
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS599_5.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      I       2           -
LGA    L       3      L       3           #
LGA    -       -      Y       4           -
LGA    -       -      D       5           -
LGA    -       -      A       6           -
LGA    Y       4      I       7          2.153
LGA    -       -      M       8           -
LGA    -       -      Y       9           -
LGA    D       5      K      10          2.250
LGA    A       6      Y      11          3.289
LGA    I       7      P      12          3.239
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      -       -           -
LGA    K      18      -       -           -
LGA    D      19      -       -           -
LGA    F      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    R      23      -       -           -
LGA    N      24      -       -           -
LGA    D      25      -       -           -
LGA    G      26      -       -           -
LGA    N      27      -       -           -
LGA    G      28      -       -           -
LGA    S      29      -       -           -
LGA    Y      30      -       -           -
LGA    I      31      -       -           -
LGA    E      32      -       -           -
LGA    K      33      -       -           -
LGA    W      34      -       -           -
LGA    N      35      -       -           -
LGA    L      36      -       -           -
LGA    R      37      -       -           -
LGA    A      38      -       -           -
LGA    P      39      -       -           -
LGA    L      40      N      13          5.369
LGA    P      41      A      14          3.855
LGA    T      42      V      15          3.281
LGA    Q      43      S      16          1.992
LGA    A      44      R      17          2.235
LGA    -       -      K      18           -
LGA    E      45      D      19          3.059
LGA    L      46      F      20          4.057
LGA    E      47      E      21          3.355
LGA    T      48      L      22           -
LGA    W      49      R      23           -
LGA    -       -      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    -       -      Y      30           -
LGA    W      50      I      31           #
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    E      51      W      34          1.040
LGA    E      52      N      35          3.343
LGA    -       -      L      36           -
LGA    -       -      R      37           -
LGA    L      53      A      38          4.696
LGA    Q      54      -       -           -
LGA    K      55      -       -           -
LGA    N      56      -       -           -
LGA    P      57      -       -           -
LGA    P      58      -       -           -
LGA    Y      59      P      39          2.415
LGA    E      60      L      40          4.409
LGA    P      61      -       -           -
LGA    P      62      -       -           -
LGA    D      63      -       -           -
LGA    Q      64      P      41          5.041
LGA    V      65      T      42          1.980
LGA    E      66      Q      43          1.806
LGA    L      67      A      44          1.454
LGA    L      68      E      45          1.148
LGA    A      69      L      46          1.184
LGA    Q      70      E      47          0.952
LGA    E      71      T      48          0.645
LGA    L      72      W      49          0.634
LGA    S      73      W      50          1.079
LGA    Q      74      E      51          1.206
LGA    E      75      E      52          0.995
LGA    K      76      L      53          0.970
LGA    L      77      Q      54          1.003
LGA    A      78      K      55          1.424
LGA    R      79      N      56          1.790
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     33    2.70     6.06     42.032     1.178

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.372676 * X  +   0.871274 * Y  +   0.319367 * Z  +  10.761537
  Y_new =  -0.726420 * X  +   0.059758 * Y  +   0.684649 * Z  +  -7.872077
  Z_new =   0.577431 * X  +  -0.487146 * Y  +   0.655180 * Z  +   5.370708 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.639347    2.502245  [ DEG:   -36.6319    143.3681 ]
  Theta =  -0.615579   -2.526014  [ DEG:   -35.2701   -144.7299 ]
  Phi   =  -1.096778    2.044815  [ DEG:   -62.8407    117.1593 ]
 
# 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_5                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS599_5.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   33   2.70    6.06  42.032
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS599_5
PFRMAT TS                                                                       
TARGET T0351                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       2.432   0.012  -7.912  1.00  0.00              
