
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS393_3-D1.T0288_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S       1           -
LGA    S       1      M       2           #
LGA    M       2      -       -           -
LGA    V       3      V       3          7.136
LGA    P       4      P       4          2.820
LGA    G       5      G       5          2.118
LGA    K       6      K       6          2.125
LGA    V       7      V       7          2.520
LGA    T       8      T       8          2.553
LGA    L       9      L       9          1.688
LGA    Q      10      Q      10          1.616
LGA    K      11      K      11          1.682
LGA    D      12      D      12          3.563
LGA    A      13      A      13          2.163
LGA    Q      14      Q      14          2.032
LGA    N      15      N      15          1.603
LGA    L      16      L      16          1.665
LGA    I      17      I      17          0.864
LGA    G      18      G      18          0.283
LGA    I      19      I      19          0.522
LGA    S      20      S      20          0.972
LGA    I      21      I      21          2.006
LGA    G      22      G      22          1.318
LGA    G      23      G      23          1.446
LGA    G      24      G      24          1.868
LGA    A      25      A      25          3.861
LGA    Q      26      Q      26          2.136
LGA    Y      27      -       -           -
LGA    C      28      -       -           -
LGA    P      29      P      29          2.448
LGA    C      30      C      30          2.322
LGA    L      31      L      31          0.478
LGA    Y      32      Y      32          0.847
LGA    I      33      I      33          1.195
LGA    V      34      V      34          1.210
LGA    Q      35      Q      35          0.654
LGA    V      36      V      36          2.108
LGA    F      37      F      37          1.556
LGA    D      38      D      38          0.923
LGA    N      39      N      39          0.630
LGA    T      40      T      40          1.306
LGA    P      41      P      41          0.595
LGA    A      42      A      42          0.613
LGA    A      43      A      43          1.807
LGA    L      44      L      44          2.861
LGA    D      45      D      45          2.090
LGA    G      46      G      46          1.806
LGA    T      47      T      47          0.741
LGA    V      48      V      48          1.171
LGA    A      49      A      49          0.830
LGA    A      50      A      50          0.948
LGA    G      51      G      51          1.255
LGA    D      52      D      52          1.361
LGA    E      53      E      53          0.578
LGA    I      54      I      54          1.512
LGA    T      55      T      55          2.346
LGA    G      56      G      56          1.782
LGA    V      57      V      57          1.873
LGA    N      58      N      58          0.952
LGA    G      59      G      59          2.669
LGA    R      60      R      60          3.328
LGA    S      61      S      61          2.940
LGA    I      62      I      62          1.291
LGA    K      63      K      63          1.705
LGA    G      64      G      64          1.522
LGA    K      65      K      65          1.996
LGA    T      66      T      66          1.841
LGA    K      67      K      67          0.986
LGA    V      68      V      68          1.139
LGA    E      69      E      69          1.596
LGA    V      70      V      70          1.284
LGA    A      71      A      71          0.549
LGA    K      72      K      72          1.376
LGA    M      73      M      73          1.311
LGA    I      74      I      74          0.894
LGA    Q      75      Q      75          1.286
LGA    E      76      E      76          1.797
LGA    V      77      V      77          0.858
LGA    K      78      K      78          2.377
LGA    G      79      G      79          1.603
LGA    E      80      E      80          3.100
LGA    V      81      V      81          0.752
LGA    T      82      T      82          0.580
LGA    I      83      I      83          0.588
