
#######################################################
#                                                     #
#                        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 T0353TS599_4
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS599_4.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      I       3           -
LGA    M       1      H       4          4.644
LGA    Q       2      V       5          4.209
LGA    I       3      Y       6          3.578
LGA    H       4      D       7          3.651
LGA    V       5      T       8           #
LGA    Y       6      -       -           -
LGA    D       7      -       -           -
LGA    T       8      -       -           -
LGA    Y       9      Y       9           #
LGA    V      10      V      10          4.489
LGA    K      11      K      11          3.601
LGA    A      12      A      12          2.027
LGA    K      13      K      13          1.809
LGA    D      14      D      14          1.576
LGA    G      15      G      15          3.456
LGA    H      16      H      16          1.949
LGA    V      17      V      17          2.452
LGA    M      18      M      18          0.266
LGA    H      19      H      19          2.112
LGA    F      20      F      20          1.980
LGA    D      21      D      21          0.643
LGA    V      22      V      22          4.451
LGA    F      23      F      23          3.461
LGA    T      24      T      24           #
LGA    D      25      -       -           -
LGA    V      26      -       -           -
LGA    R      27      -       -           -
LGA    D      28      D      25          2.475
LGA    D      29      V      26          2.038
LGA    K      30      R      27          4.448
LGA    K      31      D      28           -
LGA    A      32      D      29           -
LGA    -       -      K      30           -
LGA    I      33      K      31          4.756
LGA    E      34      -       -           -
LGA    F      35      -       -           -
LGA    A      36      -       -           -
LGA    K      37      A      32           #
LGA    Q      38      I      33           -
LGA    W      39      -       -           -
LGA    L      40      -       -           -
LGA    S      41      -       -           -
LGA    S      42      -       -           -
LGA    I      43      -       -           -
LGA    G      44      -       -           -
LGA    E      45      -       -           -
LGA    E      46      -       -           -
LGA    G      47      E      34          5.521
LGA    A      48      F      35           -
LGA    T      49      A      36           -
LGA    V      50      K      37           #
LGA    T      51      -       -           -
LGA    S      52      -       -           -
LGA    E      53      Q      38           #
LGA    E      54      W      39          4.744
LGA    C      55      L      40          3.579
LGA    R      56      S      41          1.783
LGA    F      57      S      42          3.801
LGA    C      58      I      43          2.717
LGA    -       -      G      44           -
LGA    H      59      E      45          2.313
LGA    S      60      E      46          2.176
LGA    Q      61      G      47          2.204
LGA    K      62      A      48          1.821
LGA    A      63      T      49          2.672
LGA    P      64      V      50          2.393
LGA    D      65      T      51          3.421
LGA    E      66      S      52           -
LGA    V      67      E      53           #
LGA    I      68      E      54          1.403
LGA    E      69      C      55           #
LGA    A      70      -       -           -
LGA    I      71      -       -           -
LGA    K      72      -       -           -
LGA    Q      73      -       -           -
LGA    N      74      -       -           -
LGA    G      75      -       -           -
LGA    Y      76      -       -           -
LGA    F      77      R      56          2.454
LGA    I      78      -       -           -
LGA    Y      79      F      57          5.393
LGA    K      80      C      58           -
LGA    -       -      H      59           -
