
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0378TS168_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS168_2-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    L       2      L       2           -
LGA    S       3      -       -           -
LGA    A       4      S       3           #
LGA    -       -      A       4           -
LGA    N       5      N       5          1.804
LGA    Q       6      Q       6          2.171
LGA    I       7      I       7          1.600
LGA    K       8      K       8          1.581
LGA    F       9      F       9          2.173
LGA    L      10      L      10          2.165
LGA    R      11      R      11          2.119
LGA    S      12      S      12          2.121
LGA    L      13      L      13          1.847
LGA    R      14      R      14          1.476
LGA    E      15      E      15          3.303
LGA    R      16      R      16          3.249
LGA    K      17      K      17          3.690
LGA    Y      18      Y      18          5.303
LGA    R      19      R      19          5.296
LGA    L      20      L      20          3.706
LGA    R      21      R      21          2.689
LGA    E      22      E      22          1.784
LGA    Q      23      Q      23          2.044
LGA    A      24      A      24          0.642
LGA    F      25      F      25          0.545
LGA    A      26      A      26          3.583
LGA    V      27      V      27          2.846
LGA    E      28      E      28          2.759
LGA    G      29      G      29          2.769
LGA    P      30      P      30          2.199
LGA    K      31      K      31          2.071
LGA    L      32      L      32          1.767
LGA    V      33      V      33          0.910
LGA    G      34      G      34          1.020
LGA    E      35      E      35          1.582
LGA    M      36      M      36          1.366
LGA    L      37      L      37          1.206
LGA    P      38      P      38          2.033
LGA    F      39      F      39          3.013
LGA    Y      40      Y      40          2.590
LGA    R      41      R      41          3.208
LGA    C      42      C      42          0.645
LGA    R      43      R      43          1.431
LGA    M      44      M      44          3.048
LGA    L      45      L      45          1.519
LGA    -       -      V      46           -
LGA    V      46      G      47          2.083
LGA    G      47      T      48          1.745
LGA    T      48      A      49          2.316
LGA    A      49      A      50          1.824
LGA    A      50      M      51          3.280
LGA    M      51      L      52          2.875
LGA    L      52      R      53          1.808
LGA    R      53      A      54          3.378
LGA    A      54      -       -           -
LGA    V      55      V      55          2.327
LGA    S      56      -       -           -
LGA    T      57      -       -           -
LGA    P      58      -       -           -
LGA    H      59      -       -           -
LGA    D      60      S      56          3.659
LGA    A      61      T      57          4.098
LGA    E      62      P      58          4.281
LGA    V      63      H      59          3.293
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    V      64      E      62          3.534
LGA    E      65      V      63          1.887
LGA    L      66      V      64          0.664
LGA    P      67      E      65          4.785
LGA    E      68      L      66          2.980
LGA    S      69      P      67          4.279
LGA    -       -      E      68           -
LGA    F      70      S      69           #
LGA    D      71      F      70           #
LGA    F      72      D      71           #
LGA    K      73      F      72          1.656
LGA    R      74      K      73          2.209
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    I      75      S      76          2.274
LGA    S      76      T      77          4.281
LGA    T      77      Q      78          3.270
LGA    Q      78      T      79          3.402
LGA    -       -      T      80           -
LGA    T      79      P      81          2.881
LGA    T      80      Q      82          1.196
LGA    P      81      P      83          2.407
