
#######################################################
#                                                     #
#                        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   83 (   83),  selected   83 , name T0353TS599_1-D1
# Molecule2: number of CA atoms   83 ( 1315),  selected   83 , name T0353_D1.pdb
# PARAMETERS: T0353TS599_1-D1.T0353_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.711
LGA    Q       2      Q       2          2.999
LGA    I       3      I       3          2.879
LGA    H       4      H       4          0.884
LGA    V       5      V       5          0.991
LGA    Y       6      Y       6          1.251
LGA    D       7      D       7          1.603
LGA    T       8      T       8          1.669
LGA    Y       9      Y       9          1.569
LGA    V      10      V      10          1.698
LGA    K      11      K      11          0.720
LGA    A      12      A      12          0.847
LGA    K      13      K      13          1.595
LGA    D      14      D      14          3.260
LGA    G      15      G      15           #
LGA    H      16      H      16          3.055
LGA    V      17      V      17          1.362
LGA    M      18      M      18          1.810
LGA    H      19      H      19          1.110
LGA    F      20      F      20          1.022
LGA    D      21      D      21          1.311
LGA    V      22      V      22          1.506
LGA    F      23      F      23          1.466
LGA    T      24      T      24          2.063
LGA    D      25      D      25          4.035
LGA    V      26      -       -           -
LGA    R      27      -       -           -
LGA    D      28      -       -           -
LGA    D      29      -       -           -
LGA    K      30      V      26           #
LGA    K      31      R      27           -
LGA    A      32      D      28           -
LGA    I      33      D      29           -
LGA    E      34      K      30           -
LGA    F      35      K      31           -
LGA    A      36      A      32           -
LGA    K      37      I      33           -
LGA    Q      38      E      34           -
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      -       -           -
LGA    A      48      -       -           -
LGA    T      49      -       -           -
LGA    V      50      -       -           -
LGA    T      51      -       -           -
LGA    S      52      -       -           -
LGA    E      53      -       -           -
LGA    E      54      -       -           -
LGA    C      55      -       -           -
LGA    R      56      -       -           -
LGA    F      57      -       -           -
LGA    C      58      -       -           -
LGA    H      59      -       -           -
LGA    S      60      -       -           -
LGA    Q      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      F      35          3.214
LGA    P      64      A      36          2.912
LGA    D      65      K      37          4.012
LGA    E      66      Q      38          1.517
LGA    V      67      W      39          2.474
LGA    I      68      L      40          4.335
LGA    E      69      S      41          3.094
LGA    -       -      S      42           -
LGA    A      70      I      43          5.487
LGA    I      71      G      44           #
LGA    K      72      E      45           #
LGA    Q      73      E      46          4.459
LGA    N      74      -       -           -
LGA    G      75      G      47          3.062
LGA    Y      76      A      48          3.410
LGA    F      77      T      49          3.841
LGA    I      78      V      50          3.827
LGA    Y      79      T      51           #
LGA    -       -      S      52           -
LGA    -       -      E      53           -
LGA    K      80      E      54          3.708
LGA    M      81      C      55          2.378
LGA    E      82      R      56          2.886
LGA    G      83      F      57          0.978
LGA    -       -      C      58           -
LGA    -       -      H      59           -
