
#######################################################
#                                                     #
#                        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   90 (   90),  selected   90 , name T0340TS393_1
# Molecule2: number of CA atoms   90 (  685),  selected   90 , name T0340.pdb
# PARAMETERS: T0340TS393_1.T0340.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1          3.478
LGA    M       2      M       2          3.290
LGA    L       3      L       3          2.664
LGA    R       4      R       4          1.898
LGA    P       5      P       5          2.396
LGA    R       6      R       6          0.573
LGA    L       7      L       7          1.597
LGA    C       8      C       8          0.830
LGA    H       9      H       9          0.969
LGA    L      10      L      10          0.733
LGA    R      11      R      11          0.710
LGA    K      12      K      12          1.448
LGA    G      13      G      13          2.376
LGA    P      14      P      14          1.886
LGA    Q      15      Q      15          1.653
LGA    G      16      G      16          1.120
LGA    Y      17      Y      17          1.724
LGA    G      18      G      18          1.444
LGA    F      19      F      19          2.113
LGA    N      20      N      20          1.905
LGA    L      21      L      21          1.559
LGA    H      22      H      22          0.607
LGA    S      23      S      23          1.119
LGA    D      24      D      24          4.168
LGA    K      25      K      25          3.945
LGA    S      26      S      26          4.441
LGA    R      27      R      27          3.540
LGA    P      28      P      28          1.845
LGA    G      29      G      29          2.347
LGA    Q      30      Q      30          0.882
LGA    Y      31      Y      31          0.458
LGA    I      32      I      32          0.756
LGA    R      33      R      33          1.124
LGA    S      34      S      34          1.117
LGA    V      35      V      35          1.465
LGA    D      36      D      36          2.092
LGA    P      37      P      37          1.798
LGA    G      38      G      38          1.590
LGA    S      39      S      39          1.771
LGA    P      40      P      40          1.199
LGA    A      41      A      41          0.569
LGA    A      42      A      42          1.592
LGA    R      43      R      43          2.115
LGA    S      44      S      44          2.562
LGA    G      45      G      45          2.227
LGA    L      46      L      46          1.313
LGA    R      47      R      47          1.633
LGA    A      48      A      48          1.031
LGA    Q      49      Q      49          1.667
LGA    D      50      D      50          0.856
LGA    R      51      R      51          1.224
LGA    L      52      L      52          1.214
LGA    I      53      I      53          1.113
LGA    E      54      E      54          1.215
LGA    V      55      V      55          2.868
LGA    N      56      N      56          0.874
LGA    G      57      G      57          4.122
LGA    Q      58      Q      58          3.545
LGA    N      59      N      59          2.920
LGA    V      60      V      60          2.188
LGA    E      61      E      61          0.871
LGA    G      62      G      62          1.621
LGA    L      63      L      63          1.716
LGA    R      64      R      64          2.138
LGA    H      65      H      65          1.461
LGA    A      66      A      66          1.729
LGA    E      67      E      67          1.400
LGA    V      68      V      68          1.039
LGA    V      69      V      69          1.296
LGA    A      70      A      70          1.614
LGA    S      71      S      71          1.260
LGA    I      72      I      72          1.129
LGA    K      73      K      73          1.582
LGA    A      74      A      74          1.664
LGA    R      75      R      75          2.019
LGA    E      76      E      76          2.826
LGA    D      77      D      77          3.104
LGA    E      78      E      78          3.698
LGA    A      79      A      79          1.035
LGA    R      80      R      80          0.990
LGA    L      81      L      81          1.357
LGA    L      82      L      82          1.339
