
#######################################################
#                                                     #
#                        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   85 (   85),  selected   85 , name T0353TS168_1
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS168_1.T0353.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    Q       2      Q       2           -
LGA    I       3      I       3           -
LGA    -       -      H       4           -
LGA    -       -      V       5           -
LGA    -       -      Y       6           -
LGA    -       -      D       7           -
LGA    -       -      T       8           -
LGA    H       4      Y       9          4.304
LGA    V       5      V      10          2.248
LGA    Y       6      -       -           -
LGA    D       7      -       -           -
LGA    T       8      -       -           -
LGA    Y       9      -       -           -
LGA    V      10      -       -           -
LGA    K      11      -       -           -
LGA    A      12      -       -           -
LGA    K      13      -       -           -
LGA    D      14      -       -           -
LGA    G      15      -       -           -
LGA    H      16      -       -           -
LGA    V      17      -       -           -
LGA    M      18      -       -           -
LGA    H      19      -       -           -
LGA    F      20      -       -           -
LGA    D      21      -       -           -
LGA    V      22      -       -           -
LGA    F      23      K      11          5.380
LGA    T      24      A      12          2.751
LGA    D      25      K      13          2.362
LGA    V      26      D      14          3.092
LGA    R      27      G      15           #
LGA    D      28      H      16          1.704
LGA    D      29      -       -           -
LGA    K      30      V      17          0.493
LGA    K      31      -       -           -
LGA    A      32      -       -           -
LGA    I      33      M      18          1.823
LGA    E      34      H      19          0.891
LGA    F      35      F      20          3.156
LGA    A      36      -       -           -
LGA    K      37      -       -           -
LGA    Q      38      D      21          2.880
LGA    W      39      -       -           -
LGA    L      40      V      22          1.975
LGA    S      41      F      23          4.220
LGA    S      42      -       -           -
LGA    I      43      -       -           -
LGA    G      44      T      24           #
LGA    E      45      D      25          3.144
LGA    E      46      V      26          2.804
LGA    G      47      R      27          1.279
LGA    A      48      D      28          2.162
LGA    -       -      D      29           -
LGA    T      49      K      30          3.204
LGA    -       -      K      31           -
LGA    -       -      A      32           -
LGA    V      50      I      33          3.291
LGA    T      51      E      34          4.127
LGA    -       -      F      35           -
LGA    -       -      A      36           -
LGA    S      52      K      37          5.725
LGA    E      53      Q      38           -
LGA    E      54      W      39           -
LGA    C      55      L      40           #
LGA    -       -      S      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      E      45           -
LGA    R      56      E      46          4.030
LGA    F      57      G      47          1.580
LGA    C      58      A      48          2.968
LGA    H      59      T      49          1.804
LGA    S      60      -       -           -
LGA    Q      61      V      50          5.441
LGA    K      62      T      51          3.566
LGA    A      63      S      52           -
LGA    P      64      -       -           -
LGA    D      65      E      53          2.452
LGA    E      66      E      54          3.310
LGA    V      67      C      55          2.722
LGA    I      68      -       -           -
LGA    E      69      R      56          1.026
LGA    A      70      F      57          3.770
LGA    I      71      -       -           -
LGA    K      72      -       -           -
LGA    Q      73      C      58          1.400
