
#######################################################
#                                                     #
#                        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 T0351TS599_4
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS599_4.T0351.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    -       -      I       2           -
LGA    -       -      L       3           -
LGA    -       -      Y       4           -
LGA    I       2      D       5          3.687
LGA    L       3      A       6          2.302
LGA    Y       4      I       7          1.999
LGA    -       -      M       8           -
LGA    -       -      Y       9           -
LGA    D       5      K      10          3.584
LGA    A       6      Y      11           #
LGA    I       7      -       -           -
LGA    M       8      -       -           -
LGA    Y       9      -       -           -
LGA    K      10      -       -           -
LGA    Y      11      -       -           -
LGA    P      12      -       -           -
LGA    N      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      -       -           -
LGA    S      16      -       -           -
LGA    R      17      P      12           #
LGA    K      18      N      13          2.894
LGA    D      19      A      14          2.461
LGA    F      20      V      15          2.644
LGA    E      21      S      16          3.177
LGA    -       -      R      17           -
LGA    -       -      K      18           -
LGA    L      22      D      19          4.343
LGA    R      23      F      20           -
LGA    N      24      E      21           -
LGA    D      25      L      22           -
LGA    G      26      R      23           -
LGA    N      27      N      24           -
LGA    G      28      D      25           -
LGA    S      29      G      26           -
LGA    Y      30      N      27           -
LGA    I      31      G      28           -
LGA    E      32      S      29           -
LGA    K      33      Y      30           -
LGA    W      34      I      31           -
LGA    N      35      E      32           -
LGA    -       -      K      33           -
LGA    L      36      W      34          4.786
LGA    R      37      N      35          3.007
LGA    -       -      L      36           -
LGA    -       -      R      37           -
LGA    A      38      A      38          5.601
LGA    P      39      P      39          2.690
LGA    L      40      L      40          1.368
LGA    P      41      P      41          1.319
LGA    T      42      T      42          1.025
LGA    Q      43      Q      43          1.921
LGA    A      44      A      44          2.130
LGA    E      45      E      45          0.984
LGA    L      46      L      46          1.629
LGA    E      47      E      47          2.350
LGA    T      48      T      48          1.187
LGA    W      49      W      49          1.023
LGA    W      50      W      50          1.924
LGA    E      51      E      51          1.322
LGA    E      52      E      52          0.991
LGA    L      53      L      53          2.329
LGA    Q      54      Q      54          2.563
LGA    K      55      K      55          1.200
LGA    N      56      N      56          2.074
LGA    P      57      -       -           -
LGA    P      58      -       -           -
LGA    Y      59      -       -           -
LGA    E      60      -       -           -
LGA    P      61      -       -           -
LGA    P      62      -       -           -
LGA    D      63      -       -           -
LGA    Q      64      -       -           -
LGA    V      65      -       -           -
LGA    E      66      -       -           -
LGA    L      67      -       -           -
LGA    L      68      -       -           -
LGA    A      69      -       -           -
LGA    Q      70      -       -           -
LGA    E      71      -       -           -
LGA    L      72      -       -           -
LGA    S      73      -       -           -
LGA    Q      74      -       -           -
