
#######################################################
#                                                     #
#                        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  101 (  101),  selected  101 , name T0304TS599_4-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS599_4-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    R      17      T      25          4.320
LGA    P      18      V      26          4.707
LGA    W      19      T      27          3.240
LGA    W      20      P      28          4.483
LGA    G      21      C      29          2.651
LGA    L      22      F      30           #
LGA    P      23      G      31          4.487
LGA    C      24      -       -           -
LGA    T      25      -       -           -
LGA    V      26      -       -           -
LGA    T      27      A      32           #
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    P      28      A      48          4.381
LGA    C      29      -       -           -
LGA    F      30      -       -           -
LGA    G      31      -       -           -
LGA    A      32      G      49           #
LGA    R      33      I      50           -
LGA    L      34      -       -           -
LGA    V      35      -       -           -
LGA    Q      36      -       -           -
LGA    E      37      -       -           -
LGA    G      38      -       -           -
LGA    N      39      -       -           -
LGA    R      40      -       -           -
LGA    L      41      -       -           -
LGA    H      42      -       -           -
LGA    Y      43      R      51          4.670
LGA    L      44      G      52          2.330
LGA    A      45      -       -           -
LGA    D      46      L      53          1.892
LGA    R      47      F      54          2.803
LGA    A      48      S      55           #
LGA    G      49      -       -           -
LGA    I      50      -       -           -
LGA    R      51      -       -           -
LGA    G      52      -       -           -
LGA    L      53      -       -           -
LGA    F      54      -       -           -
LGA    S      55      D      56          3.858
LGA    D      56      -       -           -
LGA    A      57      A      57          4.317
LGA    D      58      D      58          4.199
LGA    A      59      A      59          4.305
LGA    Y      60      Y      60          2.939
LGA    H      61      H      61          0.738
LGA    L      62      L      62          1.726
LGA    D      63      D      63          2.096
LGA    Q      64      Q      64          2.572
LGA    A      65      A      65          2.581
LGA    F      66      F      66          0.817
LGA    P      67      P      67          1.687
LGA    L      68      L      68          2.338
LGA    L      69      L      69          1.357
LGA    M      70      M      70          0.682
LGA    K      71      K      71          1.505
LGA    Q      72      Q      72          1.077
LGA    L      73      L      73          0.752
LGA    E      74      E      74          1.338
LGA    L      75      L      75          1.148
LGA    M      76      M      76          0.640
LGA    L      77      L      77          1.100
LGA    T      78      T      78          1.317
LGA    S      79      S      79          0.984
LGA    G      80      G      80          1.596
LGA    E      81      E      81          1.118
LGA    L      82      L      82          2.456
LGA    N      83      N      83          2.652
LGA    P      84      P      84          2.245
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    R      85      D     102          4.429
LGA    H      86      T     103          4.645
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    Q      87      C     107           #
LGA    H      88      -       -           -
LGA    T      89      -       -           -
LGA    V      90      -       -           -
LGA    T      91      -       -           -
LGA    L      92      -       -           -
LGA    Y      93      -       -           -
LGA    A      94      -       -           -
LGA    K      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    T      98      -       -           -
LGA    C      99      -       -           -
LGA    K     100      -       -           -
LGA    A     101      -       -           -
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      D     108          4.745
LGA    D     108      Y     109          3.334
LGA    Y     109      V     110           #
LGA    V     110      Y     111           #
LGA    Y     111      L     112           #
LGA    L     112      A     113           -
LGA    A     113      V     114           -
LGA    V     114      Y     115           -
