
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS168_3-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          2.112
LGA    Q       6      Q       6          2.534
LGA    I       7      I       7          2.367
LGA    K       8      K       8          2.594
LGA    F       9      F       9          3.076
LGA    L      10      L      10          3.434
LGA    R      11      R      11          3.704
LGA    S      12      S      12          3.622
LGA    L      13      L      13          3.493
LGA    R      14      R      14          3.007
LGA    E      15      E      15          4.518
LGA    R      16      R      16          4.493
LGA    K      17      K      17          4.598
LGA    Y      18      Y      18           #
LGA    R      19      R      19           #
LGA    L      20      L      20          4.711
LGA    R      21      R      21          2.589
LGA    E      22      E      22          3.007
LGA    Q      23      Q      23          1.946
LGA    A      24      A      24          1.230
LGA    F      25      F      25          2.443
LGA    A      26      A      26          4.658
LGA    V      27      V      27          2.827
LGA    E      28      E      28          2.911
LGA    G      29      G      29          2.752
LGA    P      30      P      30          3.151
LGA    K      31      K      31          3.645
LGA    L      32      L      32          3.291
LGA    V      33      V      33          2.391
LGA    G      34      G      34          2.077
LGA    E      35      E      35          2.215
LGA    M      36      M      36          1.455
LGA    L      37      L      37          2.030
LGA    P      38      P      38          2.898
LGA    F      39      F      39          2.864
LGA    Y      40      Y      40          2.375
LGA    R      41      R      41          1.032
LGA    C      42      C      42          2.229
LGA    R      43      R      43          1.599
LGA    M      44      M      44          1.888
LGA    L      45      L      45          3.946
LGA    V      46      V      46          3.070
LGA    G      47      G      47           #
LGA    T      48      -       -           -
LGA    A      49      T      48          3.690
LGA    A      50      A      49          3.042
LGA    M      51      A      50          2.132
LGA    L      52      M      51          2.440
LGA    R      53      L      52          2.268
LGA    A      54      R      53          0.909
LGA    V      55      A      54          1.288
LGA    S      56      V      55          1.909
LGA    T      57      S      56          2.509
LGA    P      58      -       -           -
LGA    H      59      -       -           -
LGA    D      60      T      57          3.449
LGA    A      61      P      58          3.782
LGA    E      62      H      59          1.887
LGA    -       -      D      60           -
LGA    V      63      A      61          3.215
LGA    V      64      E      62          3.399
LGA    E      65      V      63          2.193
LGA    L      66      V      64           #
LGA    P      67      E      65          4.784
LGA    E      68      L      66          2.520
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    S      69      S      69          4.392
LGA    F      70      F      70          2.812
LGA    D      71      D      71          4.858
LGA    F      72      F      72          1.750
LGA    K      73      K      73          2.258
LGA    R      74      R      74          0.992
LGA    I      75      I      75          1.683
LGA    S      76      S      76          2.141
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    T      77      T      79          4.047
LGA    Q      78      T      80          2.354
LGA    T      79      P      81          4.760
LGA    T      80      Q      82          2.403
LGA    P      81      P      83          2.014
LGA    Q      82      L      84          3.387
LGA    P      83      M      85          1.762
LGA    L      84      A      86          3.120
LGA    M      85      V      87           #
LGA    A      86      -       -           -