ATOM      2  CA  ILE     2       0.461   1.145  -4.368  1.00  0.00              
ATOM      3  CA  LEU     3       0.330   3.287  -0.757  1.00  0.00              
ATOM      4  CA  TYR     4       3.184   1.064   0.732  1.00  0.00              
ATOM      5  CA  ASP     5       5.203   1.232  -2.465  1.00  0.00              
ATOM      6  CA  ALA     6       4.704   4.997  -2.883  1.00  0.00              
ATOM      7  CA  ILE     7       6.140   5.397   0.660  1.00  0.00              
ATOM      8  CA  MET     8       8.878   2.877   0.392  1.00  0.00              
ATOM      9  CA  TYR     9      10.264   0.262   2.727  1.00  0.00              
ATOM     10  CA  LYS    10      13.121  -1.800   1.513  1.00  0.00              
ATOM     11  CA  TYR    11      13.725  -5.353   2.608  1.00  0.00              
ATOM     12  CA  PRO    12      17.192  -6.747   2.259  1.00  0.00              
ATOM     13  CA  ASN    13      16.696 -10.214   0.908  1.00  0.00              
ATOM     14  CA  ALA    14      13.658  -9.892  -1.058  1.00  0.00              
ATOM     15  CA  VAL    15      13.019  -7.593  -3.985  1.00  0.00              
ATOM     16  CA  SER    16      10.104  -5.415  -2.869  1.00  0.00              
ATOM     17  CA  ARG    17       8.820  -4.105  -6.162  1.00  0.00              
ATOM     18  CA  LYS    18       9.724  -0.451  -5.797  1.00  0.00              
ATOM     19  CA  ASP    19      13.141  -0.964  -4.148  1.00  0.00              
ATOM     20  CA  PHE    20      14.549  -3.869  -6.062  1.00  0.00              
ATOM     21  CA  GLU    21      18.079  -3.426  -7.275  1.00  0.00              
ATOM     22  CA  LEU    22      20.553  -6.363  -7.483  1.00  0.00              
ATOM     23  CA  ARG    23      23.973  -5.138  -8.676  1.00  0.00              
ATOM     24  CA  ASN    24      27.346  -6.564  -7.875  1.00  0.00              
ATOM     25  CA  ASP    25      29.966  -3.850  -7.230  1.00  0.00              
ATOM     26  CA  GLY    26      31.882  -5.626  -4.441  1.00  0.00              
ATOM     27  CA  ASN    27      31.899  -2.761  -1.909  1.00  0.00              
ATOM     28  CA  GLY    28      28.310  -2.628  -0.877  1.00  0.00              
ATOM     29  CA  SER    29      26.743  -0.607  -3.632  1.00  0.00              
ATOM     30  CA  TYR    30      24.047  -2.586  -5.303  1.00  0.00              
ATOM     31  CA  ILE    31      21.110  -4.326  -3.909  1.00  0.00              
ATOM     32  CA  GLU    32      22.424  -7.326  -2.104  1.00  0.00              
ATOM     33  CA  LYS    33      25.669  -6.026  -0.706  1.00  0.00              
ATOM     34  CA  TRP    34      24.428  -2.894   0.896  1.00  0.00              
ATOM     35  CA  ASN    35      21.068  -3.995   2.309  1.00  0.00              
ATOM     36  CA  LEU    36      18.647  -1.181   1.803  1.00  0.00              
ATOM     37  CA  ARG    37      15.938  -0.658   4.429  1.00  0.00              
ATOM     38  CA  ALA    38      13.938   2.420   3.756  1.00  0.00              
ATOM     39  CA  PRO    39      11.701   4.111   6.263  1.00  0.00              
ATOM     40  CA  LEU    40       8.077   3.904   5.323  1.00  0.00              
ATOM     41  CA  PRO    41       6.663   7.400   4.599  1.00  0.00              
ATOM     42  CA  THR    42       3.813   8.501   6.652  1.00  0.00              
ATOM     43  CA  GLN    43       0.148   7.846   6.273  1.00  0.00              
ATOM     44  CA  ALA    44      -0.604  11.344   4.869  1.00  0.00              
ATOM     45  CA  GLU    45       1.887  10.800   2.051  1.00  0.00              
ATOM     46  CA  LEU    46       0.302   7.445   1.228  1.00  0.00              
ATOM     47  CA  GLU    47      -3.146   9.018   0.959  1.00  0.00              
ATOM     48  CA  THR    48      -1.801  11.735  -1.341  1.00  0.00              
ATOM     49  CA  TRP    49      -0.019   9.238  -3.572  1.00  0.00              
ATOM     50  CA  TRP    50      -3.197   7.142  -3.866  1.00  0.00              
ATOM     51  CA  GLU    51      -5.351  10.158  -4.765  1.00  0.00              
ATOM     52  CA  GLU    52      -2.899  11.218  -7.478  1.00  0.00              
ATOM     53  CA  LEU    53      -2.966   7.675  -8.858  1.00  0.00              
ATOM     54  CA  GLN    54      -6.779   7.472  -8.922  1.00  0.00              
ATOM     55  CA  LYS    55      -6.955  10.700 -10.984  1.00  0.00              
ATOM     56  CA  ASN    56      -4.360   9.543 -13.480  1.00  0.00              
ATOM     57  CA  PRO    57      -5.363   7.245 -16.303  1.00  0.00              
ATOM     58  CA  PRO    58      -2.971   4.372 -16.016  1.00  0.00              
ATOM     59  CA  TYR    59      -2.993   3.766 -12.220  1.00  0.00              
