      33          1.237
LGA    A      35      G      34          1.511
LGA    G      36      A      35          3.415
LGA    E      37      G      36          2.364
LGA    F      38      E      37          3.473
LGA    -       -      F      38           -
LGA    G      39      G      39          4.056
LGA    -       -      E      40           -
LGA    E      40      V      41          0.296
LGA    V      41      C      42          3.568
LGA    C      42      S      43          2.441
LGA    S      43      -       -           -
LGA    G      44      G      44          2.867
LGA    R      45      R      45          1.490
LGA    L      46      L      46          0.637
LGA    K      47      K      47          1.475
LGA    L      48      L      48          1.452
LGA    P      49      P      49          2.105
LGA    S      50      S      50          1.440
LGA    K      51      K      51          2.588
LGA    K      52      K      52          3.391
LGA    E      53      E      53          1.152
LGA    I      54      I      54          2.673
LGA    S      55      S      55          2.448
LGA    V      56      V      56          1.810
LGA    A      57      A      57          2.409
LGA    I      58      I      58          1.868
LGA    K      59      K      59          1.165
LGA    T      60      T      60          1.437
LGA    L      61      L      61          2.065
LGA    K      62      K      62          1.865
LGA    V      63      V      63          1.001
LGA    G      64      G      64          2.172
LGA    Y      65      Y      65          2.344
LGA    T      66      T      66          1.135
LGA    E      67      E      67          0.936
LGA    K      68      K      68          1.036
LGA    Q      69      Q      69          0.521
LGA    R      70      R      70          0.346
LGA    R      71      R      71          0.862
LGA    D      72      D      72          0.579
LGA    F      73      F      73          0.576
LGA    L      74      L      74          1.712
LGA    G      75      G      75          1.320
LGA    E      76      E      76          1.275
LGA    A      77      A      77          1.212
LGA    S      78      S      78          1.418
LGA    I      79      I      79          1.893
LGA    M      80      M      80          1.402
LGA    G      81      G      81          1.631
LGA    Q      82      Q      82          2.816
LGA    F      83      F      83          3.671
LGA    D      84      D      84          4.416
LGA    H      85      H      85          3.152
LGA    P      86      P      86          3.555
LGA    N      87      N      87          1.328
LGA    I      88      I      88          1.490
LGA    I      89      I      89          1.100
LGA    R      90      R      90          1.255
LGA    L      91      L      91          1.549
LGA    E      92      E      92          1.573
LGA    G      93      G      93          0.442
LGA    V      94      V      94          0.257
LGA    V      95      V      95          0.216
LGA    T      96      T      96          1.007
LGA    K      97      K      97          2.021
LGA    S      98      S      98          2.005
LGA    K      99      K      99          1.968
LGA    P     100      P     100          1.254
LGA    V     101      V     101          2.130
LGA    M     102      M     102          1.343
LGA    I     103      I     103          1.803
LGA    V     104      V     104          1.836
LGA    T     105      T     105          0.965
LGA    E     106      E     106          1.030
LGA    Y     107      Y     107          1.632
LGA    M     108      M     108          1.415

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     96    2.29    84.38     77.236     4.024

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.193772 * X  +   0.479667 * Y  +   0.855787 * Z  +  -1.560634
  Y_new =  -0.978162 * X  +  -0.027623 * Y  +  -0.205998 * Z  +   9.165928
  Z_new =  -0.075171 * X  +  -0.877016 * Y  +   0.474545 * Z  +  54.997509 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.074819    2.066774  [ DEG:   -61.5826    118.4174 ]
  Theta =   0.075242    3.066351  [ DEG:     4.3110    175.6890 ]
  Phi   =  -1.766362    1.375230  [ DEG:  -101.2051     78.7949 ]
 
# 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: T0291TS168_2-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS168_2-D1.T0291_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  100   5.0   96   2.29   84.38  77.236
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS168_2-D1