LGA    E      75      -       -           -
LGA    K      76      -       -           -
LGA    L      77      -       -           -
LGA    A      78      -       -           -
LGA    R      79      -       -           -
LGA    K      80      -       -           -
LGA    Q      81      -       -           -
LGA    L      82      -       -           -
LGA    E      83      -       -           -
LGA    E      84      -       -           -
LGA    L      85      -       -           -
LGA    N      86      -       -           -
LGA    K      87      -       -           -
LGA    T      88      -       -           -
LGA    L      89      -       -           -
LGA    G      90      -       -           -
LGA    N      91      -       -           -
LGA    E      92      -       -           -
LGA    L      93      -       -           -
LGA    S      94      -       -           -
LGA    D      95      -       -           -
LGA    I      96      -       -           -
LGA    K      97      -       -           -
LGA    L      98      -       -           -
LGA    S      99      -       -           -
LGA    L     100      -       -           -
LGA    L     101      -       -           -
LGA    S     102      -       -           -
LGA    L     103      -       -           -
LGA    K     104      -       -           -
LGA    G     105      -       -           -
LGA    D     106      -       -           -
LGA    Y     107      -       -           -
LGA    A     108      -       -           -
LGA    E     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   56    5.0     30    2.62    63.33     40.253     1.104

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.905331 * X  +   0.266821 * Y  +  -0.330427 * Z  +  -8.454480
  Y_new =   0.239304 * X  +   0.963231 * Y  +   0.122145 * Z  +   9.438508
  Z_new =   0.350868 * X  +   0.031510 * Y  +  -0.935895 * Z  +  -2.483154 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.107938   -0.033655  [ DEG:   178.0717     -1.9283 ]
  Theta =  -0.358498   -2.783095  [ DEG:   -20.5404   -159.4596 ]
  Phi   =   2.883175   -0.258418  [ DEG:   165.1938    -14.8062 ]
 
# 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: T0351TS599_4                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS599_4.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117   56   5.0   30   2.62   63.33  40.253
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS599_4
PFRMAT TS                                                                       
TARGET T0351                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       6.039   2.792   3.656  1.00  0.00              
ATOM      2  CA  ILE     2       2.597   0.383   3.756  1.00  0.00              
ATOM      3  CA  LEU     3      -0.911  -0.173   2.588  1.00  0.00              
ATOM      4  CA  TYR     4       0.402   3.240   1.205  1.00  0.00              
ATOM      5  CA  ASP     5       2.754   1.610  -1.327  1.00  0.00              
ATOM      6  CA  ALA     6       0.204  -1.078  -2.263  1.00  0.00              
ATOM      7  CA  ILE     7      -2.174   1.775  -3.248  1.00  0.00              
ATOM      8  CA  MET     8       0.318   4.106  -4.978  1.00  0.00              
ATOM      9  CA  TYR     9       0.530   7.720  -4.066  1.00  0.00              
ATOM     10  CA  LYS    10       2.519  10.119  -6.278  1.00  0.00              
ATOM     11  CA  TYR    11       3.520  13.351  -4.609  1.00  0.00              
ATOM     12  CA  PRO    12       3.643  16.626  -6.357  1.00  0.00              
ATOM     13  CA  ASN    13       5.772  18.950  -4.171  1.00  0.00              
ATOM     14  CA  ALA    14       8.499  16.425  -3.675  1.00  0.00              
ATOM     15  CA  VAL    15       8.065  13.843  -0.997  1.00  0.00              
ATOM     16  CA  SER    16       8.784  10.504  -2.491  1.00  0.00              
ATOM     17  CA  ARG    17       6.247   7.743  -2.939  1.00  0.00              
ATOM     18  CA  LYS    18       7.269   5.591   0.002  1.00  0.00              
