
#######################################################
#                                                     #
#                        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   88 (   88),  selected   88 , name T0288TS393_5-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS393_5-D1.T0288_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    V       3      V       3           #
LGA    P       4      P       4          2.371
LGA    G       5      G       5          1.448
LGA    K       6      K       6          2.866
LGA    V       7      V       7          1.295
LGA    T       8      T       8          2.380
LGA    L       9      L       9          2.318
LGA    Q      10      Q      10          1.855
LGA    K      11      K      11          1.119
LGA    D      12      D      12          1.254
LGA    A      13      A      13          1.608
LGA    Q      14      Q      14          1.278
LGA    N      15      N      15          1.241
LGA    L      16      L      16          2.249
LGA    I      17      I      17          1.749
LGA    G      18      G      18          1.182
LGA    I      19      I      19          1.301
LGA    S      20      S      20          1.712
LGA    I      21      I      21          1.152
LGA    G      22      G      22          1.372
LGA    G      23      G      23          0.953
LGA    G      24      G      24          2.249
LGA    A      25      A      25          4.547
LGA    Q      26      Q      26          2.072
LGA    Y      27      -       -           -
LGA    C      28      P      29          2.360
LGA    P      29      C      30          2.255
LGA    C      30      -       -           -
LGA    L      31      L      31          1.706
LGA    Y      32      Y      32          1.248
LGA    I      33      I      33          0.991
LGA    V      34      V      34          1.643
LGA    Q      35      Q      35          1.034
LGA    V      36      V      36          0.688
LGA    F      37      F      37          0.522
LGA    D      38      D      38          0.870
LGA    N      39      N      39          1.736
LGA    T      40      T      40          0.864
LGA    P      41      P      41          4.409
LGA    A      42      A      42          1.501
LGA    A      43      A      43          5.212
LGA    L      44      L      44          2.054
LGA    D      45      D      45          2.002
LGA    G      46      G      46          1.393
LGA    T      47      T      47          1.320
LGA    V      48      V      48          0.929
LGA    A      49      A      49          1.251
LGA    A      50      A      50          0.806
LGA    G      51      G      51          0.869
LGA    D      52      D      52          1.472
LGA    E      53      E      53          1.118
LGA    I      54      I      54          0.879
LGA    T      55      T      55          1.720
LGA    G      56      G      56          2.254
LGA    V      57      V      57          1.985
LGA    N      58      N      58          0.320
LGA    G      59      G      59          2.285
LGA    R      60      R      60          2.545
LGA    S      61      S      61          2.188
LGA    I      62      I      62          1.450
LGA    K      63      K      63          2.584
LGA    G      64      G      64          2.486
LGA    K      65      K      65          1.173
LGA    T      66      T      66          1.480
LGA    K      67      K      67          0.961
LGA    V      68      V      68          1.221
LGA    E      69      E      69          1.206
LGA    V      70      V      70          0.994
LGA    A      71      A      71          0.726
LGA    K      72      K      72          1.161
LGA    M      73      M      73          1.041
LGA    I      74      I      74          0.861
LGA    Q      75      Q      75          0.939
LGA    E      76      E      76          1.388
LGA    V      77      V      77          0.768
LGA    K      78      K      78          2.088
LGA    G      79      G      79          0.953
LGA    E      80      E      80          1.393
LGA    V      81      V      81          0.821
LGA    T      82      T      82          1.195