LGA    V      83      V      83          1.148
LGA    V      84      V      84          1.721
LGA    G      85      G      85          1.125
LGA    P      86      P      86          2.266
LGA    S      87      S      87          2.598
LGA    T      88      T      88          3.354
LGA    R      89      R      89          1.810
LGA    L      90      L      90          6.875

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     90    2.13   100.00     87.347     4.030

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.463448 * X  +   0.857347 * Y  +   0.223991 * Z  +   9.943438
  Y_new =  -0.703963 * X  +   0.509745 * Y  +  -0.494567 * Z  +  25.809086
  Z_new =  -0.538193 * X  +   0.071525 * Y  +   0.839781 * Z  +   9.004822 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.084965   -3.056627  [ DEG:     4.8682   -175.1318 ]
  Theta =   0.568292    2.573300  [ DEG:    32.5607    147.4393 ]
  Phi   =  -0.988580    2.153013  [ DEG:   -56.6415    123.3585 ]
 
# 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: T0340TS393_1                                  
REMARK     2: T0340.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS393_1.T0340.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   90   90   5.0   90   2.13  100.00  87.347
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS393_1
PFRMAT TS
TARGET T0340
MODEL 1
PARENT N/A
ATOM      1  CA  SER     1      11.649  46.001   6.121  1.00 25.00           C
ATOM      2  CA  MET     2      14.571  45.400   8.458  1.00 25.00           C
ATOM      3  CA  LEU     3      15.996  42.590   6.324  1.00 25.00           C
ATOM      4  CA  ARG     4      16.178  39.326   8.173  1.00 25.00           C
ATOM      5  CA  PRO     5      14.031  37.922  11.038  1.00 25.00           C
ATOM      6  CA  ARG     6      10.494  36.497  10.685  1.00 25.00           C
ATOM      7  CA  LEU     7       8.805  34.489  13.499  1.00 25.00           C
ATOM      8  CA  CYS     8       6.376  31.598  13.528  1.00 25.00           C
ATOM      9  CA  HIS     9       5.561  31.168  17.276  1.00 25.00           C
ATOM     10  CA  LEU    10       3.722  27.909  16.433  1.00 25.00           C
ATOM     11  CA  ARG    11       1.622  26.454  19.175  1.00 25.00           C
ATOM     12  CA  LYS    12       1.590  22.656  19.786  1.00 25.00           C
ATOM     13  CA  GLY    13      -2.038  21.554  20.077  1.00 25.00           C
ATOM     14  CA  PRO    14      -2.667  17.850  19.482  1.00 25.00           C
ATOM     15  CA  GLN    15      -2.148  16.403  16.065  1.00 25.00           C
ATOM     16  CA  GLY    16       0.678  18.893  15.675  1.00 25.00           C
ATOM     17  CA  TYR    17       3.097  20.565  13.220  1.00 25.00           C
ATOM     18  CA  GLY    18       1.396  20.586   9.798  1.00 25.00           C
ATOM     19  CA  PHE    19       4.812  21.629   8.334  1.00 25.00           C
ATOM     20  CA  ASN    20       5.834  18.556   6.321  1.00 25.00           C
ATOM     21  CA  LEU    21       9.453  18.681   5.146  1.00 25.00           C
ATOM     22  CA  HIS    22      10.775  19.080   1.625  1.00 25.00           C
ATOM     23  CA  SER    23      14.111  19.188  -0.231  1.00 25.00           C
ATOM     24  CA  ASP    24      17.864  18.681  -0.116  1.00 25.00           C
ATOM     25  CA  LYS    25      18.999  16.562  -3.085  1.00 25.00           C
ATOM     26  CA  SER    26      21.324  19.510  -3.944  1.00 25.00           C
ATOM     27  CA  ARG    27      22.056  22.603  -1.792  1.00 25.00           C
ATOM     28  CA  PRO    28      20.835  23.157   1.779  1.00 25.00           C
ATOM     29  CA  GLY    29      17.365  24.440   0.740  1.00 25.00           C
ATOM     30  CA  GLN    30      15.163  23.241   3.601  1.00 25.00           C
ATOM     31  CA  TYR    31      11.483  24.113   3.131  1.00 25.00           C
ATOM     32  CA  ILE    32       7.776  24.826   3.063  1.00 25.00           C
ATOM     33  CA  ARG    33       5.655  22.258   1.314  1.00 25.00           C
ATOM     34  CA  SER    34       2.210  22.923   2.747  1.00 25.00           C
ATOM     35  CA  VAL    35       0.203  23.776   5.823  1.00 25.00           C
ATOM     36  CA  ASP    36      -2.732  21.300   5.997  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.281  24.162   5.794  1.00 25.00           C
