
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0324TS168_3-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS168_3-D2.T0324_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      -       -           -
LGA    Q      18      -       -           -
LGA    P      19      S      17          2.858
LGA    A      20      Q      18          2.335
LGA    Y      21      P      19          1.296
LGA    T      22      A      20          1.396
LGA    T      23      Y      21          2.049
LGA    V      24      T      22          0.960
LGA    M      25      T      23          1.030
LGA    R      26      V      24          2.123
LGA    E      27      M      25          2.758
LGA    V      28      R      26          2.889
LGA    L      29      E      27          3.379
LGA    A      30      V      28          4.279
LGA    -       -      L      29           -
LGA    T      31      A      30          2.753
LGA    Y      32      T      31          4.059
LGA    G      33      Y      32           #
LGA    K      34      G      33           #
LGA    P      35      K      34           #
LGA    F      36      -       -           -
LGA    S      37      -       -           -
LGA    P      38      -       -           -
LGA    A      39      -       -           -
LGA    Q      40      -       -           -
LGA    A      41      P      35          4.125
LGA    Q      42      -       -           -
LGA    K      43      F      36           #
LGA    T      44      S      37          4.586
LGA    F      45      P      38          4.121
LGA    P      46      A      39          2.673
LGA    M      47      Q      40          2.506
LGA    A      48      A      41          3.003
LGA    -       -      Q      42           -
LGA    -       -      K      43           -
LGA    A      49      T      44          2.088
LGA    -       -      F      45           -
LGA    -       -      P      46           -
LGA    E      50      M      47          4.316
LGA    Q      51      A      48           -
LGA    -       -      A      49           -
LGA    -       -      E      50           -
LGA    A      52      Q      51          5.104
LGA    M      53      A      52          3.324
LGA    T      54      M      53           #
LGA    E      55      T      54          2.277
LGA    L      56      E      55           -
LGA    G      57      L      56           -
LGA    -       -      G      57           -
LGA    -       -      I      58           -
LGA    -       -      A      59           -
LGA    I      58      A      60          3.954
LGA    A      59      -       -           -
LGA    A      60      -       -           -
LGA    S      61      S      61          4.176
LGA    E      62      E      62          1.124
LGA    F      63      F      63          0.674
LGA    D      64      D      64          0.478
LGA    H      65      H      65          0.555
LGA    F      66      F      66          0.417
LGA    Q      67      Q      67          0.519
LGA    A      68      A      68          0.385
LGA    Q      69      Q      69          0.985
LGA    Y      70      Y      70          1.296
LGA    E      71      E      71          1.192
LGA    D      72      D      72          1.214
LGA    V      73      V      73          2.274
LGA    M      74      M      74          2.578
LGA    A      75      A      75          1.812
LGA    S      76      S      76          1.758
LGA    H      77      H      77          2.065
LGA    Y      78      Y      78          3.123
LGA    D      79      -       -           -
LGA    Q      80      -       -           -
LGA    I      81      D      79          1.750
LGA    -       -      Q      80           -
LGA    -       -      I      81           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     45    2.65    42.22     46.971     1.634

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.781059 * X  +  -0.595215 * Y  +  -0.188852 * Z  +  28.910383
  Y_new =  -0.588732 * X  +   0.802717 * Y  +  -0.095075 * Z  +  20.665340
  Z_new =   0.208185 * X  +   0.036925 * Y  +  -0.977392 * Z  +   1.255814 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.103832   -0.037761  [ DEG:   177.8365     -2.1635 ]
  Theta =  -0.209719   -2.931874  [ DEG:   -12.0160   -167.9840 ]
  Phi   =  -2.495689    0.645904  [ DEG:  -142.9924     37.0076 ]
 
# 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: T0324TS168_3-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS168_3-D2.T0324_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   65   65   5.0   45   2.65   42.22  46.971
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS168_3-D2
PFRMAT TS
TARGET T0324
MODEL 3
PARENT N/A
ATOM     17  CA  SER    17      31.028  20.409   7.922  1.00 25.00           C
ATOM     18  CA  GLN    18      29.959  19.072  11.363  1.00 25.00           C
ATOM     19  CA  PRO    19      27.397  16.925  13.231  1.00 25.00           C