LGA    Y     115      P     116           -
LGA    P     116      T     117           -
LGA    T     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     44    2.92    63.64     30.437     1.457

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.271195 * X  +  -0.807431 * Y  +  -0.523936 * Z  +  42.194191
  Y_new =   0.930428 * X  +   0.359308 * Y  +  -0.072125 * Z  +  19.356424
  Z_new =   0.246490 * X  +  -0.467925 * Y  +   0.848698 * Z  +  40.384640 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.503874    2.637718  [ DEG:   -28.8699    151.1301 ]
  Theta =  -0.249057   -2.892535  [ DEG:   -14.2699   -165.7301 ]
  Phi   =   1.287180   -1.854412  [ DEG:    73.7500   -106.2500 ]
 
# 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: T0304TS599_4-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS599_4-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  101   5.0   44   2.92   63.64  30.437
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS599_4-D1
PFRMAT TS                                                                       
TARGET T0304                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM     17  CA  ARG    17      31.748  30.056  32.270  1.00  0.00              
ATOM     18  CA  PRO    18      34.174  29.843  29.318  1.00  0.00              
ATOM     19  CA  TRP    19      36.618  27.205  30.427  1.00  0.00              
ATOM     20  CA  TRP    20      35.106  25.556  33.431  1.00  0.00              
ATOM     21  CA  GLY    21      37.894  25.003  35.872  1.00  0.00              
ATOM     22  CA  LEU    22      36.553  22.665  38.511  1.00  0.00              
ATOM     23  CA  PRO    23      37.072  23.935  42.081  1.00  0.00              
ATOM     24  CA  CYS    24      33.661  23.605  43.745  1.00  0.00              
ATOM     25  CA  THR    25      34.508  21.801  46.987  1.00  0.00              
ATOM     26  CA  VAL    26      37.567  19.886  45.976  1.00  0.00              
ATOM     27  CA  THR    27      39.143  17.162  48.149  1.00  0.00              
ATOM     28  CA  PRO    28      40.767  14.514  45.931  1.00  0.00              
ATOM     29  CA  CYS    29      39.830  11.204  47.516  1.00  0.00              
ATOM     30  CA  PHE    30      36.158  12.137  47.167  1.00  0.00              
ATOM     31  CA  GLY    31      36.429  13.403  43.599  1.00  0.00              
ATOM     32  CA  ALA    32      37.849  10.109  42.320  1.00  0.00              
ATOM     33  CA  ARG    33      35.029   8.263  44.038  1.00  0.00              
ATOM     34  CA  LEU    34      32.385  10.504  42.426  1.00  0.00              
ATOM     35  CA  VAL    35      33.834  10.008  38.937  1.00  0.00              
ATOM     36  CA  GLN    36      33.999   6.257  39.531  1.00  0.00              
ATOM     37  CA  GLU    37      30.380   6.066  40.738  1.00  0.00              
ATOM     38  CA  GLY    38      28.967   7.684  37.689  1.00  0.00              
ATOM     39  CA  ASN    39      28.038  11.052  39.072  1.00  0.00              
ATOM     40  CA  ARG    40      28.616  13.189  35.937  1.00  0.00              
ATOM     41  CA  LEU    41      29.995  16.691  36.404  1.00  0.00              
ATOM     42  CA  HIS    42      30.110  17.930  32.843  1.00  0.00              
ATOM     43  CA  TYR    43      32.696  20.774  32.766  1.00  0.00              
ATOM     44  CA  LEU    44      35.296  19.070  35.014  1.00  0.00              
ATOM     45  CA  ALA    45      35.101  15.764  33.227  1.00  0.00              
ATOM     46  CA  ASP    46      35.508  17.174  29.695  1.00  0.00              
ATOM     47  CA  ARG    47      38.526  19.441  30.112  1.00  0.00              
ATOM     48  CA  ALA    48      40.515  16.735  31.830  1.00  0.00              
ATOM     49  CA  GLY    49      39.561  13.835  29.484  1.00  0.00              
ATOM     50  CA  ILE    50      38.075  11.668  32.205  1.00  0.00              
ATOM     51  CA  ARG    51      35.256   9.928  30.254  1.00  0.00              
ATOM     52  CA  GLY    52      37.527   9.060  27.324  1.00  0.00              
ATOM     53  CA  LEU    53      40.849   7.900  28.635  1.00  0.00              
ATOM     54  CA  PHE    54      43.248  10.855  28.431  1.00  0.00              
ATOM     55  CA  SER    55      45.910  10.764  25.824  1.00  0.00              
ATOM     56  CA  ASP    56      49.516  10.437  26.996  1.00  0.00              
ATOM     57  CA  ALA    57      50.173  13.986  25.724  1.00  0.00              
ATOM     58  CA  ASP    58      47.412  15.326  28.013  1.00  0.00              
ATOM     59  CA  ALA    59      48.882  13.442  31.012  1.00  0.00              
ATOM     60  CA  TYR    60      52.311  14.937  30.195  1.00  0.00              
