
#######################################################
#                                                     #
#                        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   75 (   75),  selected   75 , name T0349TS168_2
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS168_2.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    R       2      R       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    L       5      L       5           -
LGA    R       6      R       6           -
LGA    T       7      T       7           #
LGA    N       8      N       8          1.921
LGA    D       9      D       9          3.130
LGA    A      10      A      10          2.037
LGA    -       -      V      11           -
LGA    V      11      L      12          2.206
LGA    L      12      L      13          2.064
LGA    L      13      S      14          2.203
LGA    S      14      A      15          1.958
LGA    A      15      V      16          1.952
LGA    V      16      G      17          1.658
LGA    G      17      A      18          1.405
LGA    A      18      L      19          1.416
LGA    L      19      L      20          1.835
LGA    L      20      D      21          1.483
LGA    D      21      G      22          0.624
LGA    G      22      A      23          1.410
LGA    A      23      D      24          2.035
LGA    D      24      I      25          3.465
LGA    I      25      G      26          4.686
LGA    G      26      H      27          1.932
LGA    H      27      L      28          2.772
LGA    L      28      V      29          4.134
LGA    V      29      L      30          0.564
LGA    L      30      D      31          1.635
LGA    D      31      Q      32          1.287
LGA    Q      32      N      33          2.087
LGA    N      33      -       -           -
LGA    M      34      -       -           -
LGA    S      35      -       -           -
LGA    I      36      -       -           -
LGA    L      37      -       -           -
LGA    E      38      -       -           -
LGA    G      39      -       -           -
LGA    S      40      -       -           -
LGA    L      41      -       -           -
LGA    G      42      -       -           -
LGA    V      43      -       -           -
LGA    I      44      -       -           -
LGA    P      45      -       -           -
LGA    R      46      -       -           -
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      M      34          2.449
LGA    V      50      S      35          4.617
LGA    H      51      I      36          3.740
LGA    E      52      L      37          0.802
LGA    D      53      E      38          3.488
LGA    D      54      G      39          3.828
LGA    L      55      S      40           #
LGA    A      56      L      41           -
LGA    G      57      G      42           -
LGA    A      58      V      43           -
LGA    R      59      I      44           -
LGA    R      60      P      45           -
LGA    L      61      R      46           -
LGA    L      62      R      47           -
LGA    T      63      V      48           -
LGA    D      64      L      49           -
LGA    A      65      V      50           -
LGA    G      66      H      51           -
LGA    L      67      E      52           -
LGA    A      68      D      53           -
LGA    H      69      D      54           -
LGA    E      70      L      55           -
LGA    L      71      A      56           -
LGA    R      72      G      57           -
LGA    S      73      A      58           -
LGA    D      74      R      59           -
LGA    D      75      R      60           -
LGA    -       -      L      61           -
LGA    -       -      L      62           -
LGA    -       -      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   75    5.0     31    2.53    16.13     29.982     1.179

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.283092 * X  +  -0.303280 * Y  +   0.909879 * Z  +  -8.961905
  Y_new =   0.248966 * X  +  -0.939404 * Y  +  -0.235661 * Z  +  -1.708773
  Z_new =   0.926215 * X  +   0.159815 * Y  +   0.341444 * Z  +   5.850431 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.437768   -2.703825  [ DEG:    25.0822   -154.9178 ]
  Theta =  -1.184247   -1.957346  [ DEG:   -67.8524   -112.1476 ]
  Phi   =   2.420247   -0.721346  [ DEG:   138.6699    -41.3301 ]
 
# 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: T0349TS168_2                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS168_2.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   75   75   5.0   31   2.53   16.13  29.982
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS168_2
PFRMAT TS
TARGET T0349
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1       1.791 -19.271   8.668  1.00 25.00           C
ATOM      2  CA  ARG     2      -0.043 -16.088   7.648  1.00 25.00           C
ATOM      3  CA  GLU     3      -2.442 -15.736   4.741  1.00 25.00           C
ATOM      4  CA  LEU     4      -0.088 -13.408   2.816  1.00 25.00           C
ATOM      5  CA  LEU     5      -3.078 -11.840   1.008  1.00 25.00           C
ATOM      6  CA  ARG     6      -4.860 -11.315   4.357  1.00 25.00           C
ATOM      7  CA  THR     7      -1.718  -9.668   5.799  1.00 25.00           C
ATOM      8  CA  ASN     8      -1.494  -7.367   2.746  1.00 25.00           C