LGA    V      87      F      88           #
LGA    F      88      D      89           #
LGA    D      89      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     73    2.98    69.86     48.076     2.373

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.992851 * X  +  -0.093400 * Y  +   0.074319 * Z  +  18.113142
  Y_new =  -0.068273 * X  +  -0.066340 * Y  +  -0.995459 * Z  +  12.653564
  Z_new =   0.097906 * X  +  -0.993416 * Y  +   0.059489 * Z  +  43.115131 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.510985    1.630608  [ DEG:   -86.5731     93.4269 ]
  Theta =  -0.098063   -3.043529  [ DEG:    -5.6186   -174.3814 ]
  Phi   =  -3.072936    0.068657  [ DEG:  -176.0663      3.9337 ]
 
# 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_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS168_3-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   73   2.98   69.86  48.076
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS168_3-D1
PFRMAT TS
TARGET T0378
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      18.787  42.274  60.090  1.00 25.00           C
ATOM      2  CA  LEU     2      15.066  41.461  60.381  1.00 25.00           C
ATOM      3  CA  SER     3      12.442  40.644  57.672  1.00 25.00           C
ATOM      4  CA  ALA     4       8.716  39.758  57.878  1.00 25.00           C
ATOM      5  CA  ASN     5       9.894  36.390  56.731  1.00 25.00           C
ATOM      6  CA  GLN     6       8.883  33.117  55.021  1.00 25.00           C
ATOM      7  CA  ILE     7       9.755  34.604  51.602  1.00 25.00           C
ATOM      8  CA  LYS     8      13.163  35.732  52.933  1.00 25.00           C
ATOM      9  CA  PHE     9      13.808  32.223  54.325  1.00 25.00           C
ATOM     10  CA  LEU    10      12.875  30.684  50.945  1.00 25.00           C
ATOM     11  CA  ARG    11      15.255  33.098  49.162  1.00 25.00           C
ATOM     12  CA  SER    12      18.061  32.169  51.596  1.00 25.00           C
ATOM     13  CA  LEU    13      17.408  28.448  50.968  1.00 25.00           C
ATOM     14  CA  ARG    14      17.528  29.040  47.187  1.00 25.00           C
ATOM     15  CA  GLU    15      20.840  30.925  47.562  1.00 25.00           C
ATOM     16  CA  ARG    16      22.269  28.049  49.648  1.00 25.00           C
ATOM     17  CA  LYS    17      24.668  29.879  52.034  1.00 25.00           C
ATOM     18  CA  TYR    18      24.445  26.873  54.353  1.00 25.00           C
ATOM     19  CA  ARG    19      20.828  27.579  55.301  1.00 25.00           C
ATOM     20  CA  LEU    20      21.153  25.853  58.611  1.00 25.00           C
ATOM     21  CA  ARG    21      19.207  23.385  60.720  1.00 25.00           C
ATOM     22  CA  GLU    22      15.397  23.089  60.994  1.00 25.00           C
ATOM     23  CA  GLN    23      15.181  22.107  57.307  1.00 25.00           C
ATOM     24  CA  ALA    24      13.078  21.675  54.098  1.00 25.00           C
ATOM     25  CA  PHE    25      10.752  20.256  51.432  1.00 25.00           C
ATOM     26  CA  ALA    26       8.066  17.894  50.133  1.00 25.00           C
ATOM     27  CA  VAL    27       7.337  17.097  46.508  1.00 25.00           C
ATOM     28  CA  GLU    28       6.605  18.157  42.914  1.00 25.00           C
ATOM     29  CA  GLY    29       3.744  17.257  40.598  1.00 25.00           C
ATOM     30  CA  PRO    30       0.863  14.753  40.396  1.00 25.00           C
ATOM     31  CA  LYS    31       1.210  10.950  40.680  1.00 25.00           C
ATOM     32  CA  LEU    32       4.574  11.365  42.462  1.00 25.00           C
ATOM     33  CA  VAL    33       3.006  13.879  44.889  1.00 25.00           C
ATOM     34  CA  GLY    34       0.134  11.445  45.593  1.00 25.00           C
ATOM     35  CA  GLU    35       2.647   8.631  46.250  1.00 25.00           C
ATOM     36  CA  MET    36       4.594  10.896  48.648  1.00 25.00           C
ATOM     37  CA  LEU    37       1.352  11.778  50.486  1.00 25.00           C
ATOM     38  CA  PRO    38       0.478   8.061  50.779  1.00 25.00           C