ATOM     38  CA  GLY    38      -6.358  25.307   9.259  1.00 25.00           C
ATOM     39  CA  SER    39      -3.851  23.226  11.275  1.00 25.00           C
ATOM     40  CA  PRO    40      -1.176  24.774  13.505  1.00 25.00           C
ATOM     41  CA  ALA    41       1.242  26.108  10.852  1.00 25.00           C
ATOM     42  CA  ALA    42      -1.671  27.753   8.987  1.00 25.00           C
ATOM     43  CA  ARG    43      -2.878  29.363  12.245  1.00 25.00           C
ATOM     44  CA  SER    44      -0.139  31.877  12.907  1.00 25.00           C
ATOM     45  CA  GLY    45       0.931  32.944   9.363  1.00 25.00           C
ATOM     46  CA  LEU    46       3.787  31.100   7.669  1.00 25.00           C
ATOM     47  CA  ARG    47       3.217  31.487   3.924  1.00 25.00           C
ATOM     48  CA  ALA    48       3.940  28.260   1.943  1.00 25.00           C
ATOM     49  CA  GLN    49       7.005  29.426   0.004  1.00 25.00           C
ATOM     50  CA  ASP    50       8.953  29.934   3.212  1.00 25.00           C
ATOM     51  CA  ARG    51      12.684  29.331   3.478  1.00 25.00           C
ATOM     52  CA  LEU    52      13.395  27.341   6.626  1.00 25.00           C
ATOM     53  CA  ILE    53      16.545  28.449   8.401  1.00 25.00           C
ATOM     54  CA  GLU    54      17.089  28.792  12.160  1.00 25.00           C
ATOM     55  CA  VAL    55      16.509  27.675  15.720  1.00 25.00           C
ATOM     56  CA  ASN    56      15.067  26.123  18.938  1.00 25.00           C
ATOM     57  CA  GLY    57      18.658  25.219  19.748  1.00 25.00           C
ATOM     58  CA  GLN    58      18.504  23.130  16.527  1.00 25.00           C
ATOM     59  CA  ASN    59      19.591  24.295  13.029  1.00 25.00           C
ATOM     60  CA  VAL    60      18.503  23.892   9.440  1.00 25.00           C
ATOM     61  CA  GLU    61      21.280  25.492   7.339  1.00 25.00           C
ATOM     62  CA  GLY    62      22.918  22.109   7.027  1.00 25.00           C
ATOM     63  CA  LEU    63      20.878  18.956   7.512  1.00 25.00           C
ATOM     64  CA  ARG    64      19.417  16.430   5.047  1.00 25.00           C
ATOM     65  CA  HIS    65      15.697  17.169   5.619  1.00 25.00           C
ATOM     66  CA  ALA    66      15.072  14.094   7.814  1.00 25.00           C
ATOM     67  CA  GLU    67      17.123  15.665  10.641  1.00 25.00           C
ATOM     68  CA  VAL    68      15.115  18.910  10.327  1.00 25.00           C
ATOM     69  CA  VAL    69      11.841  16.928  10.472  1.00 25.00           C
ATOM     70  CA  ALA    70      13.067  15.087  13.599  1.00 25.00           C
ATOM     71  CA  SER    71      13.995  18.425  15.231  1.00 25.00           C
ATOM     72  CA  ILE    72      10.527  19.822  14.401  1.00 25.00           C
ATOM     73  CA  LYS    73       8.883  16.715  15.920  1.00 25.00           C
ATOM     74  CA  ALA    74      11.002  17.113  19.086  1.00 25.00           C
ATOM     75  CA  ARG    75      10.125  20.504  20.634  1.00 25.00           C
ATOM     76  CA  GLU    76       6.632  20.987  22.071  1.00 25.00           C
ATOM     77  CA  ASP    77       5.538  24.495  23.111  1.00 25.00           C
ATOM     78  CA  GLU    78       6.954  27.422  21.029  1.00 25.00           C
ATOM     79  CA  ALA    79       8.551  25.811  17.956  1.00 25.00           C
ATOM     80  CA  ARG    80      10.564  28.892  16.924  1.00 25.00           C
ATOM     81  CA  LEU    81      11.527  29.547  13.303  1.00 25.00           C
ATOM     82  CA  LEU    82      13.444  32.338  11.572  1.00 25.00           C
ATOM     83  CA  VAL    83      12.378  32.481   7.955  1.00 25.00           C
ATOM     84  CA  VAL    84      14.467  34.467   5.541  1.00 25.00           C
ATOM     85  CA  GLY    85      11.712  34.515   2.849  1.00 25.00           C
ATOM     86  CA  PRO    86      13.867  33.900  -0.173  1.00 25.00           C
ATOM     87  CA  SER    87      13.023  35.406  -3.557  1.00 25.00           C
ATOM     88  CA  THR    88      15.879  36.882  -5.620  1.00 25.00           C
ATOM     89  CA  ARG    89      19.275  36.289  -7.059  1.00 25.00           C
ATOM     90  CA  LEU    90      21.436  35.505  -4.033  1.00 25.00           C
TER
END