ATOM      9  CA  ASP     9      -5.180  -6.416   3.161  1.00 25.00           C
ATOM     10  CA  ALA    10      -4.591  -5.650   6.867  1.00 25.00           C
ATOM     11  CA  VAL    11      -1.576  -3.469   5.962  1.00 25.00           C
ATOM     12  CA  LEU    12      -3.679  -1.595   3.367  1.00 25.00           C
ATOM     13  CA  LEU    13      -6.431  -1.029   5.971  1.00 25.00           C
ATOM     14  CA  SER    14      -3.838   0.299   8.457  1.00 25.00           C
ATOM     15  CA  ALA    15      -2.455   2.669   5.788  1.00 25.00           C
ATOM     16  CA  VAL    16      -5.994   3.916   5.025  1.00 25.00           C
ATOM     17  CA  GLY    17      -6.615   4.510   8.757  1.00 25.00           C
ATOM     18  CA  ALA    18      -3.327   6.454   9.020  1.00 25.00           C
ATOM     19  CA  LEU    19      -4.314   8.583   5.994  1.00 25.00           C
ATOM     20  CA  LEU    20      -7.727   9.298   7.578  1.00 25.00           C
ATOM     21  CA  ASP    21      -6.020  10.318  10.852  1.00 25.00           C
ATOM     22  CA  GLY    22      -4.837  13.636   9.346  1.00 25.00           C
ATOM     23  CA  ALA    23      -3.661  13.781   5.713  1.00 25.00           C
ATOM     24  CA  ASP    24      -0.193  12.194   6.320  1.00 25.00           C
ATOM     25  CA  ILE    25      -0.622  10.323   3.027  1.00 25.00           C
ATOM     26  CA  GLY    26      -3.498  10.831   0.587  1.00 25.00           C
ATOM     27  CA  HIS    27      -5.237   7.664  -0.535  1.00 25.00           C
ATOM     28  CA  LEU    28      -6.112   5.599  -3.626  1.00 25.00           C
ATOM     29  CA  VAL    29      -7.121   2.004  -4.266  1.00 25.00           C
ATOM     30  CA  LEU    30      -4.441  -0.656  -4.850  1.00 25.00           C
ATOM     31  CA  ASP    31      -6.328  -2.902  -7.346  1.00 25.00           C
ATOM     32  CA  GLN    32      -8.214  -4.281  -4.299  1.00 25.00           C
ATOM     33  CA  ASN    33     -11.049  -1.975  -5.388  1.00 25.00           C
ATOM     34  CA  MET    34     -14.774  -1.033  -5.410  1.00 25.00           C
ATOM     35  CA  SER    35     -15.688   1.998  -3.301  1.00 25.00           C
ATOM     36  CA  ILE    36     -14.607   1.450   0.332  1.00 25.00           C
ATOM     37  CA  LEU    37     -14.819  -2.343  -0.152  1.00 25.00           C
ATOM     38  CA  GLU    38     -18.391  -2.058  -1.448  1.00 25.00           C
ATOM     39  CA  GLY    39     -21.240  -0.272   0.268  1.00 25.00           C
ATOM     40  CA  SER    40     -20.626   0.607   3.876  1.00 25.00           C
ATOM     41  CA  LEU    41     -21.075   4.148   2.602  1.00 25.00           C
ATOM     42  CA  GLY    42     -19.615   7.618   2.394  1.00 25.00           C
ATOM     43  CA  VAL    43     -16.508   6.361   0.511  1.00 25.00           C
ATOM     44  CA  ILE    44     -14.620   5.328   3.689  1.00 25.00           C
ATOM     45  CA  PRO    45     -10.844   4.992   4.001  1.00 25.00           C
ATOM     46  CA  ARG    46      -9.871   1.652   2.394  1.00 25.00           C
ATOM     47  CA  ARG    47      -8.413  -1.080   0.174  1.00 25.00           C
ATOM     48  CA  VAL    48     -10.036  -4.484   0.363  1.00 25.00           C
ATOM     49  CA  LEU    49     -12.594  -5.932  -2.128  1.00 25.00           C
ATOM     50  CA  VAL    50     -11.742  -9.626  -1.901  1.00 25.00           C
ATOM     51  CA  HIS    51     -15.493 -10.276  -1.948  1.00 25.00           C
ATOM     52  CA  GLU    52     -18.286 -10.862   0.643  1.00 25.00           C
ATOM     53  CA  ASP    53     -17.508 -11.646   4.310  1.00 25.00           C
ATOM     54  CA  ASP    54     -13.884 -10.514   3.810  1.00 25.00           C
ATOM     55  CA  LEU    55     -15.098  -7.261   2.194  1.00 25.00           C
ATOM     56  CA  ALA    56     -17.478  -6.660   5.135  1.00 25.00           C
ATOM     57  CA  GLY    57     -14.615  -7.259   7.606  1.00 25.00           C
ATOM     58  CA  ALA    58     -12.407  -4.789   5.686  1.00 25.00           C
ATOM     59  CA  ARG    59     -15.214  -2.185   5.758  1.00 25.00           C
ATOM     60  CA  ARG    60     -15.624  -2.698   9.532  1.00 25.00           C
ATOM     61  CA  LEU    61     -11.852  -2.261  10.026  1.00 25.00           C
ATOM     62  CA  LEU    62     -11.929   0.962   7.959  1.00 25.00           C
ATOM     63  CA  THR    63     -14.852   2.268  10.060  1.00 25.00           C
ATOM     64  CA  ASP    64     -12.937   1.454  13.276  1.00 25.00           C
ATOM     65  CA  ALA    65      -9.857   3.293  11.936  1.00 25.00           C
ATOM     66  CA  GLY    66      -7.919   1.048  14.329  1.00 25.00           C
ATOM     67  CA  LEU    67      -6.173  -2.266  14.881  1.00 25.00           C
ATOM     68  CA  ALA    68      -5.912  -0.982  18.437  1.00 25.00           C
ATOM     69  CA  HIS    69      -4.372  -1.182  21.896  1.00 25.00           C
ATOM     70  CA  GLU    70      -3.832  -4.407  23.794  1.00 25.00           C
ATOM     71  CA  LEU    71      -6.244  -5.914  21.252  1.00 25.00           C
ATOM     72  CA  ARG    72      -8.337  -6.908  24.234  1.00 25.00           C
ATOM     73  CA  SER    73      -6.242  -9.351  26.354  1.00 25.00           C
ATOM     74  CA  ASP    74      -8.730 -12.027  25.344  1.00 25.00           C
ATOM     75  CA  ASP    75      -7.998 -15.341  23.656  1.00 25.00           C
TER
END