ATOM     39  CA  PHE    39       3.763   7.904  52.784  1.00 25.00           C
ATOM     40  CA  TYR    40       5.628  11.136  53.685  1.00 25.00           C
ATOM     41  CA  ARG    41       6.094  13.838  56.336  1.00 25.00           C
ATOM     42  CA  CYS    42       6.947  17.546  55.793  1.00 25.00           C
ATOM     43  CA  ARG    43       5.761  21.141  55.424  1.00 25.00           C
ATOM     44  CA  MET    44       3.849  22.886  52.627  1.00 25.00           C
ATOM     45  CA  LEU    45       3.651  26.103  50.660  1.00 25.00           C
ATOM     46  CA  VAL    46       1.200  28.836  49.834  1.00 25.00           C
ATOM     47  CA  GLY    47      -2.492  29.271  50.571  1.00 25.00           C
ATOM     48  CA  THR    48      -5.991  29.065  49.180  1.00 25.00           C
ATOM     49  CA  ALA    49      -7.705  27.406  46.166  1.00 25.00           C
ATOM     50  CA  ALA    50     -10.623  25.036  46.891  1.00 25.00           C
ATOM     51  CA  MET    51      -9.769  22.989  43.768  1.00 25.00           C
ATOM     52  CA  LEU    52      -6.106  22.791  44.870  1.00 25.00           C
ATOM     53  CA  ARG    53      -7.192  21.624  48.353  1.00 25.00           C
ATOM     54  CA  ALA    54      -9.437  18.948  46.784  1.00 25.00           C
ATOM     55  CA  VAL    55      -6.532  17.763  44.589  1.00 25.00           C
ATOM     56  CA  SER    56      -4.255  17.570  47.663  1.00 25.00           C
ATOM     57  CA  THR    57      -6.912  15.542  49.533  1.00 25.00           C
ATOM     58  CA  PRO    58     -10.004  15.007  51.743  1.00 25.00           C
ATOM     59  CA  HIS    59      -8.251  16.586  54.727  1.00 25.00           C
ATOM     60  CA  ASP    60      -5.348  14.088  54.591  1.00 25.00           C
ATOM     61  CA  ALA    61      -4.184  15.776  57.803  1.00 25.00           C
ATOM     62  CA  GLU    62      -0.501  16.605  57.790  1.00 25.00           C
ATOM     63  CA  VAL    63       1.095  19.229  55.463  1.00 25.00           C
ATOM     64  CA  VAL    64      -0.874  22.459  55.126  1.00 25.00           C
ATOM     65  CA  GLU    65      -2.034  24.372  52.045  1.00 25.00           C
ATOM     66  CA  LEU    66      -1.066  24.367  48.314  1.00 25.00           C
ATOM     67  CA  PRO    67      -2.202  26.877  45.681  1.00 25.00           C
ATOM     68  CA  GLU    68      -2.479  30.519  44.683  1.00 25.00           C
ATOM     69  CA  SER    69      -0.936  32.272  41.697  1.00 25.00           C
ATOM     70  CA  PHE    70       1.585  35.107  42.214  1.00 25.00           C
ATOM     71  CA  ASP    71       3.274  33.124  45.023  1.00 25.00           C
ATOM     72  CA  PHE    72       3.471  30.040  42.761  1.00 25.00           C
ATOM     73  CA  LYS    73       5.020  32.156  39.970  1.00 25.00           C
ATOM     74  CA  ARG    74       7.590  33.568  42.432  1.00 25.00           C
ATOM     75  CA  ILE    75       8.455  30.024  43.600  1.00 25.00           C
ATOM     76  CA  SER    76       7.761  27.288  41.069  1.00 25.00           C
ATOM     77  CA  THR    77       9.302  28.862  37.995  1.00 25.00           C
ATOM     78  CA  GLN    78       6.238  28.385  35.776  1.00 25.00           C
ATOM     79  CA  THR    79       2.858  27.951  34.148  1.00 25.00           C
ATOM     80  CA  THR    80       1.815  25.210  36.646  1.00 25.00           C
ATOM     81  CA  PRO    81       2.274  25.433  40.402  1.00 25.00           C
ATOM     82  CA  GLN    82       3.811  22.312  42.034  1.00 25.00           C
ATOM     83  CA  PRO    83       3.473  22.020  45.852  1.00 25.00           C
ATOM     84  CA  LEU    84       7.045  21.952  47.061  1.00 25.00           C
ATOM     85  CA  MET    85      10.599  20.683  46.401  1.00 25.00           C
ATOM     86  CA  ALA    86      12.623  17.666  47.413  1.00 25.00           C
ATOM     87  CA  VAL    87      12.717  14.967  50.066  1.00 25.00           C
ATOM     88  CA  PHE    88      11.157  13.191  53.068  1.00 25.00           C
ATOM     89  CA  ASP    89      14.312  11.603  54.564  1.00 25.00           C
TER
END