LGA    -       -      S      60           -
LGA    -       -      E      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    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    -       -      I      78           -
LGA    -       -      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   83   83    5.0     41    2.76    60.98     33.258     1.434

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.857940 * X  +  -0.166505 * Y  +   0.486019 * Z  +  -3.378782
  Y_new =   0.467174 * X  +   0.646440 * Y  +  -0.603212 * Z  +  -4.692626
  Z_new =  -0.213744 * X  +   0.744575 * Y  +   0.632393 * Z  +  -1.373210 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.866688   -2.274904  [ DEG:    49.6576   -130.3424 ]
  Theta =   0.215406    2.926186  [ DEG:    12.3419    167.6581 ]
  Phi   =   0.498634   -2.642959  [ DEG:    28.5696   -151.4304 ]
 
# 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_1-D1                               
REMARK     2: T0353_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_1-D1.T0353_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   83   83   5.0   41   2.76   60.98  33.258
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_1-D1
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      14.128   4.275 -10.294  1.00  0.00              
ATOM      2  CA  GLN     2      10.703   4.816  -9.323  1.00  0.00              
ATOM      3  CA  ILE     3       9.667   4.139  -5.824  1.00  0.00              
ATOM      4  CA  HIS     4       6.097   4.627  -4.767  1.00  0.00              
ATOM      5  CA  VAL     5       5.094   4.450  -1.156  1.00  0.00              
ATOM      6  CA  TYR     6       1.553   3.664  -0.224  1.00  0.00              
ATOM      7  CA  ASP     7       0.424   4.175   3.205  1.00  0.00              
ATOM      8  CA  THR     8      -2.492   2.409   4.309  1.00  0.00              
ATOM      9  CA  TYR     9      -3.977   3.360   7.468  1.00  0.00              
ATOM     10  CA  VAL    10      -6.387   1.088   9.003  1.00  0.00              
ATOM     11  CA  LYS    11      -8.737   2.364  11.513  1.00  0.00              
ATOM     12  CA  ALA    12     -10.589  -0.119  13.592  1.00  0.00              
ATOM     13  CA  LYS    13     -14.017   0.812  15.036  1.00  0.00              
ATOM     14  CA  ASP    14     -12.526   1.309  18.486  1.00  0.00              
ATOM     15  CA  GLY    15      -9.915   3.795  17.352  1.00  0.00              
ATOM     16  CA  HIS    16      -6.928   1.568  17.097  1.00  0.00              
ATOM     17  CA  VAL    17      -4.790   2.683  14.364  1.00  0.00              
ATOM     18  CA  MET    18      -3.100   0.121  12.212  1.00  0.00              
ATOM     19  CA  HIS    19      -0.357   1.191   9.865  1.00  0.00              
ATOM     20  CA  PHE    20       0.211  -0.687   6.660  1.00  0.00              
ATOM     21  CA  ASP    21       3.013   0.244   4.478  1.00  0.00              
ATOM     22  CA  VAL    22       2.955  -0.806   0.864  1.00  0.00              
ATOM     23  CA  PHE    23       5.972  -0.146  -1.251  1.00  0.00              
ATOM     24  CA  THR    24       5.661  -0.046  -4.916  1.00  0.00              
ATOM     25  CA  ASP    25       8.676  -0.365  -7.080  1.00  0.00              
ATOM     26  CA  VAL    26       8.164   0.303 -10.729  1.00  0.00              
ATOM     27  CA  ARG    27      10.008  -2.540 -12.367  1.00  0.00              
ATOM     28  CA  ASP    28       8.902  -4.942  -9.606  1.00  0.00              
ATOM     29  CA  ASP    29       5.289  -3.756  -9.350  1.00  0.00              
ATOM     30  CA  LYS    30       4.521  -4.543 -12.979  1.00  0.00              
ATOM     31  CA  LYS    31       5.990  -8.052 -12.571  1.00  0.00              
ATOM     32  CA  ALA    32       3.997  -8.784  -9.437  1.00  0.00              
ATOM     33  CA  ILE    33       0.770  -7.675 -11.073  1.00  0.00              
ATOM     34  CA  GLU    34       1.395  -9.869 -14.093  1.00  0.00              
