
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS168_4-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          2.387
LGA    A      20      Q      18          2.034
LGA    Y      21      P      19          1.687
LGA    T      22      A      20          1.741
LGA    T      23      Y      21          2.418
LGA    V      24      T      22          2.014
LGA    M      25      T      23          1.681
LGA    R      26      V      24          2.431
LGA    E      27      M      25          3.416
LGA    V      28      R      26          3.439
LGA    L      29      E      27          3.341
LGA    A      30      V      28          4.194
LGA    T      31      L      29           #
LGA    Y      32      A      30          2.252
LGA    -       -      T      31           -
LGA    -       -      Y      32           -
LGA    G      33      G      33          2.109
LGA    K      34      K      34          3.758
LGA    P      35      P      35          5.003
LGA    F      36      F      36           #
LGA    S      37      -       -           -
LGA    P      38      -       -           -
LGA    A      39      -       -           -
LGA    Q      40      -       -           -
LGA    A      41      S      37          3.128
LGA    Q      42      P      38          5.374
LGA    K      43      A      39          4.118
LGA    T      44      Q      40          0.698
LGA    F      45      A      41          2.943
LGA    P      46      Q      42          1.697
LGA    M      47      K      43          0.784
LGA    A      48      T      44           #
LGA    A      49      F      45          3.184
LGA    E      50      P      46          2.978
LGA    Q      51      M      47          2.327
LGA    A      52      A      48          4.769
LGA    M      53      A      49          3.429
LGA    T      54      E      50          4.936
LGA    E      55      Q      51          0.934
LGA    L      56      A      52          4.052
LGA    G      57      M      53           #
LGA    I      58      T      54           #
LGA    A      59      E      55           -
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    -       -      I      58           -
LGA    -       -      A      59           -
LGA    A      60      A      60          3.215
LGA    S      61      S      61          3.262
LGA    E      62      E      62          0.956
LGA    F      63      F      63          1.135
LGA    D      64      D      64          0.901
LGA    H      65      H      65          0.584
LGA    F      66      F      66          0.689
LGA    Q      67      Q      67          0.620
LGA    A      68      A      68          0.791
LGA    Q      69      Q      69          0.963
LGA    Y      70      Y      70          1.099
LGA    E      71      E      71          1.257
LGA    D      72      D      72          1.357
LGA    V      73      V      73          1.971
LGA    M      74      M      74          2.466
LGA    A      75      A      75          2.260
LGA    S      76      S      76          2.521
LGA    H      77      H      77          2.584
LGA    Y      78      Y      78          3.816
LGA    D      79      -       -           -
LGA    Q      80      -       -           -
LGA    I      81      D      79          3.065
LGA    -       -      Q      80           -
LGA    -       -      I      81           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     51    2.76    45.10     51.215     1.785

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.150700 * X  +  -0.762377 * Y  +   0.629341 * Z  +  30.558578
  Y_new =  -0.987565 * X  +   0.144935 * Y  +  -0.060907 * Z  +  20.233971
  Z_new =  -0.044780 * X  +  -0.630694 * Y  +  -0.774739 * Z  +   1.396445 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.458329    0.683264  [ DEG:  -140.8519     39.1481 ]
  Theta =   0.044795    3.096798  [ DEG:     2.5665    177.4335 ]
  Phi   =  -1.722226    1.419367  [ DEG:   -98.6763     81.3237 ]
 
# 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_4-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS168_4-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   51   2.76   45.10  51.215
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS168_4-D2
PFRMAT TS
TARGET T0324
MODEL 4
PARENT N/A
ATOM     17  CA  SER    17      30.256  17.535   7.115  1.00 25.00           C
ATOM     18  CA  GLN    18      29.157  19.536  10.208  1.00 25.00           C
ATOM     19  CA  PRO    19      26.572  17.661  12.321  1.00 25.00           C
ATOM     20  CA  ALA    20      23.730  19.342  10.381  1.00 25.00           C
ATOM     21  CA  TYR    21      25.377  18.357   7.066  1.00 25.00           C
ATOM     22  CA  THR    22      25.723  14.742   8.284  1.00 25.00           C