ATOM     61  CA  HIS    61      50.741  18.434  29.967  1.00  0.00              
ATOM     62  CA  LEU    62      49.258  18.073  33.468  1.00  0.00              
ATOM     63  CA  ASP    63      52.614  16.955  34.869  1.00  0.00              
ATOM     64  CA  GLN    64      54.380  19.955  33.258  1.00  0.00              
ATOM     65  CA  ALA    65      51.803  22.360  34.677  1.00  0.00              
ATOM     66  CA  PHE    66      51.968  21.062  38.285  1.00  0.00              
ATOM     67  CA  PRO    67      55.785  21.183  38.550  1.00  0.00              
ATOM     68  CA  LEU    68      55.707  24.670  37.146  1.00  0.00              
ATOM     69  CA  LEU    69      53.028  25.762  39.682  1.00  0.00              
ATOM     70  CA  MET    70      54.847  24.411  42.705  1.00  0.00              
ATOM     71  CA  LYS    71      58.172  26.032  41.634  1.00  0.00              
ATOM     72  CA  GLN    72      56.446  29.325  41.139  1.00  0.00              
ATOM     73  CA  LEU    73      54.780  29.206  44.455  1.00  0.00              
ATOM     74  CA  GLU    74      58.011  28.466  46.281  1.00  0.00              
ATOM     75  CA  LEU    75      59.859  31.271  44.481  1.00  0.00              
ATOM     76  CA  MET    76      57.107  33.741  45.369  1.00  0.00              
ATOM     77  CA  LEU    77      57.020  32.703  49.082  1.00  0.00              
ATOM     78  CA  THR    78      60.787  33.100  49.356  1.00  0.00              
ATOM     79  CA  SER    79      60.662  36.525  47.623  1.00  0.00              
ATOM     80  CA  GLY    80      58.007  38.133  49.702  1.00  0.00              
ATOM     81  CA  GLU    81      55.247  38.049  47.071  1.00  0.00              
ATOM     82  CA  LEU    82      53.255  36.093  49.578  1.00  0.00              
ATOM     83  CA  ASN    83      49.545  35.822  49.021  1.00  0.00              
ATOM     84  CA  PRO    84      47.648  34.015  51.704  1.00  0.00              
ATOM     85  CA  ARG    85      46.679  30.937  49.633  1.00  0.00              
ATOM     86  CA  HIS    86      50.303  30.444  48.581  1.00  0.00              
ATOM     87  CA  GLN    87      51.863  30.638  52.055  1.00  0.00              
ATOM     88  CA  HIS    88      50.262  27.366  52.965  1.00  0.00              
ATOM     89  CA  THR    89      51.780  25.256  50.276  1.00  0.00              
ATOM     90  CA  VAL    90      50.291  24.139  47.028  1.00  0.00              
ATOM     91  CA  THR    91      51.420  20.795  45.805  1.00  0.00              
ATOM     92  CA  LEU    92      50.533  19.339  42.564  1.00  0.00              
ATOM     93  CA  TYR    93      51.450  15.643  42.042  1.00  0.00              
ATOM     94  CA  ALA    94      51.309  14.102  38.730  1.00  0.00              
ATOM     95  CA  LYS    95      51.059  10.498  39.399  1.00  0.00              
ATOM     96  CA  GLY    96      48.529  10.130  42.043  1.00  0.00              
ATOM     97  CA  LEU    97      48.746  11.866  45.449  1.00  0.00              
ATOM     98  CA  THR    98      45.290  12.724  46.821  1.00  0.00              
ATOM     99  CA  CYS    99      44.664  15.544  49.231  1.00  0.00              
ATOM    100  CA  LYS   100      42.016  15.151  51.924  1.00  0.00              
ATOM    101  CA  ALA   101      39.905  18.297  52.147  1.00  0.00              
ATOM    102  CA  ASP   102      40.158  18.788  55.858  1.00  0.00              
ATOM    103  CA  THR   103      43.873  18.489  56.542  1.00  0.00              
ATOM    104  CA  LEU   104      45.282  20.469  53.587  1.00  0.00              
ATOM    105  CA  SER   105      42.763  23.214  54.333  1.00  0.00              
ATOM    106  CA  SER   106      43.023  23.628  58.110  1.00  0.00              
ATOM    107  CA  CYS   107      46.815  23.867  58.201  1.00  0.00              
ATOM    108  CA  ASP   108      46.942  25.758  54.901  1.00  0.00              
ATOM    109  CA  TYR   109      48.351  23.090  52.512  1.00  0.00              
ATOM    110  CA  VAL   110      46.906  22.194  49.189  1.00  0.00              
ATOM    111  CA  TYR   111      47.776  18.853  47.661  1.00  0.00              
ATOM    112  CA  LEU   112      46.410  17.940  44.336  1.00  0.00              
ATOM    113  CA  ALA   113      46.853  14.580  42.949  1.00  0.00              
ATOM    114  CA  VAL   114      46.386  13.939  39.196  1.00  0.00              
ATOM    115  CA  TYR   115      45.576  10.570  37.994  1.00  0.00              
ATOM    116  CA  PRO   116      45.667   7.828  35.550  1.00  0.00              
ATOM    117  CA  THR   117      43.021   8.199  32.898  1.00  0.00              
TER                                                                             
END