LGA    Q      82      L      84          2.923
LGA    P      83      M      85          3.407
LGA    L      84      A      86          2.300
LGA    M      85      V      87          2.818
LGA    A      86      F      88          3.765
LGA    V      87      D      89          3.215
LGA    F      88      -       -           -
LGA    D      89      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     75    2.75    58.67     52.038     2.635

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.696941 * X  +  -0.111488 * Y  +   0.708409 * Z  +  17.760210
  Y_new =  -0.208534 * X  +  -0.913647 * Y  +  -0.348945 * Z  +   9.723938
  Z_new =   0.686139 * X  +  -0.390921 * Y  +   0.613509 * Z  +  46.618946 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.567317    2.574276  [ DEG:   -32.5048    147.4952 ]
  Theta =  -0.756169   -2.385424  [ DEG:   -43.3253   -136.6747 ]
  Phi   =  -2.850858    0.290734  [ DEG:  -163.3421     16.6578 ]
 
# 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: T0378TS168_2-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS168_2-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89   89   5.0   75   2.75   58.67  52.038
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS168_2-D1
PFRMAT TS
TARGET T0378
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      11.592  29.372  67.143  1.00 25.00           C
ATOM      2  CA  LEU     2      11.583  31.629  64.126  1.00 25.00           C
ATOM      3  CA  SER     3       9.059  33.898  62.414  1.00 25.00           C
ATOM      4  CA  ALA     4       8.024  36.497  59.907  1.00 25.00           C
ATOM      5  CA  ASN     5       9.810  35.757  56.676  1.00 25.00           C
ATOM      6  CA  GLN     6       8.491  32.467  55.224  1.00 25.00           C
ATOM      7  CA  ILE     7       9.098  33.762  51.672  1.00 25.00           C
ATOM      8  CA  LYS     8      12.667  34.773  52.624  1.00 25.00           C
ATOM      9  CA  PHE     9      13.281  31.300  54.114  1.00 25.00           C
ATOM     10  CA  LEU    10      11.960  29.666  50.912  1.00 25.00           C
ATOM     11  CA  ARG    11      14.265  31.880  48.801  1.00 25.00           C
ATOM     12  CA  SER    12      17.247  30.916  51.003  1.00 25.00           C
ATOM     13  CA  LEU    13      16.366  27.209  50.617  1.00 25.00           C
ATOM     14  CA  ARG    14      16.150  27.632  46.816  1.00 25.00           C
ATOM     15  CA  GLU    15      19.566  29.364  46.792  1.00 25.00           C
ATOM     16  CA  ARG    16      21.056  26.512  48.867  1.00 25.00           C
ATOM     17  CA  LYS    17      23.445  28.684  50.881  1.00 25.00           C
ATOM     18  CA  TYR    18      24.072  27.650  54.490  1.00 25.00           C
ATOM     19  CA  ARG    19      20.424  27.172  55.244  1.00 25.00           C
ATOM     20  CA  LEU    20      21.880  24.781  57.881  1.00 25.00           C
ATOM     21  CA  ARG    21      19.679  26.776  60.299  1.00 25.00           C
ATOM     22  CA  GLU    22      16.227  25.615  59.058  1.00 25.00           C
ATOM     23  CA  GLN    23      15.035  22.163  58.103  1.00 25.00           C
ATOM     24  CA  ALA    24      12.965  21.206  54.988  1.00 25.00           C
ATOM     25  CA  PHE    25      13.476  20.234  51.313  1.00 25.00           C
ATOM     26  CA  ALA    26      11.968  18.288  48.488  1.00 25.00           C
ATOM     27  CA  VAL    27       9.174  16.745  46.339  1.00 25.00           C
ATOM     28  CA  GLU    28       7.328  18.414  43.464  1.00 25.00           C
ATOM     29  CA  GLY    29       5.432  18.161  40.175  1.00 25.00           C
ATOM     30  CA  PRO    30       2.320  16.290  41.092  1.00 25.00           C
ATOM     31  CA  LYS    31       2.925  12.508  41.115  1.00 25.00           C
ATOM     32  CA  LEU    32       6.034  12.994  43.298  1.00 25.00           C
ATOM     33  CA  VAL    33       4.023  15.176  45.718  1.00 25.00           C
ATOM     34  CA  GLY    34       1.286  12.503  45.895  1.00 25.00           C
ATOM     35  CA  GLU    35       3.922   9.818  46.614  1.00 25.00           C
ATOM     36  CA  MET    36       5.417  11.994  49.388  1.00 25.00           C