ATOM     19  CA  ASP    19       7.228   8.448   2.562  1.00  0.00              
ATOM     20  CA  PHE    20       4.295  10.456   1.387  1.00  0.00              
ATOM     21  CA  GLU    21       1.765  11.821   3.826  1.00  0.00              
ATOM     22  CA  LEU    22       0.320  15.301   3.157  1.00  0.00              
ATOM     23  CA  ARG    23      -1.492  16.904   6.072  1.00  0.00              
ATOM     24  CA  ASN    24      -4.213  19.420   5.467  1.00  0.00              
ATOM     25  CA  ASP    25      -3.675  22.095   8.084  1.00  0.00              
ATOM     26  CA  GLY    26      -7.062  23.460   8.918  1.00  0.00              
ATOM     27  CA  ASN    27      -7.440  26.063   6.136  1.00  0.00              
ATOM     28  CA  GLY    28      -6.665  23.641   3.272  1.00  0.00              
ATOM     29  CA  SER    29      -3.119  24.485   2.458  1.00  0.00              
ATOM     30  CA  TYR    30      -1.031  21.292   2.562  1.00  0.00              
ATOM     31  CA  ILE    31      -2.839  18.642   0.503  1.00  0.00              
ATOM     32  CA  GLU    32      -4.107  21.169  -2.088  1.00  0.00              
ATOM     33  CA  LYS    33      -0.668  22.755  -2.564  1.00  0.00              
ATOM     34  CA  TRP    34       1.037  19.365  -2.979  1.00  0.00              
ATOM     35  CA  ASN    35      -1.087  17.447  -5.429  1.00  0.00              
ATOM     36  CA  LEU    36      -1.488  13.919  -4.579  1.00  0.00              
ATOM     37  CA  ARG    37      -1.718  11.428  -7.371  1.00  0.00              
ATOM     38  CA  ALA    38      -2.973   8.072  -6.368  1.00  0.00              
ATOM     39  CA  PRO    39      -2.147   5.092  -8.483  1.00  0.00              
ATOM     40  CA  LEU    40      -5.095   2.743  -8.116  1.00  0.00              
ATOM     41  CA  PRO    41      -4.048  -0.469  -6.437  1.00  0.00              
ATOM     42  CA  THR    42      -4.597  -3.436  -8.712  1.00  0.00              
ATOM     43  CA  GLN    43      -5.968  -6.598  -7.253  1.00  0.00              
ATOM     44  CA  ALA    44      -2.655  -8.362  -8.047  1.00  0.00              
ATOM     45  CA  GLU    45      -0.725  -5.774  -6.001  1.00  0.00              
ATOM     46  CA  LEU    46      -3.133  -6.192  -3.047  1.00  0.00              
ATOM     47  CA  GLU    47      -2.781  -9.983  -3.130  1.00  0.00              
ATOM     48  CA  THR    48       0.999  -9.585  -3.208  1.00  0.00              
ATOM     49  CA  TRP    49       0.960  -7.132  -0.254  1.00  0.00              
ATOM     50  CA  TRP    50      -1.239  -9.455   1.788  1.00  0.00              
ATOM     51  CA  GLU    51       0.894 -12.468   1.132  1.00  0.00              
ATOM     52  CA  GLU    52       4.048 -10.585   2.161  1.00  0.00              
ATOM     53  CA  LEU    53       2.414  -9.649   5.456  1.00  0.00              
ATOM     54  CA  GLN    54       1.321 -13.209   6.219  1.00  0.00              
ATOM     55  CA  LYS    55       4.855 -14.510   5.643  1.00  0.00              
ATOM     56  CA  ASN    56       6.671 -12.019   7.876  1.00  0.00              
ATOM     57  CA  PRO    57       7.513 -13.611  11.256  1.00  0.00              
ATOM     58  CA  PRO    58       5.999 -11.223  13.741  1.00  0.00              
ATOM     59  CA  TYR    59       3.013 -10.361  11.538  1.00  0.00              
ATOM     60  CA  GLU    60       1.779 -13.944  10.933  1.00  0.00              
ATOM     61  CA  PRO    61      -0.095 -13.939  14.256  1.00  0.00              
ATOM     62  CA  PRO    62      -3.784 -14.583  13.551  1.00  0.00              
ATOM     63  CA  ASP    63      -5.298 -11.447  15.076  1.00  0.00              
ATOM     64  CA  GLN    64      -3.068  -8.886  13.337  1.00  0.00              
ATOM     65  CA  VAL    65      -2.950 -10.314   9.777  1.00  0.00              
ATOM     66  CA  GLU    66      -6.743 -10.730   9.417  1.00  0.00              
ATOM     67  CA  LEU    67      -7.458  -7.309  10.967  1.00  0.00              
ATOM     68  CA  LEU    68      -4.940  -5.509   8.714  1.00  0.00              