LGA    I      83      I      83          0.817
LGA    H      84      H      84          0.511
LGA    Y      85      Y      85          1.054
LGA    N      86      N      86          1.356
LGA    K      87      K      87          1.591
LGA    L      88      L      88          0.706

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     83    1.76    97.59     87.668     4.454

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.198512 * X  +  -0.392615 * Y  +  -0.898023 * Z  +  27.489759
  Y_new =   0.426488 * X  +  -0.790358 * Y  +   0.439821 * Z  +  17.298861
  Z_new =  -0.882440 * X  +  -0.470306 * Y  +   0.010551 * Z  +  13.229816 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.548366    1.593226  [ DEG:   -88.7149     91.2851 ]
  Theta =   1.081024    2.060568  [ DEG:    61.9381    118.0619 ]
  Phi   =   1.135164   -2.006429  [ DEG:    65.0401   -114.9599 ]
 
# 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: T0288TS393_5-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS393_5-D1.T0288_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   88   86   5.0   83   1.76   97.59  87.668
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS393_5-D1
PFRMAT TS
TARGET T0288
MODEL 5
PARENT N/A
ATOM      1  CA  SER     1      22.884   9.941  32.036  1.00 25.00           C
ATOM      2  CA  MET     2      25.880  10.665  29.806  1.00 25.00           C
ATOM      3  CA  VAL     3      23.627  10.674  26.812  1.00 25.00           C
ATOM      4  CA  PRO     4      24.442  13.729  24.620  1.00 25.00           C
ATOM      5  CA  GLY     5      21.513  15.943  23.636  1.00 25.00           C
ATOM      6  CA  LYS     6      22.636  18.824  21.417  1.00 25.00           C
ATOM      7  CA  VAL     7      21.440  20.643  18.368  1.00 25.00           C
ATOM      8  CA  THR     8      19.143  22.739  16.209  1.00 25.00           C
ATOM      9  CA  LEU     9      21.568  23.613  13.375  1.00 25.00           C
ATOM     10  CA  GLN    10      18.563  25.511  11.969  1.00 25.00           C
ATOM     11  CA  LYS    11      18.426  25.657   8.114  1.00 25.00           C
ATOM     12  CA  ASP    12      18.825  29.081   6.488  1.00 25.00           C
ATOM     13  CA  ALA    13      20.560  30.406   3.370  1.00 25.00           C
ATOM     14  CA  GLN    14      23.355  28.446   1.739  1.00 25.00           C
ATOM     15  CA  ASN    15      21.741  25.386   3.357  1.00 25.00           C
ATOM     16  CA  LEU    16      24.557  23.194   4.631  1.00 25.00           C
ATOM     17  CA  ILE    17      23.380  23.069   8.264  1.00 25.00           C
ATOM     18  CA  GLY    18      26.618  25.048   8.920  1.00 25.00           C
ATOM     19  CA  ILE    19      29.674  22.747   8.597  1.00 25.00           C
ATOM     20  CA  SER    20      32.196  20.898   6.414  1.00 25.00           C
ATOM     21  CA  ILE    21      32.185  17.262   7.655  1.00 25.00           C
ATOM     22  CA  GLY    22      35.227  14.978   7.686  1.00 25.00           C
ATOM     23  CA  GLY    23      36.406  12.235  10.055  1.00 25.00           C
ATOM     24  CA  GLY    24      38.054  10.471   7.152  1.00 25.00           C
ATOM     25  CA  ALA    25      37.195   6.901   6.330  1.00 25.00           C
ATOM     26  CA  GLN    26      40.106   5.715   8.448  1.00 25.00           C
ATOM     27  CA  TYR    27      38.868   7.760  11.365  1.00 25.00           C
ATOM     28  CA  CYS    28      37.021   4.644  12.653  1.00 25.00           C
ATOM     29  CA  PRO    29      35.220   6.945  15.141  1.00 25.00           C
ATOM     30  CA  CYS    30      32.834   8.685  12.743  1.00 25.00           C
ATOM     31  CA  LEU    31      31.573  12.072  11.470  1.00 25.00           C
ATOM     32  CA  TYR    32      33.295  15.290  12.563  1.00 25.00           C
ATOM     33  CA  ILE    33      33.443  19.062  12.598  1.00 25.00           C
ATOM     34  CA  VAL    34      35.788  21.358  10.578  1.00 25.00           C
ATOM     35  CA  GLN    35      34.212  24.737  11.299  1.00 25.00           C
ATOM     36  CA  VAL    36      31.292  26.526  12.963  1.00 25.00           C