LGA    N      74      H      59          2.810
LGA    G      75      S      60           #
LGA    -       -      Q      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    Y      76      I      71           #
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    F      77      Y      76           #
LGA    I      78      F      77           -
LGA    Y      79      I      78           -
LGA    K      80      Y      79           -
LGA    M      81      K      80           -
LGA    E      82      M      81           -
LGA    G      83      E      82           -
LGA    C      84      G      83           -
LGA    N      85      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   85    5.0     35    3.12     8.57     25.347     1.088

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.859347 * X  +  -0.451097 * Y  +   0.240904 * Z  +  -4.541739
  Y_new =  -0.372735 * X  +   0.875021 * Y  +   0.308880 * Z  +   2.091076
  Z_new =  -0.350131 * X  +   0.175642 * Y  +  -0.920086 * Z  +   2.372550 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.952965   -0.188628  [ DEG:   169.1924    -10.8076 ]
  Theta =   0.357711    2.783882  [ DEG:    20.4953    159.5047 ]
  Phi   =  -2.732341    0.409252  [ DEG:  -156.5516     23.4484 ]
 
# 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: T0353TS168_1                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS168_1.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   85   5.0   35   3.12    8.57  25.347
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS168_1
PFRMAT TS
TARGET T0353
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -4.097  17.182  13.828  1.00 25.00           C
ATOM      2  CA  GLN     2      -5.109  14.559  11.277  1.00 25.00           C
ATOM      3  CA  ILE     3      -5.278  11.151   9.480  1.00 25.00           C
ATOM      4  CA  HIS     4      -6.386   7.539  10.131  1.00 25.00           C
ATOM      5  CA  VAL     5      -6.251   4.266   8.269  1.00 25.00           C
ATOM      6  CA  TYR     6      -6.536   1.718   5.445  1.00 25.00           C
ATOM      7  CA  ASP     7      -4.259  -0.288   3.163  1.00 25.00           C
ATOM      8  CA  THR     8      -7.049  -1.588   0.890  1.00 25.00           C
ATOM      9  CA  TYR     9      -4.762  -0.952  -2.002  1.00 25.00           C
ATOM     10  CA  VAL    10      -5.476  -4.327  -3.483  1.00 25.00           C
ATOM     11  CA  LYS    11      -6.557  -6.773  -0.802  1.00 25.00           C
ATOM     12  CA  ALA    12      -4.987 -10.231  -0.969  1.00 25.00           C
ATOM     13  CA  LYS    13      -3.083 -13.116  -2.582  1.00 25.00           C
ATOM     14  CA  ASP    14      -1.183 -14.691  -5.456  1.00 25.00           C
ATOM     15  CA  GLY    15      -1.541 -13.124  -8.902  1.00 25.00           C
ATOM     16  CA  HIS    16      -1.906  -9.659  -7.469  1.00 25.00           C
ATOM     17  CA  VAL    17      -1.251  -5.975  -6.884  1.00 25.00           C
ATOM     18  CA  MET    18      -1.262  -7.032  -3.259  1.00 25.00           C
ATOM     19  CA  HIS    19      -0.969  -6.797   0.561  1.00 25.00           C
ATOM     20  CA  PHE    20      -2.891  -5.172   3.486  1.00 25.00           C
ATOM     21  CA  ASP    21      -3.352  -5.932   7.226  1.00 25.00           C
ATOM     22  CA  VAL    22      -6.515  -3.784   6.946  1.00 25.00           C
ATOM     23  CA  PHE    23      -8.894  -2.234   9.446  1.00 25.00           C
ATOM     24  CA  THR    24      -9.503   1.295  10.744  1.00 25.00           C
ATOM     25  CA  ASP    25     -11.616   1.281  13.937  1.00 25.00           C
ATOM     26  CA  VAL    26      -9.816   0.671  17.226  1.00 25.00           C
ATOM     27  CA  ARG    27      -6.289   1.810  18.190  1.00 25.00           C
ATOM     28  CA  ASP    28      -4.911  -1.664  17.352  1.00 25.00           C
ATOM     29  CA  ASP    29      -6.683  -1.575  13.958  1.00 25.00           C
ATOM     30  CA  LYS    30      -5.210   1.890  13.253  1.00 25.00           C
ATOM     31  CA  LYS    31      -1.717   0.619  14.170  1.00 25.00           C
ATOM     32  CA  ALA    32      -2.168  -2.382  11.836  1.00 25.00           C
