
#######################################################
#                                                     #
#                        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   67 (   67),  selected   67 , name T0379TS168_2-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS168_2-D2.T0379_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          1.465
LGA    R      18      R      18          1.537
LGA    E      19      E      19          2.739
LGA    E      20      -       -           -
LGA    S      21      E      20          2.395
LGA    I      22      S      21          2.610
LGA    R      23      I      22          2.632
LGA    R      24      R      23          2.391
LGA    F      25      R      24          1.230
LGA    K      26      F      25          2.965
LGA    A      27      K      26          4.425
LGA    I      28      A      27          1.355
LGA    G      29      I      28           #
LGA    V      30      G      29          4.492
LGA    A      31      V      30           #
LGA    D      32      A      31          1.735
LGA    -       -      D      32           -
LGA    I      33      I      33          2.651
LGA    E      34      E      34          2.691
LGA    E      35      E      35          4.549
LGA    M      36      M      36          2.832
LGA    L      37      L      37          2.318
LGA    D      38      D      38          4.624
LGA    P      39      P      39          5.175
LGA    Y      40      K      43          3.762
LGA    L      41      G      44          3.174
LGA    -       -      L      45           -
LGA    Q      42      F      46          2.792
LGA    K      43      L      47          2.954
LGA    G      44      D      48          2.649
LGA    L      45      L      49          2.157
LGA    F      46      E      50          4.626
LGA    L      47      S      51           #
LGA    D      48      -       -           -
LGA    L      49      G      52          1.036
LGA    E      50      R      53          3.956
LGA    S      51      K      54           -
LGA    G      52      -       -           -
LGA    R      53      -       -           -
LGA    K      54      -       -           -
LGA    S      55      S      55          4.112
LGA    E      56      E      56          1.091
LGA    E      57      E      57          0.814
LGA    E      58      E      58          1.759
LGA    F      59      F      59          1.957
LGA    R      60      R      60          1.193
LGA    T      61      T      61          2.349
LGA    E      62      E      62          3.204
LGA    L      63      L      63          2.041
LGA    S      64      S      64          2.224
LGA    R      65      R      65          3.742
LGA    Y      66      Y      66          3.354
LGA    I      67      I      67          2.205
LGA    G      68      G      68          3.222
LGA    K      69      K      69          2.952
LGA    E      70      -       -           -
LGA    L      71      E      70          3.487
LGA    T      72      -       -           -
LGA    Y      73      L      71          2.005
LGA    Q      74      T      72          3.146
LGA    Q      75      Y      73           -
LGA    -       -      Q      74           -
LGA    V      76      Q      75          2.732
LGA    Y      77      V      76          2.083
LGA    D      78      Y      77          4.375
LGA    A      79      D      78          1.931
LGA    L      80      A      79          2.600
LGA    L      81      L      80           #
LGA    G      82      L      81          3.573
LGA    F      83      G      82          2.609
LGA    -       -      F      83           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   67   64    5.0     54    2.94    50.00     53.217     1.775

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.810233 * X  +   0.322762 * Y  +  -0.489231 * Z  +  62.754963
  Y_new =   0.327104 * X  +  -0.941638 * Y  +  -0.079502 * Z  +   9.028146
  Z_new =  -0.486339 * X  +  -0.095614 * Y  +  -0.868523 * Z  +   8.382463 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.031946    0.109647  [ DEG:  -173.7177      6.2823 ]
  Theta =   0.507895    2.633698  [ DEG:    29.1002    150.8998 ]
  Phi   =   0.383706   -2.757887  [ DEG:    21.9847   -158.0153 ]
 
# 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: T0379TS168_2-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS168_2-D2.T0379_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   67   64   5.0   54   2.94   50.00  53.217
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS168_2-D2
PFRMAT TS
TARGET T0379
MODEL 2
PARENT N/A
ATOM     17  CA  ASN    17      67.821   8.383  13.681  1.00 25.00           C
ATOM     18  CA  ARG    18      65.319   5.683  14.638  1.00 25.00           C
ATOM     19  CA  GLU    19      66.559   2.409  16.189  1.00 25.00           C
ATOM     20  CA  GLU    20      69.916   4.051  17.027  1.00 25.00           C
ATOM     21  CA  SER    21      68.096   7.006  18.647  1.00 25.00           C
