
#######################################################
#                                                     #
#                        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   75 (   75),  selected   75 , name T0349TS599_2
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS599_2.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    M       1      N       8           #
LGA    R       2      D       9          2.050
LGA    E       3      -       -           -
LGA    L       4      -       -           -
LGA    L       5      -       -           -
LGA    R       6      -       -           -
LGA    T       7      -       -           -
LGA    N       8      -       -           -
LGA    D       9      -       -           -
LGA    A      10      A      10          2.897
LGA    V      11      V      11          1.132
LGA    L      12      L      12          1.759
LGA    L      13      L      13          1.649
LGA    S      14      S      14          0.986
LGA    A      15      A      15          0.781
LGA    V      16      V      16          1.170
LGA    G      17      G      17          1.284
LGA    A      18      A      18          1.097
LGA    L      19      L      19          0.811
LGA    L      20      L      20          0.738
LGA    D      21      D      21          1.840
LGA    G      22      G      22          2.486
LGA    A      23      A      23          2.094
LGA    D      24      D      24          1.835
LGA    I      25      I      25          0.621
LGA    G      26      G      26          2.790
LGA    H      27      H      27          2.005
LGA    L      28      L      28          2.843
LGA    V      29      V      29          2.969
LGA    L      30      L      30          0.821
LGA    D      31      D      31          1.393
LGA    Q      32      Q      32          1.745
LGA    N      33      N      33          3.786
LGA    M      34      M      34          4.591
LGA    S      35      S      35          5.131
LGA    I      36      I      36           #
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      I      44           -
LGA    -       -      P      45           -
LGA    L      37      R      46           #
LGA    E      38      -       -           -
LGA    G      39      -       -           -
LGA    S      40      -       -           -
LGA    L      41      -       -           -
LGA    G      42      -       -           -
LGA    V      43      -       -           -
LGA    I      44      -       -           -
LGA    P      45      -       -           -
LGA    R      46      -       -           -
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      -       -           -
LGA    V      50      -       -           -
LGA    H      51      -       -           -
LGA    E      52      -       -           -
LGA    D      53      -       -           -
LGA    D      54      -       -           -
LGA    L      55      R      47           #
LGA    A      56      -       -           -
LGA    G      57      -       -           -
LGA    A      58      V      48           #
LGA    R      59      L      49          4.639
LGA    R      60      -       -           -
LGA    L      61      -       -           -
LGA    L      62      V      50          2.621
LGA    T      63      H      51          4.111
LGA    D      64      E      52          2.245
LGA    A      65      D      53          2.583
LGA    G      66      D      54          2.059
LGA    L      67      L      55          3.860
LGA    A      68      -       -           -
LGA    H      69      A      56          2.056
LGA    E      70      G      57          2.071
LGA    L      71      A      58          2.828
LGA    R      72      R      59          2.475
LGA    S      73      R      60          1.777
LGA    D      74      L      61          5.819
LGA    -       -      L      62           -
LGA    -       -      T      63           -
LGA    D      75      D      64          3.599
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   75    5.0     41    2.66    70.73     38.713     1.488

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.918880 * X  +   0.382786 * Y  +   0.095570 * Z  +  -4.028867
  Y_new =  -0.138351 * X  +   0.539478 * Y  +  -0.830555 * Z  +   3.842148
  Z_new =  -0.369483 * X  +   0.749959 * Y  +   0.548675 * Z  +   0.854240 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.939171   -2.202421  [ DEG:    53.8106   -126.1894 ]
  Theta =   0.378453    2.763140  [ DEG:    21.6838    158.3162 ]
  Phi   =  -0.149443    2.992150  [ DEG:    -8.5624    171.4376 ]
 
# 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: T0349TS599_2                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_2.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   75   75   5.0   41   2.66   70.73  38.713
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_2
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -3.542  -8.099   6.806  1.00  0.00              
ATOM      2  CA  ARG     2      -1.900  -8.215   3.267  1.00  0.00              
ATOM      3  CA  GLU     3      -2.731 -11.206   6.101  1.00  0.00              
ATOM      4  CA  LEU     4      -5.626  -9.261   5.271  1.00  0.00              
ATOM      5  CA  LEU     5      -5.818 -10.399   1.669  1.00  0.00              
ATOM      6  CA  ARG     6      -5.505 -14.075   2.396  1.00  0.00              
ATOM      7  CA  THR     7      -8.165 -14.240   5.045  1.00  0.00              
ATOM      8  CA  ASN     8     -10.562 -11.569   3.815  1.00  0.00              