ATOM     33  CA  ILE    33      -3.271  -0.047   9.007  1.00 25.00           C
ATOM     34  CA  GLU    34      -0.203   2.165   9.603  1.00 25.00           C
ATOM     35  CA  PHE    35       2.070  -0.917   9.503  1.00 25.00           C
ATOM     36  CA  ALA    36       0.446  -2.037   6.221  1.00 25.00           C
ATOM     37  CA  LYS    37       0.972   1.455   4.740  1.00 25.00           C
ATOM     38  CA  GLN    38       4.647   1.384   5.815  1.00 25.00           C
ATOM     39  CA  TRP    39       5.078  -2.062   4.201  1.00 25.00           C
ATOM     40  CA  LEU    40       3.488  -0.772   0.965  1.00 25.00           C
ATOM     41  CA  SER    41       5.842   2.248   0.981  1.00 25.00           C
ATOM     42  CA  SER    42       8.849  -0.068   1.491  1.00 25.00           C
ATOM     43  CA  ILE    43      10.196   1.350  -1.815  1.00 25.00           C
ATOM     44  CA  GLY    44       8.218   2.732  -4.774  1.00 25.00           C
ATOM     45  CA  GLU    45       6.892   3.151  -8.310  1.00 25.00           C
ATOM     46  CA  GLU    46       3.855   4.461 -10.095  1.00 25.00           C
ATOM     47  CA  GLY    47       0.672   6.261  -9.191  1.00 25.00           C
ATOM     48  CA  ALA    48      -2.524   4.607  -7.955  1.00 25.00           C
ATOM     49  CA  THR    49      -6.167   3.615  -8.424  1.00 25.00           C
ATOM     50  CA  VAL    50      -7.781   2.515  -5.215  1.00 25.00           C
ATOM     51  CA  THR    51     -11.301   2.857  -3.706  1.00 25.00           C
ATOM     52  CA  SER    52     -13.903   1.151  -1.472  1.00 25.00           C
ATOM     53  CA  GLU    53     -17.721   0.819  -1.127  1.00 25.00           C
ATOM     54  CA  GLU    54     -18.729  -0.996   2.026  1.00 25.00           C
ATOM     55  CA  CYS    55     -15.338  -2.811   2.328  1.00 25.00           C
ATOM     56  CA  ARG    56     -16.432  -3.145   5.990  1.00 25.00           C
ATOM     57  CA  PHE    57     -13.730  -1.326   7.845  1.00 25.00           C
ATOM     58  CA  CYS    58     -11.389  -0.204   5.006  1.00 25.00           C
ATOM     59  CA  HIS    59     -12.054   3.349   6.185  1.00 25.00           C
ATOM     60  CA  SER    60     -15.501   4.958   6.288  1.00 25.00           C
ATOM     61  CA  GLN    61     -15.899   4.755   2.569  1.00 25.00           C
ATOM     62  CA  LYS    62     -12.577   5.521   0.922  1.00 25.00           C
ATOM     63  CA  ALA    63      -9.652   3.168   1.686  1.00 25.00           C
ATOM     64  CA  PRO    64      -8.379   6.121   3.751  1.00 25.00           C
ATOM     65  CA  ASP    65      -6.505   9.378   4.493  1.00 25.00           C
ATOM     66  CA  GLU    66      -3.579   7.388   5.958  1.00 25.00           C
ATOM     67  CA  VAL    67      -3.502   5.161   2.844  1.00 25.00           C
ATOM     68  CA  ILE    68      -3.486   8.261   0.597  1.00 25.00           C
ATOM     69  CA  GLU    69      -0.601   9.749   2.628  1.00 25.00           C
ATOM     70  CA  ALA    70       1.349   6.469   2.306  1.00 25.00           C
ATOM     71  CA  ILE    71       0.755   6.457  -1.478  1.00 25.00           C
ATOM     72  CA  LYS    72       1.979  10.079  -1.705  1.00 25.00           C
ATOM     73  CA  GLN    73       5.117   9.171   0.294  1.00 25.00           C
ATOM     74  CA  ASN    74       6.736   7.023  -2.477  1.00 25.00           C
ATOM     75  CA  GLY    75       4.262   6.446  -5.319  1.00 25.00           C
ATOM     76  CA  TYR    76       3.155   2.973  -4.222  1.00 25.00           C
ATOM     77  CA  PHE    77      -0.416   1.766  -3.904  1.00 25.00           C
ATOM     78  CA  ILE    78      -3.364   3.913  -2.774  1.00 25.00           C
ATOM     79  CA  TYR    79      -4.384   7.298  -4.140  1.00 25.00           C
ATOM     80  CA  LYS    80      -7.893   7.206  -2.630  1.00 25.00           C
ATOM     81  CA  MET    81     -11.515   8.069  -3.618  1.00 25.00           C
ATOM     82  CA  GLU    82     -13.940  10.690  -2.208  1.00 25.00           C
ATOM     83  CA  GLY    83     -12.343  14.145  -1.968  1.00 25.00           C
ATOM     84  CA  CYS    84     -12.021  15.486   1.620  1.00 25.00           C
ATOM     85  CA  ASN    85     -12.459  19.261   1.352  1.00 25.00           C
TER
END