LGA    -       -      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    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    M      81      G      75           #
LGA    E      82      Y      76          1.189
LGA    G      83      F      77          3.917
LGA    C      84      I      78           #
LGA    N      85      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -
LGA    -       -      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   85    5.0     40    3.21    37.50     27.638     1.210

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.852159 * X  +   0.377886 * Y  +  -0.361976 * Z  +  -4.967870
  Y_new =   0.325653 * X  +   0.924435 * Y  +   0.198420 * Z  +   0.479849
  Z_new =   0.409603 * X  +   0.051207 * Y  +  -0.910825 * Z  +   0.599127 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.085431   -0.056162  [ DEG:   176.7822     -3.2178 ]
  Theta =  -0.422019   -2.719573  [ DEG:   -24.1799   -155.8201 ]
  Phi   =   2.776568   -0.365024  [ DEG:   159.0856    -20.9144 ]
 
# 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: T0353TS599_4                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_4.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   40   3.21   37.50  27.638
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_4
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       6.918   8.643  -4.634  1.00  0.00              
ATOM      2  CA  GLN     2       7.322   7.922  -0.773  1.00  0.00              
ATOM      3  CA  ILE     3       5.184   5.830   1.214  1.00  0.00              
ATOM      4  CA  HIS     4       4.380   6.891   5.137  1.00  0.00              
ATOM      5  CA  VAL     5       2.526   4.523   7.227  1.00  0.00              
ATOM      6  CA  TYR     6       0.376   5.504  10.127  1.00  0.00              
ATOM      7  CA  ASP     7      -1.015   2.709  12.362  1.00  0.00              
ATOM      8  CA  THR     8      -2.215   4.831  15.243  1.00  0.00              
ATOM      9  CA  TYR     9      -3.824   7.472  12.994  1.00  0.00              
ATOM     10  CA  VAL    10      -6.001   4.646  11.577  1.00  0.00              
ATOM     11  CA  LYS    11      -7.785   3.281  14.472  1.00  0.00              
ATOM     12  CA  ALA    12     -10.875   1.275  13.928  1.00  0.00              
ATOM     13  CA  LYS    13     -13.723   1.384  16.509  1.00  0.00              
ATOM     14  CA  ASP    14     -12.624  -1.919  17.991  1.00  0.00              
ATOM     15  CA  GLY    15      -9.055  -0.756  18.644  1.00  0.00              
ATOM     16  CA  HIS    16      -7.354  -2.451  15.770  1.00  0.00              
ATOM     17  CA  VAL    17      -4.523  -0.468  14.357  1.00  0.00              
ATOM     18  CA  MET    18      -4.131  -0.359  10.628  1.00  0.00              
ATOM     19  CA  HIS    19      -0.707   0.044   9.188  1.00  0.00              
ATOM     20  CA  PHE    20      -0.226   1.438   5.631  1.00  0.00              
ATOM     21  CA  ASP    21       3.007   0.870   3.846  1.00  0.00              
ATOM     22  CA  VAL    22       4.407   3.334   1.533  1.00  0.00              
ATOM     23  CA  PHE    23       6.682   2.076  -1.401  1.00  0.00              
ATOM     24  CA  THR    24       6.990   4.478  -4.259  1.00  0.00              
ATOM     25  CA  ASP    25       9.414   4.023  -7.130  1.00  0.00              
ATOM     26  CA  VAL    26       7.635   5.966  -9.929  1.00  0.00              
ATOM     27  CA  ARG    27       7.985   3.431 -12.791  1.00  0.00              
ATOM     28  CA  ASP    28       6.835   0.598 -10.510  1.00  0.00              
ATOM     29  CA  ASP    29       3.865   2.447  -8.980  1.00  0.00              
ATOM     30  CA  LYS    30       2.156   3.038 -12.274  1.00  0.00              
ATOM     31  CA  LYS    31       2.539  -0.648 -13.153  1.00  0.00              
ATOM     32  CA  ALA    32       1.123  -1.851  -9.786  1.00  0.00              
ATOM     33  CA  ILE    33      -1.911   0.379 -10.006  1.00  0.00              
ATOM     34  CA  GLU    34      -2.593  -0.840 -13.515  1.00  0.00              
ATOM     35  CA  PHE    35      -2.298  -4.487 -12.664  1.00  0.00              