LGA    H      84      H      84          0.985
LGA    Y      85      Y      85          1.052
LGA    N      86      N      86          1.775
LGA    K      87      K      87          3.432
LGA    L      88      L      88          1.050

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     84    1.93   100.00     87.568     4.145

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.536456 * X  +   0.186164 * Y  +  -0.823139 * Z  +  27.534304
  Y_new =   0.279851 * X  +  -0.880937 * Y  +  -0.381620 * Z  +  17.388376
  Z_new =  -0.796177 * X  +  -0.435078 * Y  +   0.420486 * Z  +  13.329571 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.802452    2.339141  [ DEG:   -45.9771    134.0229 ]
  Theta =   0.920951    2.220642  [ DEG:    52.7666    127.2334 ]
  Phi   =   2.660763   -0.480829  [ DEG:   152.4505    -27.5495 ]
 
# 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_3-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS393_3-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   84   1.93  100.00  87.568
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS393_3-D1
PFRMAT TS
TARGET T0288
MODEL 3
PARENT N/A
ATOM      1  CA  SER     1      23.755  13.889  33.084  1.00 25.00           C
ATOM      2  CA  MET     2      24.962  12.545  29.792  1.00 25.00           C
ATOM      3  CA  VAL     3      22.279  11.919  27.219  1.00 25.00           C
ATOM      4  CA  PRO     4      24.111  13.478  24.288  1.00 25.00           C
ATOM      5  CA  GLY     5      22.371  16.898  24.665  1.00 25.00           C
ATOM      6  CA  LYS     6      21.216  18.408  21.336  1.00 25.00           C
ATOM      7  CA  VAL     7      21.740  21.697  19.572  1.00 25.00           C
ATOM      8  CA  THR     8      18.673  22.325  17.394  1.00 25.00           C
ATOM      9  CA  LEU     9      20.415  23.931  14.428  1.00 25.00           C
ATOM     10  CA  GLN    10      17.695  25.361  12.148  1.00 25.00           C
ATOM     11  CA  LYS    11      19.229  25.905   8.779  1.00 25.00           C
ATOM     12  CA  ASP    12      16.725  28.270   7.288  1.00 25.00           C
ATOM     13  CA  ALA    13      18.708  29.150   4.184  1.00 25.00           C
ATOM     14  CA  GLN    14      22.259  29.572   2.892  1.00 25.00           C
ATOM     15  CA  ASN    15      22.529  25.792   2.459  1.00 25.00           C
ATOM     16  CA  LEU    16      22.852  23.959   5.758  1.00 25.00           C
ATOM     17  CA  ILE    17      23.988  24.153   9.381  1.00 25.00           C
ATOM     18  CA  GLY    18      27.326  25.898   9.234  1.00 25.00           C
ATOM     19  CA  ILE    19      29.323  22.820  10.174  1.00 25.00           C
ATOM     20  CA  SER    20      31.407  20.787   7.771  1.00 25.00           C
ATOM     21  CA  ILE    21      31.322  16.993   7.194  1.00 25.00           C
ATOM     22  CA  GLY    22      35.030  16.284   7.996  1.00 25.00           C
ATOM     23  CA  GLY    23      36.514  12.912   9.092  1.00 25.00           C
ATOM     24  CA  GLY    24      38.622   9.813   8.285  1.00 25.00           C
ATOM     25  CA  ALA    25      37.810   6.214   7.452  1.00 25.00           C
ATOM     26  CA  GLN    26      40.626   5.071   9.750  1.00 25.00           C
ATOM     27  CA  TYR    27      39.288   6.805  12.889  1.00 25.00           C
ATOM     28  CA  CYS    28      36.800   5.157  15.240  1.00 25.00           C
ATOM     29  CA  PRO    29      33.544   5.537  13.241  1.00 25.00           C
ATOM     30  CA  CYS    30      32.068   8.802  14.562  1.00 25.00           C
ATOM     31  CA  LEU    31      33.036  11.903  12.591  1.00 25.00           C
ATOM     32  CA  TYR    32      34.088  15.469  13.136  1.00 25.00           C
ATOM     33  CA  ILE    33      33.177  19.002  12.205  1.00 25.00           C
ATOM     34  CA  VAL    34      36.382  20.449  10.749  1.00 25.00           C
ATOM     35  CA  GLN    35      35.388  23.951  11.854  1.00 25.00           C
ATOM     36  CA  VAL    36      32.729  26.437  10.930  1.00 25.00           C
ATOM     37  CA  PHE    37      31.758  29.582   8.940  1.00 25.00           C
