
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS168_4-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    N       5      A       4          2.930
LGA    -       -      N       5           -
LGA    Q       6      Q       6          1.606
LGA    I       7      I       7          1.882
LGA    K       8      K       8          1.736
LGA    F       9      F       9          1.280
LGA    L      10      L      10          2.576
LGA    R      11      R      11          3.239
LGA    S      12      S      12          2.243
LGA    L      13      L      13          2.198
LGA    R      14      R      14          3.353
LGA    E      15      E      15          4.078
LGA    R      16      R      16          3.970
LGA    K      17      K      17          3.091
LGA    Y      18      Y      18          4.656
LGA    R      19      R      19          4.336
LGA    L      20      L      20          1.517
LGA    R      21      R      21          4.125
LGA    E      22      E      22          2.922
LGA    Q      23      Q      23          2.436
LGA    A      24      A      24          1.349
LGA    F      25      F      25          1.450
LGA    A      26      A      26          1.047
LGA    V      27      V      27          2.383
LGA    E      28      E      28          3.019
LGA    G      29      G      29          2.408
LGA    P      30      P      30          1.456
LGA    K      31      K      31          2.391
LGA    L      32      L      32          1.490
LGA    V      33      V      33          1.118
LGA    G      34      G      34          1.822
LGA    E      35      E      35          2.145
LGA    M      36      M      36          1.846
LGA    L      37      L      37          1.437
LGA    P      38      P      38          1.216
LGA    F      39      F      39          1.160
LGA    Y      40      Y      40          1.838
LGA    R      41      R      41          2.503
LGA    C      42      C      42          1.388
LGA    R      43      R      43          2.351
LGA    M      44      M      44          3.360
LGA    L      45      L      45          3.901
LGA    V      46      V      46          1.419
LGA    G      47      G      47          4.172
LGA    T      48      T      48          3.264
LGA    A      49      A      49          1.795
LGA    A      50      A      50          1.957
LGA    M      51      M      51          1.819
LGA    L      52      L      52          1.811
LGA    R      53      R      53          1.507
LGA    A      54      A      54          1.702
LGA    V      55      V      55          2.150
LGA    S      56      S      56          3.531
LGA    T      57      -       -           -
LGA    P      58      -       -           -
LGA    H      59      -       -           -
LGA    D      60      T      57          5.606
LGA    A      61      P      58          2.310
LGA    E      62      H      59          1.963
LGA    -       -      D      60           -
LGA    V      63      A      61          3.279
LGA    -       -      E      62           -
LGA    V      64      V      63          2.674
LGA    E      65      V      64           #
LGA    L      66      E      65           #
LGA    P      67      L      66          5.001
LGA    E      68      P      67          4.180
LGA    -       -      E      68           -
LGA    S      69      S      69          3.975
LGA    F      70      F      70          3.929
LGA    D      71      D      71          4.496
LGA    F      72      F      72          1.897
LGA    K      73      K      73          3.038
LGA    R      74      R      74          3.034
LGA    I      75      I      75          3.549
LGA    S      76      S      76          3.581
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    T      77      T      79          1.882
LGA    Q      78      T      80          2.516
LGA    T      79      P      81          3.469
LGA    T      80      Q      82          3.546
LGA    P      81      P      83           #
LGA    Q      82      L      84          4.480
LGA    P      83      M      85          4.245
LGA    L      84      A      86           #