ATOM     36  CA  ALA    36      -4.625  -4.193  -9.727  1.00  0.00              
ATOM     37  CA  LYS    37      -7.221  -2.318 -11.762  1.00  0.00              
ATOM     38  CA  GLN    38      -7.031  -4.972 -14.525  1.00  0.00              
ATOM     39  CA  TRP    39      -7.423  -7.883 -12.105  1.00  0.00              
ATOM     40  CA  LEU    40     -10.344  -6.320 -10.322  1.00  0.00              
ATOM     41  CA  SER    41     -12.082  -5.612 -13.586  1.00  0.00              
ATOM     42  CA  SER    42     -11.560  -9.115 -14.860  1.00  0.00              
ATOM     43  CA  ILE    43     -13.073 -10.698 -11.808  1.00  0.00              
ATOM     44  CA  GLY    44     -16.150  -8.407 -11.856  1.00  0.00              
ATOM     45  CA  GLU    45     -15.081  -6.228  -8.983  1.00  0.00              
ATOM     46  CA  GLU    46     -15.491  -2.508  -9.119  1.00  0.00              
ATOM     47  CA  GLY    47     -12.565  -1.157  -7.119  1.00  0.00              
ATOM     48  CA  ALA    48     -14.902   0.137  -4.391  1.00  0.00              
ATOM     49  CA  THR    49     -16.499  -3.145  -3.602  1.00  0.00              
ATOM     50  CA  VAL    50     -13.497  -5.343  -3.110  1.00  0.00              
ATOM     51  CA  THR    51     -13.900  -9.041  -3.590  1.00  0.00              
ATOM     52  CA  SER    52     -13.225 -11.462  -0.787  1.00  0.00              
ATOM     53  CA  GLU    53      -9.813 -12.577  -2.144  1.00  0.00              
ATOM     54  CA  GLU    54      -8.460  -9.116  -2.679  1.00  0.00              
ATOM     55  CA  CYS    55      -8.819  -6.450  -0.070  1.00  0.00              
ATOM     56  CA  ARG    56     -12.253  -5.835   1.306  1.00  0.00              
ATOM     57  CA  PHE    57     -12.384  -9.376   2.701  1.00  0.00              
ATOM     58  CA  CYS    58      -9.640  -8.520   5.224  1.00  0.00              
ATOM     59  CA  HIS    59     -10.446  -4.839   5.782  1.00  0.00              
ATOM     60  CA  SER    60     -14.127  -5.101   6.696  1.00  0.00              
ATOM     61  CA  GLN    61     -13.911  -3.038   9.894  1.00  0.00              
ATOM     62  CA  LYS    62     -12.058  -0.008   8.670  1.00  0.00              
ATOM     63  CA  ALA    63     -13.764   1.202   5.546  1.00  0.00              
ATOM     64  CA  PRO    64     -11.348   2.598   2.933  1.00  0.00              
ATOM     65  CA  ASP    65     -12.830   6.083   2.895  1.00  0.00              
ATOM     66  CA  GLU    66     -12.728   6.459   6.641  1.00  0.00              
ATOM     67  CA  VAL    67      -9.174   5.316   6.961  1.00  0.00              
ATOM     68  CA  ILE    68      -7.875   7.674   4.269  1.00  0.00              
ATOM     69  CA  GLU    69      -9.673  10.636   5.748  1.00  0.00              
ATOM     70  CA  ALA    70      -8.327  10.031   9.267  1.00  0.00              
ATOM     71  CA  ILE    71      -4.781   9.648   7.910  1.00  0.00              
ATOM     72  CA  LYS    72      -5.018  12.868   5.891  1.00  0.00              
ATOM     73  CA  GLN    73      -6.281  14.909   8.828  1.00  0.00              
ATOM     74  CA  ASN    74      -3.456  13.617  11.061  1.00  0.00              
ATOM     75  CA  GLY    75      -0.682  14.279   8.537  1.00  0.00              
ATOM     76  CA  TYR    76      -0.032  10.596   7.656  1.00  0.00              
ATOM     77  CA  PHE    77       0.136   9.304   4.105  1.00  0.00              
ATOM     78  CA  ILE    78      -0.683   5.702   3.474  1.00  0.00              
ATOM     79  CA  TYR    79       0.430   4.116   0.357  1.00  0.00              
ATOM     80  CA  LYS    80      -0.030   0.443  -0.087  1.00  0.00              
ATOM     81  CA  MET    81       2.188  -1.354  -2.552  1.00  0.00              
ATOM     82  CA  GLU    82       0.774  -4.522  -4.113  1.00  0.00              
ATOM     83  CA  GLY    83       3.663  -6.355  -5.210  1.00  0.00              
ATOM     84  CA  CYS    84      -0.410  -5.563  -4.887  1.00  0.00              
ATOM     85  CA  ASN    85      -4.270  -7.036  -5.001  1.00  0.00              
TER                                                                             
END