ATOM     37  CA  LEU    37       1.937  12.493  50.907  1.00 25.00           C
ATOM     38  CA  PRO    38       1.325   8.713  50.806  1.00 25.00           C
ATOM     39  CA  PHE    39       3.692   8.162  53.708  1.00 25.00           C
ATOM     40  CA  TYR    40       5.924  10.883  55.222  1.00 25.00           C
ATOM     41  CA  ARG    41       3.628  13.897  55.710  1.00 25.00           C
ATOM     42  CA  CYS    42       4.722  17.432  54.606  1.00 25.00           C
ATOM     43  CA  ARG    43       4.459  21.004  55.913  1.00 25.00           C
ATOM     44  CA  MET    44       1.813  21.275  53.190  1.00 25.00           C
ATOM     45  CA  LEU    45       0.458  23.522  50.465  1.00 25.00           C
ATOM     46  CA  VAL    46      -2.049  25.022  48.007  1.00 25.00           C
ATOM     47  CA  GLY    47      -4.966  26.236  45.915  1.00 25.00           C
ATOM     48  CA  THR    48      -8.117  26.901  43.859  1.00 25.00           C
ATOM     49  CA  ALA    49      -9.398  23.924  41.778  1.00 25.00           C
ATOM     50  CA  ALA    50      -6.367  21.876  40.643  1.00 25.00           C
ATOM     51  CA  MET    51      -5.261  21.450  44.285  1.00 25.00           C
ATOM     52  CA  LEU    52      -8.785  20.300  45.247  1.00 25.00           C
ATOM     53  CA  ARG    53      -8.776  17.780  42.363  1.00 25.00           C
ATOM     54  CA  ALA    54      -5.364  16.459  43.494  1.00 25.00           C
ATOM     55  CA  VAL    55      -6.667  16.092  47.076  1.00 25.00           C
ATOM     56  CA  SER    56      -9.736  14.194  45.793  1.00 25.00           C
ATOM     57  CA  THR    57      -7.476  11.876  43.748  1.00 25.00           C
ATOM     58  CA  PRO    58      -6.669  10.500  47.240  1.00 25.00           C
ATOM     59  CA  HIS    59      -8.566  11.124  50.489  1.00 25.00           C
ATOM     60  CA  ASP    60      -8.696  14.293  52.659  1.00 25.00           C
ATOM     61  CA  ALA    61      -5.734  13.605  54.944  1.00 25.00           C
ATOM     62  CA  GLU    62      -4.533  15.439  58.061  1.00 25.00           C
ATOM     63  CA  VAL    63      -2.543  18.437  56.918  1.00 25.00           C
ATOM     64  CA  VAL    64      -1.919  22.147  57.013  1.00 25.00           C
ATOM     65  CA  GLU    65      -2.523  25.654  55.710  1.00 25.00           C
ATOM     66  CA  LEU    66      -2.087  28.055  52.834  1.00 25.00           C
ATOM     67  CA  PRO    67      -0.304  29.564  49.783  1.00 25.00           C
ATOM     68  CA  GLU    68      -2.585  32.516  48.879  1.00 25.00           C
ATOM     69  CA  SER    69      -1.717  32.305  45.182  1.00 25.00           C
ATOM     70  CA  PHE    70       0.999  34.450  43.539  1.00 25.00           C
ATOM     71  CA  ASP    71       3.656  32.843  45.779  1.00 25.00           C
ATOM     72  CA  PHE    72       2.375  29.358  44.843  1.00 25.00           C
ATOM     73  CA  LYS    73       2.517  30.276  41.128  1.00 25.00           C
ATOM     74  CA  ARG    74       6.106  31.542  41.554  1.00 25.00           C
ATOM     75  CA  ILE    75       7.072  28.286  43.321  1.00 25.00           C
ATOM     76  CA  SER    76       8.375  26.115  40.445  1.00 25.00           C
ATOM     77  CA  THR    77       9.784  29.013  38.411  1.00 25.00           C
ATOM     78  CA  GLN    78       7.595  28.223  35.438  1.00 25.00           C
ATOM     79  CA  THR    79       3.938  27.009  35.465  1.00 25.00           C
ATOM     80  CA  THR    80       2.421  24.160  37.467  1.00 25.00           C
ATOM     81  CA  PRO    81       2.289  24.082  41.271  1.00 25.00           C
ATOM     82  CA  GLN    82       4.190  22.756  44.351  1.00 25.00           C
ATOM     83  CA  PRO    83       3.806  20.199  47.151  1.00 25.00           C
ATOM     84  CA  LEU    84       7.044  21.758  48.345  1.00 25.00           C
ATOM     85  CA  MET    85       7.806  19.006  50.836  1.00 25.00           C
ATOM     86  CA  ALA    86       8.737  15.345  51.168  1.00 25.00           C
ATOM     87  CA  VAL    87      11.614  16.136  53.490  1.00 25.00           C
ATOM     88  CA  PHE    88      11.835  14.173  56.752  1.00 25.00           C
ATOM     89  CA  ASP    89      14.384  11.719  58.074  1.00 25.00           C
TER
END