ATOM     37  CA  PHE    37      31.114  29.377  10.374  1.00 25.00           C
ATOM     38  CA  ASP    38      30.057  32.995  10.937  1.00 25.00           C
ATOM     39  CA  ASN    39      26.947  33.642   8.878  1.00 25.00           C
ATOM     40  CA  THR    40      26.053  30.062   9.742  1.00 25.00           C
ATOM     41  CA  PRO    41      26.653  30.150  13.484  1.00 25.00           C
ATOM     42  CA  ALA    42      25.575  27.006  15.290  1.00 25.00           C
ATOM     43  CA  ALA    43      22.104  28.579  14.894  1.00 25.00           C
ATOM     44  CA  LEU    44      22.900  31.092  17.673  1.00 25.00           C
ATOM     45  CA  ASP    45      23.501  28.252  20.145  1.00 25.00           C
ATOM     46  CA  GLY    46      27.077  27.056  20.363  1.00 25.00           C
ATOM     47  CA  THR    47      25.482  23.561  20.074  1.00 25.00           C
ATOM     48  CA  VAL    48      28.343  22.880  17.684  1.00 25.00           C
ATOM     49  CA  ALA    49      31.784  24.324  18.600  1.00 25.00           C
ATOM     50  CA  ALA    50      34.480  22.600  16.470  1.00 25.00           C
ATOM     51  CA  GLY    51      35.356  19.111  17.606  1.00 25.00           C
ATOM     52  CA  ASP    52      31.640  18.497  18.309  1.00 25.00           C
ATOM     53  CA  GLU    53      32.177  14.799  17.798  1.00 25.00           C
ATOM     54  CA  ILE    54      29.292  14.056  15.461  1.00 25.00           C
ATOM     55  CA  THR    55      26.533  11.469  14.927  1.00 25.00           C
ATOM     56  CA  GLY    56      23.418  12.419  12.900  1.00 25.00           C
ATOM     57  CA  VAL    57      20.560  12.006  10.384  1.00 25.00           C
ATOM     58  CA  ASN    58      17.379  12.964  12.243  1.00 25.00           C
ATOM     59  CA  GLY    59      17.167   9.235  13.043  1.00 25.00           C
ATOM     60  CA  ARG    60      19.251   7.119  10.575  1.00 25.00           C
ATOM     61  CA  SER    61      22.755   6.118  11.718  1.00 25.00           C
ATOM     62  CA  ILE    62      25.641   8.403  10.688  1.00 25.00           C
ATOM     63  CA  LYS    63      27.757   6.524  13.230  1.00 25.00           C
ATOM     64  CA  GLY    64      29.256   3.488  11.497  1.00 25.00           C
ATOM     65  CA  LYS    65      28.616   5.198   8.196  1.00 25.00           C
ATOM     66  CA  THR    66      31.765   6.477   6.585  1.00 25.00           C
ATOM     67  CA  LYS    67      32.173  10.304   6.711  1.00 25.00           C
ATOM     68  CA  VAL    68      31.010  10.643   3.078  1.00 25.00           C
ATOM     69  CA  GLU    69      27.673   8.987   3.967  1.00 25.00           C
ATOM     70  CA  VAL    70      27.241  11.386   6.921  1.00 25.00           C
ATOM     71  CA  ALA    71      27.973  14.371   4.634  1.00 25.00           C
ATOM     72  CA  LYS    72      25.397  13.096   2.104  1.00 25.00           C
ATOM     73  CA  MET    73      22.805  12.716   4.898  1.00 25.00           C
ATOM     74  CA  ILE    74      23.527  16.284   6.087  1.00 25.00           C
ATOM     75  CA  GLN    75      23.114  17.587   2.510  1.00 25.00           C
ATOM     76  CA  GLU    76      19.780  15.729   2.192  1.00 25.00           C
ATOM     77  CA  VAL    77      17.862  18.190   4.290  1.00 25.00           C
ATOM     78  CA  LYS    78      16.898  21.786   3.525  1.00 25.00           C
ATOM     79  CA  GLY    79      14.797  22.533   6.624  1.00 25.00           C
ATOM     80  CA  GLU    80      15.194  20.986  10.001  1.00 25.00           C
ATOM     81  CA  VAL    81      18.443  19.407  11.113  1.00 25.00           C
ATOM     82  CA  THR    82      18.063  17.826  14.527  1.00 25.00           C
ATOM     83  CA  ILE    83      21.790  16.923  14.544  1.00 25.00           C
ATOM     84  CA  HIS    84      22.947  14.652  17.353  1.00 25.00           C
ATOM     85  CA  TYR    85      26.170  15.966  18.890  1.00 25.00           C
ATOM     86  CA  ASN    86      28.304  13.541  20.793  1.00 25.00           C
ATOM     87  CA  LYS    87      30.699  14.943  23.324  1.00 25.00           C
ATOM     88  CA  LEU    88      34.407  14.331  23.896  1.00 25.00           C
TER
END