ATOM     60  CA  GLU    60      -6.775   3.882 -11.983  1.00  0.00              
ATOM     61  CA  PRO    61      -7.263   0.494 -13.724  1.00  0.00              
ATOM     62  CA  PRO    62      -9.148  -1.728 -11.313  1.00  0.00              
ATOM     63  CA  ASP    63      -6.954  -4.772 -11.986  1.00  0.00              
ATOM     64  CA  GLN    64      -3.528  -3.347 -11.188  1.00  0.00              
ATOM     65  CA  VAL    65      -4.412  -1.309  -8.078  1.00  0.00              
ATOM     66  CA  GLU    66      -6.333  -4.000  -6.213  1.00  0.00              
ATOM     67  CA  LEU    67      -3.912  -6.835  -7.026  1.00  0.00              
ATOM     68  CA  LEU    68      -0.938  -4.740  -5.899  1.00  0.00              
ATOM     69  CA  ALA    69      -2.513  -3.666  -2.609  1.00  0.00              
ATOM     70  CA  GLN    70      -3.428  -7.302  -1.807  1.00  0.00              
ATOM     71  CA  GLU    71       0.068  -8.490  -2.662  1.00  0.00              
ATOM     72  CA  LEU    72       1.747  -5.828  -0.469  1.00  0.00              
ATOM     73  CA  SER    73      -0.483  -6.648   2.438  1.00  0.00              
ATOM     74  CA  GLN    74       0.245 -10.379   2.171  1.00  0.00              
ATOM     75  CA  GLU    75       3.991  -9.736   2.027  1.00  0.00              
ATOM     76  CA  LYS    76       3.840  -7.440   4.994  1.00  0.00              
ATOM     77  CA  LEU    77       1.821  -9.945   7.026  1.00  0.00              
ATOM     78  CA  ALA    78       4.207 -12.806   6.290  1.00  0.00              
ATOM     79  CA  ARG    79       7.224 -10.712   7.280  1.00  0.00              
ATOM     80  CA  LYS    80       5.453  -9.793  10.549  1.00  0.00              
ATOM     81  CA  GLN    81       4.572 -13.422  11.289  1.00  0.00              
ATOM     82  CA  LEU    82       8.170 -14.483  10.683  1.00  0.00              
ATOM     83  CA  GLU    83       9.422 -11.741  13.001  1.00  0.00              
ATOM     84  CA  GLU    84       6.992 -12.889  15.698  1.00  0.00              
ATOM     85  CA  LEU    85       8.244 -16.469  15.225  1.00  0.00              
ATOM     86  CA  ASN    86      11.851 -15.305  15.520  1.00  0.00              
ATOM     87  CA  LYS    87      10.974 -13.528  18.775  1.00  0.00              
ATOM     88  CA  THR    88       9.282 -16.705  20.063  1.00  0.00              
ATOM     89  CA  LEU    89      12.249 -18.925  19.137  1.00  0.00              
ATOM     90  CA  GLY    90      14.831 -16.545  20.677  1.00  0.00              
ATOM     91  CA  ASN    91      12.956 -16.345  23.985  1.00  0.00              
ATOM     92  CA  GLU    92      12.722 -20.154  24.110  1.00  0.00              
ATOM     93  CA  LEU    93      16.420 -20.560  23.377  1.00  0.00              
ATOM     94  CA  SER    94      17.577 -18.089  26.066  1.00  0.00              
ATOM     95  CA  ASP    95      15.424 -19.714  28.697  1.00  0.00              
ATOM     96  CA  ILE    96      16.789 -23.191  27.792  1.00  0.00              
ATOM     97  CA  LYS    97      20.526 -22.511  28.311  1.00  0.00              
ATOM     98  CA  LEU    98      22.561 -24.942  26.332  1.00  0.00              
ATOM     99  CA  SER    99      26.233 -25.177  27.248  1.00  0.00              
ATOM    100  CA  LEU   100      28.599 -26.929  24.798  1.00  0.00              
ATOM    101  CA  LEU   101      31.723 -28.151  27.094  1.00  0.00              
ATOM    102  CA  SER   102      34.466 -29.000  24.550  1.00  0.00              
ATOM    103  CA  LEU   103      32.243 -30.020  21.639  1.00  0.00              
ATOM    104  CA  LYS   104      30.536 -32.767  23.608  1.00  0.00              
ATOM    105  CA  GLY   105      29.278 -30.876  26.578  1.00  0.00              
ATOM    106  CA  ASP   106      27.902 -27.834  24.240  1.00  0.00              
ATOM    107  CA  TYR   107      26.376 -29.713  21.253  1.00  0.00              
ATOM    108  CA  ALA   108      24.581 -32.541  22.938  1.00  0.00              
ATOM    109  CA  GLU   109      23.131 -30.291  25.582  1.00  0.00              
ATOM    110  CA  LEU   110      21.770 -27.646  23.191  1.00  0.00              
ATOM    111  CA  GLU   111      20.010 -30.118  20.914  1.00  0.00              
ATOM    112  CA  HIS   112      17.770 -31.618  23.595  1.00  0.00              
ATOM    113  CA  HIS   113      14.479 -30.827  21.781  1.00  0.00              
ATOM    114  CA  HIS   114      15.506 -27.140  21.714  1.00  0.00              
ATOM    115  CA  HIS   115      17.213 -27.391  25.578  1.00  0.00              
ATOM    116  CA  HIS   116      17.041 -26.805  29.753  1.00  0.00              
ATOM    117  CA  HIS   117      21.218 -26.545  30.241  1.00  0.00              
TER                                                                             
END