LGA    M      85      V      87           -
LGA    A      86      F      88           #
LGA    V      87      D      89           #
LGA    F      88      -       -           -
LGA    D      89      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     73    2.89    83.56     49.870     2.443

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.938930 * X  +   0.255052 * Y  +  -0.230998 * Z  +  17.507833
  Y_new =   0.247673 * X  +   0.034862 * Y  +  -0.968216 * Z  +  10.731833
  Z_new =  -0.238892 * X  +  -0.966299 * Y  +  -0.095902 * Z  +  42.569233 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.669719    1.471874  [ DEG:   -95.6679     84.3321 ]
  Theta =   0.241225    2.900368  [ DEG:    13.8212    166.1788 ]
  Phi   =   2.883685   -0.257908  [ DEG:   165.2230    -14.7770 ]
 
# 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_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS168_4-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   2.89   83.56  49.870
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS168_4-D1
PFRMAT TS
TARGET T0378
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       8.002  37.160  66.384  1.00 25.00           C
ATOM      2  CA  LEU     2       7.130  34.452  63.833  1.00 25.00           C
ATOM      3  CA  SER     3       8.174  36.830  61.082  1.00 25.00           C
ATOM      4  CA  ALA     4       7.622  38.989  57.993  1.00 25.00           C
ATOM      5  CA  ASN     5       6.851  36.026  55.694  1.00 25.00           C
ATOM      6  CA  GLN     6       6.061  33.415  53.006  1.00 25.00           C
ATOM      7  CA  ILE     7       8.115  35.391  50.449  1.00 25.00           C
ATOM      8  CA  LYS     8      11.044  35.579  52.909  1.00 25.00           C
ATOM      9  CA  PHE     9      10.826  31.801  53.497  1.00 25.00           C
ATOM     10  CA  LEU    10      10.825  31.188  49.717  1.00 25.00           C
ATOM     11  CA  ARG    11      13.897  33.442  49.327  1.00 25.00           C
ATOM     12  CA  SER    12      15.682  31.535  52.127  1.00 25.00           C
ATOM     13  CA  LEU    13      14.842  28.206  50.428  1.00 25.00           C
ATOM     14  CA  ARG    14      16.202  29.532  47.102  1.00 25.00           C
ATOM     15  CA  GLU    15      19.421  30.664  48.840  1.00 25.00           C
ATOM     16  CA  ARG    16      19.797  27.208  50.448  1.00 25.00           C
ATOM     17  CA  LYS    17      23.058  28.649  51.757  1.00 25.00           C
ATOM     18  CA  TYR    18      23.231  27.577  55.441  1.00 25.00           C
ATOM     19  CA  ARG    19      21.741  24.218  54.403  1.00 25.00           C
ATOM     20  CA  LEU    20      20.620  22.318  57.499  1.00 25.00           C
ATOM     21  CA  ARG    21      19.446  21.421  60.953  1.00 25.00           C
ATOM     22  CA  GLU    22      16.010  21.529  59.412  1.00 25.00           C
ATOM     23  CA  GLN    23      14.370  18.576  57.661  1.00 25.00           C
ATOM     24  CA  ALA    24      14.238  20.027  54.146  1.00 25.00           C
ATOM     25  CA  PHE    25      13.265  19.279  50.598  1.00 25.00           C
ATOM     26  CA  ALA    26      10.647  20.629  48.123  1.00 25.00           C
ATOM     27  CA  VAL    27       6.916  20.121  47.421  1.00 25.00           C
ATOM     28  CA  GLU    28       5.226  18.625  44.304  1.00 25.00           C
ATOM     29  CA  GLY    29       4.204  17.645  40.805  1.00 25.00           C
ATOM     30  CA  PRO    30       0.913  16.142  42.150  1.00 25.00           C
ATOM     31  CA  LYS    31       2.148  12.523  41.943  1.00 25.00           C
ATOM     32  CA  LEU    32       5.377  13.495  43.758  1.00 25.00           C
ATOM     33  CA  VAL    33       3.344  15.246  46.489  1.00 25.00           C
ATOM     34  CA  GLY    34       1.144  12.136  46.881  1.00 25.00           C
ATOM     35  CA  GLU    35       4.265   9.935  47.168  1.00 25.00           C
ATOM     36  CA  MET    36       5.704  12.279  49.831  1.00 25.00           C
ATOM     37  CA  LEU    37       2.408  12.137  51.774  1.00 25.00           C
ATOM     38  CA  PRO    38       2.436   8.311  51.590  1.00 25.00           C