PFRMAT TS
TARGET T0291
MODEL 2
PARENT N/A
ATOM      1  CA  THR     1      -4.520  36.125  44.313  1.00 25.00           C
ATOM      2  CA  TYR     2      -4.922  32.952  46.362  1.00 25.00           C
ATOM      3  CA  VAL     3      -7.237  31.806  49.156  1.00 25.00           C
ATOM      4  CA  ASP     4      -8.923  28.957  50.928  1.00 25.00           C
ATOM      5  CA  PRO     5     -12.712  29.031  51.586  1.00 25.00           C
ATOM      6  CA  HIS     6     -12.691  30.659  55.052  1.00 25.00           C
ATOM      7  CA  THR     7     -11.934  34.381  54.438  1.00 25.00           C
ATOM      8  CA  TYR     8     -15.685  34.725  54.183  1.00 25.00           C
ATOM      9  CA  GLU     9     -18.448  34.869  56.874  1.00 25.00           C
ATOM     10  CA  ASP    10     -21.342  33.124  55.061  1.00 25.00           C
ATOM     11  CA  PRO    11     -19.719  31.038  52.406  1.00 25.00           C
ATOM     12  CA  THR    12     -21.841  28.121  51.118  1.00 25.00           C
ATOM     13  CA  GLN    13     -21.855  29.648  47.606  1.00 25.00           C
ATOM     14  CA  ALA    14     -18.047  30.048  47.740  1.00 25.00           C
ATOM     15  CA  VAL    15     -17.676  26.396  48.832  1.00 25.00           C
ATOM     16  CA  HIS    16     -19.932  25.279  45.946  1.00 25.00           C
ATOM     17  CA  GLU    17     -17.841  27.333  43.483  1.00 25.00           C
ATOM     18  CA  PHE    18     -14.632  25.752  44.851  1.00 25.00           C
ATOM     19  CA  ALA    19     -16.159  22.261  44.466  1.00 25.00           C
ATOM     20  CA  LYS    20     -17.157  23.069  40.858  1.00 25.00           C
ATOM     21  CA  GLU    21     -20.314  21.092  41.821  1.00 25.00           C
ATOM     22  CA  LEU    22     -21.917  17.685  42.354  1.00 25.00           C
ATOM     23  CA  ASP    23     -24.619  17.178  39.723  1.00 25.00           C
ATOM     24  CA  ALA    24     -26.473  15.154  42.274  1.00 25.00           C
ATOM     25  CA  THR    25     -28.736  12.498  40.807  1.00 25.00           C
ATOM     26  CA  ASN    26     -26.220  12.005  37.960  1.00 25.00           C
ATOM     27  CA  ILE    27     -25.811   8.287  38.746  1.00 25.00           C
ATOM     28  CA  SER    28     -24.347   6.174  41.627  1.00 25.00           C
ATOM     29  CA  ILE    29     -23.980   2.861  43.478  1.00 25.00           C
ATOM     30  CA  ASP    30     -20.757   1.060  42.559  1.00 25.00           C
ATOM     31  CA  LYS    31     -20.974  -1.344  45.472  1.00 25.00           C
ATOM     32  CA  VAL    32     -19.139  -1.561  48.814  1.00 25.00           C
ATOM     33  CA  VAL    33     -15.367  -1.378  49.134  1.00 25.00           C
ATOM     34  CA  GLY    34     -14.710   0.454  52.422  1.00 25.00           C
ATOM     35  CA  ALA    35     -15.182   0.635  56.240  1.00 25.00           C
ATOM     36  CA  GLY    36     -13.746   2.366  59.351  1.00 25.00           C
ATOM     37  CA  GLU    37     -14.149   5.683  61.192  1.00 25.00           C
ATOM     38  CA  PHE    38     -16.975   7.615  59.447  1.00 25.00           C
ATOM     39  CA  GLY    39     -18.478   4.759  57.432  1.00 25.00           C
ATOM     40  CA  GLU    40     -16.639   4.931  54.098  1.00 25.00           C
ATOM     41  CA  VAL    41     -14.558   5.648  51.032  1.00 25.00           C
ATOM     42  CA  CYS    42     -17.071   3.824  48.905  1.00 25.00           C
ATOM     43  CA  SER    43     -16.325   3.347  45.220  1.00 25.00           C
ATOM     44  CA  GLY    44     -19.211   5.567  44.241  1.00 25.00           C
ATOM     45  CA  ARG    45     -18.984   5.349  40.410  1.00 25.00           C
ATOM     46  CA  LEU    46     -18.690   8.998  39.257  1.00 25.00           C
ATOM     47  CA  LYS    47     -20.455   8.715  35.899  1.00 25.00           C
ATOM     48  CA  LEU    48     -18.765  12.050  35.061  1.00 25.00           C
ATOM     49  CA  PRO    49     -20.416  13.856  32.141  1.00 25.00           C
ATOM     50  CA  SER    50     -16.931  14.594  30.890  1.00 25.00           C
ATOM     51  CA  LYS    51     -16.472  11.057  29.431  1.00 25.00           C
ATOM     52  CA  LYS    52     -18.428   7.872  30.112  1.00 25.00           C
ATOM     53  CA  GLU    53     -16.611   6.767  33.271  1.00 25.00           C