ATOM     38  CA  ASP    38      30.512  32.841  10.519  1.00 25.00           C
ATOM     39  CA  ASN    39      26.715  33.446  10.368  1.00 25.00           C
ATOM     40  CA  THR    40      24.316  30.626   9.629  1.00 25.00           C
ATOM     41  CA  PRO    41      22.154  28.771  12.234  1.00 25.00           C
ATOM     42  CA  ALA    42      25.107  27.032  13.958  1.00 25.00           C
ATOM     43  CA  ALA    43      28.513  28.782  14.042  1.00 25.00           C
ATOM     44  CA  LEU    44      26.949  31.793  15.820  1.00 25.00           C
ATOM     45  CA  ASP    45      24.563  29.937  18.036  1.00 25.00           C
ATOM     46  CA  GLY    46      27.389  27.426  18.747  1.00 25.00           C
ATOM     47  CA  THR    47      26.506  24.223  20.596  1.00 25.00           C
ATOM     48  CA  VAL    48      27.869  22.625  17.424  1.00 25.00           C
ATOM     49  CA  ALA    49      31.308  22.957  18.872  1.00 25.00           C
ATOM     50  CA  ALA    50      34.516  22.674  16.882  1.00 25.00           C
ATOM     51  CA  GLY    51      36.626  19.493  17.195  1.00 25.00           C
ATOM     52  CA  ASP    52      33.228  17.769  17.498  1.00 25.00           C
ATOM     53  CA  GLU    53      31.491  14.322  17.594  1.00 25.00           C
ATOM     54  CA  ILE    54      29.068  14.816  14.692  1.00 25.00           C
ATOM     55  CA  THR    55      26.298  12.211  14.855  1.00 25.00           C
ATOM     56  CA  GLY    56      22.904  11.938  13.209  1.00 25.00           C
ATOM     57  CA  VAL    57      20.880  13.665  10.469  1.00 25.00           C
ATOM     58  CA  ASN    58      17.336  12.816  11.509  1.00 25.00           C
ATOM     59  CA  GLY    59      17.519   9.175  12.651  1.00 25.00           C
ATOM     60  CA  ARG    60      20.128   8.642   9.869  1.00 25.00           C
ATOM     61  CA  SER    61      23.014   6.352  10.950  1.00 25.00           C
ATOM     62  CA  ILE    62      26.435   7.718  11.941  1.00 25.00           C
ATOM     63  CA  LYS    63      28.212   4.839  13.765  1.00 25.00           C
ATOM     64  CA  GLY    64      29.213   3.289  10.438  1.00 25.00           C
ATOM     65  CA  LYS    65      29.628   6.302   8.140  1.00 25.00           C
ATOM     66  CA  THR    66      32.729   7.247   6.206  1.00 25.00           C
ATOM     67  CA  LYS    67      32.455  10.977   6.623  1.00 25.00           C
ATOM     68  CA  VAL    68      31.027  10.757   3.076  1.00 25.00           C
ATOM     69  CA  GLU    69      27.831   9.146   4.436  1.00 25.00           C
ATOM     70  CA  VAL    70      27.511  11.928   7.048  1.00 25.00           C
ATOM     71  CA  ALA    71      27.960  14.576   4.319  1.00 25.00           C
ATOM     72  CA  LYS    72      25.266  12.877   2.192  1.00 25.00           C
ATOM     73  CA  MET    73      22.893  12.821   5.198  1.00 25.00           C
ATOM     74  CA  ILE    74      23.553  16.543   5.818  1.00 25.00           C
ATOM     75  CA  GLN    75      22.837  17.308   2.134  1.00 25.00           C
ATOM     76  CA  GLU    76      19.567  15.325   2.331  1.00 25.00           C
ATOM     77  CA  VAL    77      17.952  17.597   4.898  1.00 25.00           C
ATOM     78  CA  LYS    78      17.383  21.264   4.224  1.00 25.00           C
ATOM     79  CA  GLY    79      14.570  21.749   6.798  1.00 25.00           C
ATOM     80  CA  GLU    80      14.753  19.092   9.562  1.00 25.00           C
ATOM     81  CA  VAL    81      18.501  18.593   9.979  1.00 25.00           C
ATOM     82  CA  THR    82      18.396  17.450  13.634  1.00 25.00           C
ATOM     83  CA  ILE    83      22.096  17.097  14.471  1.00 25.00           C
ATOM     84  CA  HIS    84      22.475  14.791  17.438  1.00 25.00           C
ATOM     85  CA  TYR    85      25.939  15.739  18.837  1.00 25.00           C
ATOM     86  CA  ASN    86      28.592  15.670  21.553  1.00 25.00           C
ATOM     87  CA  LYS    87      31.281  13.151  22.518  1.00 25.00           C
ATOM     88  CA  LEU    88      34.154  15.486  23.589  1.00 25.00           C
TER
END