ATOM     22  CA  ILE    22      65.958   4.589  20.709  1.00 25.00           C
ATOM     23  CA  ARG    23      69.107   2.724  21.836  1.00 25.00           C
ATOM     24  CA  ARG    24      70.738   6.039  22.845  1.00 25.00           C
ATOM     25  CA  PHE    25      67.609   7.003  24.830  1.00 25.00           C
ATOM     26  CA  LYS    26      67.652   3.604  26.595  1.00 25.00           C
ATOM     27  CA  ALA    27      71.353   4.071  27.459  1.00 25.00           C
ATOM     28  CA  ILE    28      69.818   4.387  30.887  1.00 25.00           C
ATOM     29  CA  GLY    29      70.544   0.676  31.079  1.00 25.00           C
ATOM     30  CA  VAL    30      67.034  -0.662  31.446  1.00 25.00           C
ATOM     31  CA  ALA    31      65.823  -1.394  27.877  1.00 25.00           C
ATOM     32  CA  ASP    32      62.613   0.356  29.017  1.00 25.00           C
ATOM     33  CA  ILE    33      62.604   2.472  25.825  1.00 25.00           C
ATOM     34  CA  GLU    34      63.064  -0.683  23.703  1.00 25.00           C
ATOM     35  CA  GLU    35      60.161  -2.373  25.541  1.00 25.00           C
ATOM     36  CA  MET    36      57.956   0.699  24.935  1.00 25.00           C
ATOM     37  CA  LEU    37      58.872   0.652  21.217  1.00 25.00           C
ATOM     38  CA  ASP    38      55.822  -1.685  20.854  1.00 25.00           C
ATOM     39  CA  PRO    39      53.255   0.225  18.726  1.00 25.00           C
ATOM     40  CA  TYR    40      51.154   0.444  21.920  1.00 25.00           C
ATOM     41  CA  LEU    41      52.968   3.666  22.922  1.00 25.00           C
ATOM     42  CA  GLN    42      52.320   5.139  19.447  1.00 25.00           C
ATOM     43  CA  LYS    43      48.612   4.218  19.719  1.00 25.00           C
ATOM     44  CA  GLY    44      48.429   5.876  23.167  1.00 25.00           C
ATOM     45  CA  LEU    45      50.081   9.032  21.764  1.00 25.00           C
ATOM     46  CA  PHE    46      47.573   9.090  18.871  1.00 25.00           C
ATOM     47  CA  LEU    47      44.674   8.725  21.346  1.00 25.00           C
ATOM     48  CA  ASP    48      46.071  11.606  23.446  1.00 25.00           C
ATOM     49  CA  LEU    49      46.367  13.782  20.309  1.00 25.00           C
ATOM     50  CA  GLU    50      42.748  12.957  19.365  1.00 25.00           C
ATOM     51  CA  SER    51      40.037  14.511  21.584  1.00 25.00           C
ATOM     52  CA  GLY    52      42.815  16.952  22.375  1.00 25.00           C
ATOM     53  CA  ARG    53      43.432  17.432  26.105  1.00 25.00           C
ATOM     54  CA  LYS    54      47.237  17.839  26.183  1.00 25.00           C
ATOM     55  CA  SER    55      50.160  18.725  23.923  1.00 25.00           C
ATOM     56  CA  GLU    56      52.524  16.360  25.812  1.00 25.00           C
ATOM     57  CA  GLU    57      51.375  15.591  29.385  1.00 25.00           C
ATOM     58  CA  GLU    58      49.210  12.707  28.093  1.00 25.00           C
ATOM     59  CA  PHE    59      52.185  11.327  26.115  1.00 25.00           C
ATOM     60  CA  ARG    60      54.391  11.539  29.239  1.00 25.00           C
ATOM     61  CA  THR    61      51.724   9.695  31.277  1.00 25.00           C
ATOM     62  CA  GLU    62      51.518   6.972  28.591  1.00 25.00           C
ATOM     63  CA  LEU    63      55.331   6.611  28.631  1.00 25.00           C
ATOM     64  CA  SER    64      55.286   6.307  32.449  1.00 25.00           C
ATOM     65  CA  ARG    65      52.564   3.623  32.229  1.00 25.00           C
ATOM     66  CA  TYR    66      54.629   1.707  29.633  1.00 25.00           C
ATOM     67  CA  ILE    67      57.708   1.906  31.901  1.00 25.00           C
ATOM     68  CA  GLY    68      56.630   0.861  35.411  1.00 25.00           C
ATOM     69  CA  LYS    69      57.901   4.026  37.090  1.00 25.00           C
ATOM     70  CA  GLU    70      61.029   4.447  39.128  1.00 25.00           C
ATOM     71  CA  LEU    71      62.375   7.673  37.726  1.00 25.00           C
ATOM     72  CA  THR    72      65.165   9.900  36.406  1.00 25.00           C
ATOM     73  CA  TYR    73      62.571  11.038  33.866  1.00 25.00           C
ATOM     74  CA  GLN    74      63.858  14.583  33.202  1.00 25.00           C
ATOM     75  CA  GLN    75      67.063  13.159  31.663  1.00 25.00           C
ATOM     76  CA  VAL    76      64.990  10.836  29.433  1.00 25.00           C
ATOM     77  CA  TYR    77      62.831  13.796  28.316  1.00 25.00           C
ATOM     78  CA  ASP    78      65.980  15.819  27.506  1.00 25.00           C
ATOM     79  CA  ALA    79      67.372  12.885  25.474  1.00 25.00           C
ATOM     80  CA  LEU    80      64.066  12.610  23.561  1.00 25.00           C
ATOM     81  CA  LEU    81      64.149  16.368  22.827  1.00 25.00           C
ATOM     82  CA  GLY    82      67.753  16.067  21.566  1.00 25.00           C
ATOM     83  CA  PHE    83      66.744  13.142  19.308  1.00 25.00           C
TER
END