ATOM      9  CA  ASP     9     -10.499  -9.787   7.126  1.00  0.00              
ATOM     10  CA  ALA    10      -9.040  -6.239   6.726  1.00  0.00              
ATOM     11  CA  VAL    11      -6.079  -5.633   9.004  1.00  0.00              
ATOM     12  CA  LEU    12      -3.199  -3.967   7.065  1.00  0.00              
ATOM     13  CA  LEU    13      -5.489  -1.571   5.171  1.00  0.00              
ATOM     14  CA  SER    14      -7.177  -0.518   8.428  1.00  0.00              
ATOM     15  CA  ALA    15      -3.890   0.159  10.241  1.00  0.00              
ATOM     16  CA  VAL    16      -2.621   2.159   7.264  1.00  0.00              
ATOM     17  CA  GLY    17      -5.849   4.138   7.136  1.00  0.00              
ATOM     18  CA  ALA    18      -5.695   5.210  10.706  1.00  0.00              
ATOM     19  CA  LEU    19      -2.077   6.407  10.308  1.00  0.00              
ATOM     20  CA  LEU    20      -2.950   8.334   7.163  1.00  0.00              
ATOM     21  CA  ASP    21      -5.986  10.084   8.706  1.00  0.00              
ATOM     22  CA  GLY    22      -3.836  11.134  11.650  1.00  0.00              
ATOM     23  CA  ALA    23      -1.401  12.960   9.348  1.00  0.00              
ATOM     24  CA  ASP    24      -4.184  14.842   7.548  1.00  0.00              
ATOM     25  CA  ILE    25      -3.219  13.459   4.121  1.00  0.00              
ATOM     26  CA  GLY    26      -6.165  12.761   1.880  1.00  0.00              
ATOM     27  CA  HIS    27      -4.689  10.200  -0.585  1.00  0.00              
ATOM     28  CA  LEU    28      -6.405   6.948  -1.343  1.00  0.00              
ATOM     29  CA  VAL    29      -4.913   4.372  -3.639  1.00  0.00              
ATOM     30  CA  LEU    30      -6.948   1.460  -4.684  1.00  0.00              
ATOM     31  CA  ASP    31      -5.082  -1.644  -5.940  1.00  0.00              
ATOM     32  CA  GLN    32      -7.090  -3.743  -8.309  1.00  0.00              
ATOM     33  CA  ASN    33      -7.850  -6.473  -5.720  1.00  0.00              
ATOM     34  CA  MET    34      -8.664  -4.265  -2.778  1.00  0.00              
ATOM     35  CA  SER    35     -11.895  -4.761  -0.845  1.00  0.00              
ATOM     36  CA  ILE    36     -10.668  -3.920   2.684  1.00  0.00              
ATOM     37  CA  LEU    37      -8.699  -0.989   1.313  1.00  0.00              
ATOM     38  CA  GLU    38     -11.738   0.435  -0.509  1.00  0.00              
ATOM     39  CA  GLY    39     -14.179   0.734   2.397  1.00  0.00              
ATOM     40  CA  SER    40     -11.637   2.553   4.626  1.00  0.00              
ATOM     41  CA  LEU    41     -10.363   4.874   1.942  1.00  0.00              
ATOM     42  CA  GLY    42     -13.905   6.020   0.972  1.00  0.00              
ATOM     43  CA  VAL    43     -14.116   7.842   4.330  1.00  0.00              
ATOM     44  CA  ILE    44     -10.963   9.892   3.387  1.00  0.00              
ATOM     45  CA  PRO    45     -11.234  10.523  -0.379  1.00  0.00              
ATOM     46  CA  ARG    46      -9.220  13.674  -0.813  1.00  0.00              
ATOM     47  CA  ARG    47      -7.319  12.330  -3.831  1.00  0.00              
ATOM     48  CA  VAL    48      -8.391   8.896  -4.896  1.00  0.00              
ATOM     49  CA  LEU    49      -6.344   6.855  -7.137  1.00  0.00              
ATOM     50  CA  VAL    50      -8.003   3.869  -8.683  1.00  0.00              
ATOM     51  CA  HIS    51      -7.204   1.029 -10.744  1.00  0.00              
ATOM     52  CA  GLU    52      -4.459  -1.501 -10.938  1.00  0.00              
ATOM     53  CA  ASP    53      -3.524  -0.574 -14.561  1.00  0.00              
ATOM     54  CA  ASP    54      -3.161   3.097 -13.465  1.00  0.00              
ATOM     55  CA  LEU    55      -0.974   2.422 -10.498  1.00  0.00              
ATOM     56  CA  ALA    56       1.976   4.558 -11.722  1.00  0.00              
ATOM     57  CA  GLY    57      -0.317   7.598 -12.061  1.00  0.00              
ATOM     58  CA  ALA    58      -1.775   7.051  -8.556  1.00  0.00              
ATOM     59  CA  ARG    59       1.662   6.684  -6.984  1.00  0.00              
ATOM     60  CA  ARG    60       2.730   9.907  -8.737  1.00  0.00              
ATOM     61  CA  LEU    61      -0.244  11.788  -7.263  1.00  0.00              
ATOM     62  CA  LEU    62       0.582  10.519  -3.738  1.00  0.00              
ATOM     63  CA  THR    63       4.246  11.536  -4.192  1.00  0.00              
ATOM     64  CA  ASP    64       3.309  14.997  -5.394  1.00  0.00              
ATOM     65  CA  ALA    65       1.106  15.435  -2.310  1.00  0.00              
ATOM     66  CA  GLY    66       3.898  14.244   0.057  1.00  0.00              
ATOM     67  CA  LEU    67       2.106  11.303   1.553  1.00  0.00              
ATOM     68  CA  ALA    68       5.117   8.948   1.967  1.00  0.00              
ATOM     69  CA  HIS    69       7.204  11.589   3.691  1.00  0.00              
ATOM     70  CA  GLU    70       4.363  12.421   6.127  1.00  0.00              
ATOM     71  CA  LEU    71       3.752   8.768   7.047  1.00  0.00              
ATOM     72  CA  ARG    72       7.359   7.757   7.249  1.00  0.00              
ATOM     73  CA  SER    73       8.591  10.773   9.649  1.00  0.00              
ATOM     74  CA  ASP    74       8.401  14.261  10.465  1.00  0.00              
ATOM     75  CA  ASP    75       6.614  10.991  11.902  1.00  0.00              
TER                                                                             
END