ATOM     54  CA  ILE    54     -14.549   8.989  35.652  1.00 25.00           C
ATOM     55  CA  SER    55     -13.681   6.756  38.616  1.00 25.00           C
ATOM     56  CA  VAL    56     -14.236   8.221  42.063  1.00 25.00           C
ATOM     57  CA  ALA    57     -15.032   8.247  45.768  1.00 25.00           C
ATOM     58  CA  ILE    58     -18.125   9.074  47.798  1.00 25.00           C
ATOM     59  CA  LYS    59     -18.414   9.291  51.562  1.00 25.00           C
ATOM     60  CA  THR    60     -21.060   8.639  54.230  1.00 25.00           C
ATOM     61  CA  LEU    61     -21.223  10.379  57.578  1.00 25.00           C
ATOM     62  CA  LYS    62     -24.664   8.667  57.826  1.00 25.00           C
ATOM     63  CA  VAL    63     -27.713   9.307  59.987  1.00 25.00           C
ATOM     64  CA  GLY    64     -28.933  12.946  60.132  1.00 25.00           C
ATOM     65  CA  TYR    65     -26.966  12.965  63.436  1.00 25.00           C
ATOM     66  CA  THR    66     -25.551  16.412  64.016  1.00 25.00           C
ATOM     67  CA  GLU    67     -24.843  20.038  63.000  1.00 25.00           C
ATOM     68  CA  LYS    68     -21.370  19.935  64.611  1.00 25.00           C
ATOM     69  CA  GLN    69     -20.512  16.780  62.617  1.00 25.00           C
ATOM     70  CA  ARG    70     -21.675  18.476  59.386  1.00 25.00           C
ATOM     71  CA  ARG    71     -19.521  21.539  60.189  1.00 25.00           C
ATOM     72  CA  ASP    72     -16.499  19.276  60.829  1.00 25.00           C
ATOM     73  CA  PHE    73     -17.093  17.496  57.492  1.00 25.00           C
ATOM     74  CA  LEU    74     -17.302  20.874  55.699  1.00 25.00           C
ATOM     75  CA  GLY    75     -14.026  21.978  57.346  1.00 25.00           C
ATOM     76  CA  GLU    76     -12.347  18.713  56.255  1.00 25.00           C
ATOM     77  CA  ALA    77     -13.598  19.240  52.674  1.00 25.00           C
ATOM     78  CA  SER    78     -12.234  22.818  52.697  1.00 25.00           C
ATOM     79  CA  ILE    79      -8.849  21.546  53.958  1.00 25.00           C
ATOM     80  CA  MET    80      -8.780  18.906  51.183  1.00 25.00           C
ATOM     81  CA  GLY    81      -9.581  21.592  48.574  1.00 25.00           C
ATOM     82  CA  GLN    82      -6.763  23.796  49.941  1.00 25.00           C
ATOM     83  CA  PHE    83      -4.151  21.096  49.616  1.00 25.00           C
ATOM     84  CA  ASP    84      -2.232  20.271  46.457  1.00 25.00           C
ATOM     85  CA  HIS    85       0.832  18.601  44.901  1.00 25.00           C
ATOM     86  CA  PRO    86       2.524  15.505  43.397  1.00 25.00           C
ATOM     87  CA  ASN    87       0.907  13.678  46.350  1.00 25.00           C
ATOM     88  CA  ILE    88      -1.772  15.405  48.432  1.00 25.00           C
ATOM     89  CA  ILE    89      -4.749  13.114  47.733  1.00 25.00           C
ATOM     90  CA  ARG    90      -6.862  14.458  44.794  1.00 25.00           C
ATOM     91  CA  LEU    91      -9.916  16.402  46.018  1.00 25.00           C
ATOM     92  CA  GLU    92     -13.099  15.994  43.940  1.00 25.00           C
ATOM     93  CA  GLY    93     -16.824  16.671  44.300  1.00 25.00           C
ATOM     94  CA  VAL    94     -19.437  16.766  47.063  1.00 25.00           C
ATOM     95  CA  VAL    95     -23.131  16.026  47.280  1.00 25.00           C
ATOM     96  CA  THR    96     -24.059  18.274  50.148  1.00 25.00           C
ATOM     97  CA  LYS    97     -27.687  19.536  49.873  1.00 25.00           C
ATOM     98  CA  SER    98     -29.945  16.615  50.593  1.00 25.00           C
ATOM     99  CA  LYS    99     -30.640  13.340  52.390  1.00 25.00           C
ATOM    100  CA  PRO   100     -26.913  12.939  53.117  1.00 25.00           C
ATOM    101  CA  VAL   101     -23.271  13.328  53.854  1.00 25.00           C
ATOM    102  CA  MET   102     -20.645  14.003  51.221  1.00 25.00           C
ATOM    103  CA  ILE   103     -16.894  14.455  51.381  1.00 25.00           C
ATOM    104  CA  VAL   104     -15.510  13.370  47.972  1.00 25.00           C
ATOM    105  CA  THR   105     -12.050  12.026  47.194  1.00 25.00           C
ATOM    106  CA  GLU   106      -9.767   9.865  45.053  1.00 25.00           C
ATOM    107  CA  TYR   107      -9.107   6.802  42.994  1.00 25.00           C
ATOM    108  CA  MET   108      -7.597   4.344  45.401  1.00 25.00           C
TER
END