ATOM     39  CA  PHE    39       5.668   8.830  53.590  1.00 25.00           C
ATOM     40  CA  TYR    40       6.782  11.850  55.511  1.00 25.00           C
ATOM     41  CA  ARG    41       4.090  14.289  56.777  1.00 25.00           C
ATOM     42  CA  CYS    42       5.649  16.855  54.443  1.00 25.00           C
ATOM     43  CA  ARG    43       4.917  20.579  54.720  1.00 25.00           C
ATOM     44  CA  MET    44       4.336  22.149  51.368  1.00 25.00           C
ATOM     45  CA  LEU    45       3.618  24.759  48.723  1.00 25.00           C
ATOM     46  CA  VAL    46       0.791  27.294  49.236  1.00 25.00           C
ATOM     47  CA  GLY    47      -2.946  28.090  49.176  1.00 25.00           C
ATOM     48  CA  THR    48      -6.051  28.039  46.882  1.00 25.00           C
ATOM     49  CA  ALA    49      -9.288  26.419  45.685  1.00 25.00           C
ATOM     50  CA  ALA    50      -9.770  23.610  43.128  1.00 25.00           C
ATOM     51  CA  MET    51      -6.113  22.556  43.557  1.00 25.00           C
ATOM     52  CA  LEU    52      -6.545  22.519  47.363  1.00 25.00           C
ATOM     53  CA  ARG    53      -9.697  20.373  47.008  1.00 25.00           C
ATOM     54  CA  ALA    54      -7.815  17.943  44.724  1.00 25.00           C
ATOM     55  CA  VAL    55      -4.962  17.721  47.268  1.00 25.00           C
ATOM     56  CA  SER    56      -7.480  17.016  50.067  1.00 25.00           C
ATOM     57  CA  THR    57      -9.104  14.270  47.946  1.00 25.00           C
ATOM     58  CA  PRO    58      -8.827  11.848  50.869  1.00 25.00           C
ATOM     59  CA  HIS    59      -7.617  12.890  54.299  1.00 25.00           C
ATOM     60  CA  ASP    60      -4.212  12.251  55.904  1.00 25.00           C
ATOM     61  CA  ALA    61      -3.522  15.793  54.751  1.00 25.00           C
ATOM     62  CA  GLU    62      -0.776  16.151  57.383  1.00 25.00           C
ATOM     63  CA  VAL    63       0.063  19.346  55.402  1.00 25.00           C
ATOM     64  CA  VAL    64      -0.620  22.526  53.363  1.00 25.00           C
ATOM     65  CA  GLU    65      -1.395  22.314  49.634  1.00 25.00           C
ATOM     66  CA  LEU    66      -1.037  23.514  46.001  1.00 25.00           C
ATOM     67  CA  PRO    67      -1.243  27.022  44.546  1.00 25.00           C
ATOM     68  CA  GLU    68      -2.107  30.667  43.844  1.00 25.00           C
ATOM     69  CA  SER    69      -0.755  33.571  41.846  1.00 25.00           C
ATOM     70  CA  PHE    70       2.593  35.416  41.628  1.00 25.00           C
ATOM     71  CA  ASP    71       4.032  33.183  44.386  1.00 25.00           C
ATOM     72  CA  PHE    72       2.818  30.062  42.527  1.00 25.00           C
ATOM     73  CA  LYS    73       4.435  31.329  39.295  1.00 25.00           C
ATOM     74  CA  ARG    74       7.722  31.959  41.157  1.00 25.00           C
ATOM     75  CA  ILE    75       7.597  28.423  42.623  1.00 25.00           C
ATOM     76  CA  SER    76       8.108  27.461  39.021  1.00 25.00           C
ATOM     77  CA  THR    77       9.222  27.831  35.418  1.00 25.00           C
ATOM     78  CA  GLN    78       6.022  29.246  34.013  1.00 25.00           C
ATOM     79  CA  THR    79       3.034  27.600  35.784  1.00 25.00           C
ATOM     80  CA  THR    80       1.646  24.062  35.249  1.00 25.00           C
ATOM     81  CA  PRO    81       4.125  21.915  37.178  1.00 25.00           C
ATOM     82  CA  GLN    82       4.379  23.046  40.830  1.00 25.00           C
ATOM     83  CA  PRO    83       7.380  23.333  43.162  1.00 25.00           C
ATOM     84  CA  LEU    84       9.313  20.096  42.960  1.00 25.00           C
ATOM     85  CA  MET    85       9.950  16.756  44.773  1.00 25.00           C
ATOM     86  CA  ALA    86       9.370  15.639  48.356  1.00 25.00           C
ATOM     87  CA  VAL    87      12.506  13.975  49.729  1.00 25.00           C
ATOM     88  CA  PHE    88      10.496  10.921  50.952  1.00 25.00           C
ATOM     89  CA  ASP    89      12.028   8.560  53.522  1.00 25.00           C
TER
END