ATOM     20  CA  ALA    20      24.538  18.980  11.721  1.00 25.00           C
ATOM     21  CA  TYR    21      26.035  18.536   8.224  1.00 25.00           C
ATOM     22  CA  THR    22      26.314  14.761   8.795  1.00 25.00           C
ATOM     23  CA  THR    23      22.662  14.638   9.940  1.00 25.00           C
ATOM     24  CA  VAL    24      21.592  16.582   6.818  1.00 25.00           C
ATOM     25  CA  MET    25      23.557  14.152   4.604  1.00 25.00           C
ATOM     26  CA  ARG    26      21.885  11.177   6.342  1.00 25.00           C
ATOM     27  CA  GLU    27      18.443  12.763   5.799  1.00 25.00           C
ATOM     28  CA  VAL    28      19.251  13.312   2.096  1.00 25.00           C
ATOM     29  CA  LEU    29      20.355   9.658   1.771  1.00 25.00           C
ATOM     30  CA  ALA    30      17.103   8.503   3.433  1.00 25.00           C
ATOM     31  CA  THR    31      15.070  10.681   1.028  1.00 25.00           C
ATOM     32  CA  TYR    32      11.915   9.002   2.331  1.00 25.00           C
ATOM     33  CA  GLY    33      11.763   6.155  -0.199  1.00 25.00           C
ATOM     34  CA  LYS    34      13.461   8.085  -2.963  1.00 25.00           C
ATOM     35  CA  PRO    35      11.055  10.120  -5.019  1.00 25.00           C
ATOM     36  CA  PHE    36      10.656  13.172  -2.808  1.00 25.00           C
ATOM     37  CA  SER    37       9.559  14.880  -5.986  1.00 25.00           C
ATOM     38  CA  PRO    38       8.509  18.528  -5.382  1.00 25.00           C
ATOM     39  CA  ALA    39       6.432  20.224  -2.647  1.00 25.00           C
ATOM     40  CA  GLN    40       7.375  17.453  -0.178  1.00 25.00           C
ATOM     41  CA  ALA    41      11.074  17.878  -1.076  1.00 25.00           C
ATOM     42  CA  GLN    42      10.795  21.659  -0.540  1.00 25.00           C
ATOM     43  CA  LYS    43       9.142  21.080   2.865  1.00 25.00           C
ATOM     44  CA  THR    44      11.944  18.659   3.840  1.00 25.00           C
ATOM     45  CA  PHE    45      14.573  21.238   2.790  1.00 25.00           C
ATOM     46  CA  PRO    46      13.110  24.339   4.513  1.00 25.00           C
ATOM     47  CA  MET    47      12.404  23.019   8.010  1.00 25.00           C
ATOM     48  CA  ALA    48      15.523  21.624   9.745  1.00 25.00           C
ATOM     49  CA  ALA    49      15.342  23.974  12.739  1.00 25.00           C
ATOM     50  CA  GLU    50      12.678  25.129  15.236  1.00 25.00           C
ATOM     51  CA  GLN    51      10.001  23.166  13.326  1.00 25.00           C
ATOM     52  CA  ALA    52      12.223  20.048  13.368  1.00 25.00           C
ATOM     53  CA  MET    53      12.756  20.448  17.139  1.00 25.00           C
ATOM     54  CA  THR    54       8.977  20.783  17.663  1.00 25.00           C
ATOM     55  CA  GLU    55       8.385  17.621  15.585  1.00 25.00           C
ATOM     56  CA  LEU    56      10.998  15.739  17.659  1.00 25.00           C
ATOM     57  CA  GLY    57       8.412  14.522  20.127  1.00 25.00           C
ATOM     58  CA  ILE    58       5.304  13.344  18.177  1.00 25.00           C
ATOM     59  CA  ALA    59       4.450  10.350  20.352  1.00 25.00           C
ATOM     60  CA  ALA    60       4.830   6.972  18.635  1.00 25.00           C
ATOM     61  CA  SER    61       6.597   3.830  17.342  1.00 25.00           C
ATOM     62  CA  GLU    62       7.554   5.665  14.120  1.00 25.00           C
ATOM     63  CA  PHE    63       8.932   8.594  16.168  1.00 25.00           C
ATOM     64  CA  ASP    64      10.972   6.165  18.314  1.00 25.00           C
ATOM     65  CA  HIS    65      12.362   4.504  15.156  1.00 25.00           C
ATOM     66  CA  PHE    66      13.315   7.933  13.742  1.00 25.00           C
ATOM     67  CA  GLN    67      15.070   8.827  17.026  1.00 25.00           C
ATOM     68  CA  ALA    68      16.984   5.511  16.934  1.00 25.00           C
ATOM     69  CA  GLN    69      18.040   6.193  13.317  1.00 25.00           C
ATOM     70  CA  TYR    70      19.236   9.695  14.300  1.00 25.00           C
ATOM     71  CA  GLU    71      21.240   8.222  17.211  1.00 25.00           C
ATOM     72  CA  ASP    72      22.825   5.654  14.853  1.00 25.00           C
ATOM     73  CA  VAL    73      23.747   8.443  12.396  1.00 25.00           C
ATOM     74  CA  MET    74      25.319  10.466  15.243  1.00 25.00           C
ATOM     75  CA  ALA    75      27.327   7.398  16.346  1.00 25.00           C
ATOM     76  CA  SER    76      28.534   6.864  12.751  1.00 25.00           C
ATOM     77  CA  HIS    77      29.582  10.542  12.531  1.00 25.00           C
ATOM     78  CA  TYR    78      31.487  10.221  15.839  1.00 25.00           C
ATOM     79  CA  ASP    79      33.254   7.080  14.545  1.00 25.00           C
ATOM     80  CA  GLN    80      36.689   8.318  13.311  1.00 25.00           C
ATOM     81  CA  ILE    81      34.883  11.081  11.406  1.00 25.00           C
TER
END