ATOM     23  CA  THR    23      22.030  14.705   9.302  1.00 25.00           C
ATOM     24  CA  VAL    24      21.043  16.056   5.857  1.00 25.00           C
ATOM     25  CA  MET    25      23.154  13.347   4.162  1.00 25.00           C
ATOM     26  CA  ARG    26      21.483  10.661   6.322  1.00 25.00           C
ATOM     27  CA  GLU    27      18.028  12.027   5.393  1.00 25.00           C
ATOM     28  CA  VAL    28      18.974  11.962   1.682  1.00 25.00           C
ATOM     29  CA  LEU    29      20.176   8.343   2.025  1.00 25.00           C
ATOM     30  CA  ALA    30      16.888   7.388   3.743  1.00 25.00           C
ATOM     31  CA  THR    31      14.904   9.063   0.928  1.00 25.00           C
ATOM     32  CA  TYR    32      12.832  10.603   3.762  1.00 25.00           C
ATOM     33  CA  GLY    33      10.112  10.565   1.133  1.00 25.00           C
ATOM     34  CA  LYS    34      11.830  13.467  -0.640  1.00 25.00           C
ATOM     35  CA  PRO    35      10.900  15.940  -3.410  1.00 25.00           C
ATOM     36  CA  PHE    36       9.575  18.156  -0.622  1.00 25.00           C
ATOM     37  CA  SER    37       8.896  21.570  -2.244  1.00 25.00           C
ATOM     38  CA  PRO    38      11.208  24.605  -2.405  1.00 25.00           C
ATOM     39  CA  ALA    39       9.554  26.522   0.467  1.00 25.00           C
ATOM     40  CA  GLN    40       9.364  23.306   2.537  1.00 25.00           C
ATOM     41  CA  ALA    41      13.068  22.616   1.851  1.00 25.00           C
ATOM     42  CA  GLN    42      13.957  26.183   2.925  1.00 25.00           C
ATOM     43  CA  LYS    43      11.929  25.744   6.145  1.00 25.00           C
ATOM     44  CA  THR    44      13.730  22.441   6.858  1.00 25.00           C
ATOM     45  CA  PHE    45      17.117  24.138   6.298  1.00 25.00           C
ATOM     46  CA  PRO    46      18.146  23.967   9.953  1.00 25.00           C
ATOM     47  CA  MET    47      15.000  25.706  11.044  1.00 25.00           C
ATOM     48  CA  ALA    48      16.295  26.486  14.494  1.00 25.00           C
ATOM     49  CA  ALA    49      18.730  23.843  15.744  1.00 25.00           C
ATOM     50  CA  GLU    50      17.595  23.663  19.397  1.00 25.00           C
ATOM     51  CA  GLN    51      13.956  24.167  18.315  1.00 25.00           C
ATOM     52  CA  ALA    52      14.317  21.381  15.713  1.00 25.00           C
ATOM     53  CA  MET    53      15.793  19.054  18.373  1.00 25.00           C
ATOM     54  CA  THR    54      12.881  19.859  20.727  1.00 25.00           C
ATOM     55  CA  GLU    55      10.379  19.115  17.925  1.00 25.00           C
ATOM     56  CA  LEU    56      12.121  15.779  17.220  1.00 25.00           C
ATOM     57  CA  GLY    57      11.005  15.018  20.777  1.00 25.00           C
ATOM     58  CA  ILE    58       7.511  14.384  19.555  1.00 25.00           C
ATOM     59  CA  ALA    59       6.341  10.848  20.513  1.00 25.00           C
ATOM     60  CA  ALA    60       4.774   8.376  18.041  1.00 25.00           C
ATOM     61  CA  SER    61       6.360   4.978  17.261  1.00 25.00           C
ATOM     62  CA  GLU    62       7.567   6.291  13.872  1.00 25.00           C
ATOM     63  CA  PHE    63       9.071   9.374  15.575  1.00 25.00           C
ATOM     64  CA  ASP    64      10.851   7.130  18.119  1.00 25.00           C
ATOM     65  CA  HIS    65      12.237   4.968  15.279  1.00 25.00           C
ATOM     66  CA  PHE    66      13.485   8.103  13.467  1.00 25.00           C
ATOM     67  CA  GLN    67      15.175   9.317  16.682  1.00 25.00           C
ATOM     68  CA  ALA    68      16.849   5.901  17.123  1.00 25.00           C
ATOM     69  CA  GLN    69      18.086   6.013  13.501  1.00 25.00           C
ATOM     70  CA  TYR    70      19.492   9.530  14.064  1.00 25.00           C
ATOM     71  CA  GLU    71      21.275   8.337  17.237  1.00 25.00           C
ATOM     72  CA  ASP    72      22.759   5.374  15.318  1.00 25.00           C
ATOM     73  CA  VAL    73      23.971   7.738  12.558  1.00 25.00           C
ATOM     74  CA  MET    74      25.574  10.020  15.181  1.00 25.00           C
ATOM     75  CA  ALA    75      27.315   7.005  16.777  1.00 25.00           C
ATOM     76  CA  SER    76      28.616   5.910  13.345  1.00 25.00           C
ATOM     77  CA  HIS    77      29.932   9.446  12.688  1.00 25.00           C
ATOM     78  CA  TYR    78      31.683   9.453  16.093  1.00 25.00           C
ATOM     79  CA  ASP    79      33.268   6.055  15.314  1.00 25.00           C
ATOM     80  CA  GLN    80      35.404   7.412  12.416  1.00 25.00           C
ATOM     81  CA  ILE    81      36.192  11.092  12.723  1.00 25.00           C
TER
END