ATOM     69  CA  ALA    69      -6.292  -7.128   5.522  1.00  0.00              
ATOM     70  CA  GLN    70      -9.814  -6.113   6.638  1.00  0.00              
ATOM     71  CA  GLU    71      -8.755  -2.527   7.391  1.00  0.00              
ATOM     72  CA  LEU    72      -7.036  -2.169   3.976  1.00  0.00              
ATOM     73  CA  SER    73     -10.057  -3.551   2.206  1.00  0.00              
ATOM     74  CA  GLN    74     -12.433  -1.145   3.993  1.00  0.00              
ATOM     75  CA  GLU    75     -10.166   1.834   3.155  1.00  0.00              
ATOM     76  CA  LYS    76      -9.890   0.792  -0.452  1.00  0.00              
ATOM     77  CA  LEU    77     -13.715   0.391  -0.779  1.00  0.00              
ATOM     78  CA  ALA    78     -14.306   3.789   0.777  1.00  0.00              
ATOM     79  CA  ARG    79     -11.879   5.497  -1.621  1.00  0.00              
ATOM     80  CA  LYS    80     -13.605   3.744  -4.546  1.00  0.00              
ATOM     81  CA  GLN    81     -17.086   4.805  -3.387  1.00  0.00              
ATOM     82  CA  LEU    82     -15.949   8.433  -2.963  1.00  0.00              
ATOM     83  CA  GLU    83     -14.462   8.365  -6.478  1.00  0.00              
ATOM     84  CA  GLU    84     -17.729   7.021  -7.879  1.00  0.00              
ATOM     85  CA  LEU    85     -19.606   9.760  -6.038  1.00  0.00              
ATOM     86  CA  ASN    86     -17.265  12.422  -7.430  1.00  0.00              
ATOM     87  CA  LYS    87     -17.801  11.103 -10.981  1.00  0.00              
ATOM     88  CA  THR    88     -21.586  11.187 -10.457  1.00  0.00              
ATOM     89  CA  LEU    89     -21.495  14.745  -9.082  1.00  0.00              
ATOM     90  CA  GLY    90     -19.298  15.936 -11.978  1.00  0.00              
ATOM     91  CA  ASN    91     -21.766  14.411 -14.481  1.00  0.00              
ATOM     92  CA  GLU    92     -24.719  16.077 -12.729  1.00  0.00              
ATOM     93  CA  LEU    93     -22.856  19.414 -12.833  1.00  0.00              
ATOM     94  CA  SER    94     -22.097  18.939 -16.581  1.00  0.00              
ATOM     95  CA  ASP    95     -25.660  17.987 -17.424  1.00  0.00              
ATOM     96  CA  ILE    96     -26.973  21.107 -15.574  1.00  0.00              
ATOM     97  CA  LYS    97     -24.516  23.570 -17.203  1.00  0.00              
ATOM     98  CA  LEU    98     -24.096  26.449 -14.871  1.00  0.00              
ATOM     99  CA  SER    99     -23.112  29.905 -16.242  1.00  0.00              
ATOM    100  CA  LEU   100     -22.831  32.508 -13.484  1.00  0.00              
ATOM    101  CA  LEU   101     -23.799  36.011 -14.750  1.00  0.00              
ATOM    102  CA  SER   102     -23.310  38.807 -12.212  1.00  0.00              
ATOM    103  CA  LEU   103     -25.717  41.751 -12.376  1.00  0.00              
ATOM    104  CA  LYS   104     -25.455  42.973  -8.765  1.00  0.00              
ATOM    105  CA  GLY   105     -25.411  39.484  -7.263  1.00  0.00              
ATOM    106  CA  ASP   106     -28.444  37.954  -8.888  1.00  0.00              
ATOM    107  CA  TYR   107     -27.427  35.934 -11.868  1.00  0.00              
ATOM    108  CA  ALA   108     -24.038  34.927 -10.317  1.00  0.00              
ATOM    109  CA  GLU   109     -25.755  33.334  -7.357  1.00  0.00              
ATOM    110  CA  LEU   110     -28.224  31.281  -9.337  1.00  0.00              
ATOM    111  CA  GLU   111     -25.698  29.832 -11.754  1.00  0.00              
ATOM    112  CA  HIS   112     -23.360  28.845  -8.995  1.00  0.00              
ATOM    113  CA  HIS   113     -26.057  27.070  -6.857  1.00  0.00              
ATOM    114  CA  HIS   114     -26.105  24.582  -9.667  1.00  0.00              
ATOM    115  CA  HIS   115     -29.196  24.669 -11.442  1.00  0.00              
ATOM    116  CA  HIS   116     -27.995  25.081 -15.461  1.00  0.00              
ATOM    117  CA  HIS   117     -27.209  27.948 -18.374  1.00  0.00              
TER                                                                             
END