ATOM     35  CA  PHE    35       2.176 -12.948 -12.031  1.00  0.00              
ATOM     36  CA  ALA    36      -0.952 -12.398  -9.908  1.00  0.00              
ATOM     37  CA  LYS    37      -3.145 -11.982 -13.012  1.00  0.00              
ATOM     38  CA  GLN    38      -1.797 -15.196 -14.578  1.00  0.00              
ATOM     39  CA  TRP    39      -2.420 -17.176 -11.361  1.00  0.00              
ATOM     40  CA  LEU    40      -5.892 -15.898 -10.861  1.00  0.00              
ATOM     41  CA  SER    41      -6.849 -16.709 -14.480  1.00  0.00              
ATOM     42  CA  SER    42      -5.514 -20.211 -14.351  1.00  0.00              
ATOM     43  CA  ILE    43      -7.487 -20.970 -11.160  1.00  0.00              
ATOM     44  CA  GLY    44     -10.739 -19.556 -12.545  1.00  0.00              
ATOM     45  CA  GLU    45     -10.709 -16.306 -10.670  1.00  0.00              
ATOM     46  CA  GLU    46     -11.519 -13.090 -12.485  1.00  0.00              
ATOM     47  CA  GLY    47      -9.214 -10.368 -11.137  1.00  0.00              
ATOM     48  CA  ALA    48     -12.084  -8.479  -9.452  1.00  0.00              
ATOM     49  CA  THR    49     -13.319 -11.480  -7.566  1.00  0.00              
ATOM     50  CA  VAL    50     -10.032 -12.943  -6.394  1.00  0.00              
ATOM     51  CA  THR    51     -10.295 -15.340  -3.519  1.00  0.00              
ATOM     52  CA  SER    52      -8.016 -14.875  -0.515  1.00  0.00              
ATOM     53  CA  GLU    53      -6.006 -18.038  -1.268  1.00  0.00              
ATOM     54  CA  GLU    54      -5.428 -17.199  -4.908  1.00  0.00              
ATOM     55  CA  CYS    55      -4.215 -13.703  -4.243  1.00  0.00              
ATOM     56  CA  ARG    56      -1.961 -14.016  -1.217  1.00  0.00              
ATOM     57  CA  PHE    57       0.589 -16.163  -2.946  1.00  0.00              
ATOM     58  CA  CYS    58       1.765 -13.217  -5.131  1.00  0.00              
ATOM     59  CA  HIS    59       0.227 -10.283  -3.406  1.00  0.00              
ATOM     60  CA  SER    60       2.054  -9.963  -0.131  1.00  0.00              
ATOM     61  CA  GLN    61       1.236  -6.258   0.092  1.00  0.00              
ATOM     62  CA  LYS    62      -2.528  -6.707  -0.340  1.00  0.00              
ATOM     63  CA  ALA    63      -3.921  -4.896  -3.322  1.00  0.00              
ATOM     64  CA  PRO    64      -6.225  -1.977  -2.757  1.00  0.00              
ATOM     65  CA  ASP    65      -9.507  -3.524  -3.804  1.00  0.00              
ATOM     66  CA  GLU    66      -9.042  -6.571  -1.662  1.00  0.00              
ATOM     67  CA  VAL    67      -7.972  -4.686   1.395  1.00  0.00              
ATOM     68  CA  ILE    68     -10.900  -2.313   1.214  1.00  0.00              
ATOM     69  CA  GLU    69     -13.382  -5.108   0.890  1.00  0.00              
ATOM     70  CA  ALA    70     -11.896  -6.999   3.863  1.00  0.00              
ATOM     71  CA  ILE    71     -11.800  -3.972   6.088  1.00  0.00              
ATOM     72  CA  LYS    72     -15.368  -3.025   5.381  1.00  0.00              
ATOM     73  CA  GLN    73     -16.613  -6.510   6.053  1.00  0.00              
ATOM     74  CA  ASN    74     -14.742  -6.584   9.334  1.00  0.00              
ATOM     75  CA  GLY    75     -15.768  -3.145  10.639  1.00  0.00              
ATOM     76  CA  TYR    76     -12.399  -1.583   9.723  1.00  0.00              
ATOM     77  CA  PHE    77     -12.025   1.796   8.072  1.00  0.00              
ATOM     78  CA  ILE    78      -9.327   2.155   5.465  1.00  0.00              
ATOM     79  CA  TYR    79      -7.484   5.323   5.105  1.00  0.00              
ATOM     80  CA  LYS    80      -5.086   5.608   2.246  1.00  0.00              
ATOM     81  CA  MET    81      -2.204   8.043   2.362  1.00  0.00              
ATOM     82  CA  GLU    82      -0.467   8.739  -0.877  1.00  0.00              
ATOM     83  CA  GLY    83       2.876   9.856  -0.271  1.00  0.00              
TER                                                                             
END
