
#######################################################
#                                                     #
#                        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   82 (   82),  selected   82 , name T0340TS393_2-D1
# Molecule2: number of CA atoms   82 (  626),  selected   82 , name T0340_D1.pdb
# PARAMETERS: T0340TS393_2-D1.T0340_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       4      R       4          1.929
LGA    P       5      P       5          2.412
LGA    R       6      R       6          2.004
LGA    L       7      L       7          2.149
LGA    C       8      C       8          0.163
LGA    H       9      H       9          0.612
LGA    L      10      L      10          0.848
LGA    R      11      R      11          0.857
LGA    K      12      K      12          0.929
LGA    G      13      G      13          1.581
LGA    P      14      P      14          2.340
LGA    Q      15      Q      15          1.887
LGA    G      16      G      16          1.147
LGA    Y      17      Y      17          1.362
LGA    G      18      G      18          1.379
LGA    F      19      F      19          1.173
LGA    N      20      N      20          1.496
LGA    L      21      L      21          0.201
LGA    H      22      H      22          0.452
LGA    S      23      S      23          2.149
LGA    D      24      D      24          3.018
LGA    K      25      K      25          3.041
LGA    S      26      S      26          5.418
LGA    R      27      R      27          2.376
LGA    P      28      P      28          2.266
LGA    G      29      G      29          0.939
LGA    Q      30      Q      30          1.795
LGA    Y      31      Y      31          1.453
LGA    I      32      I      32          1.711
LGA    R      33      R      33          1.777
LGA    S      34      S      34          1.374
LGA    V      35      V      35          1.117
LGA    D      36      D      36          0.550
LGA    P      37      P      37          1.872
LGA    G      38      G      38          2.659
LGA    S      39      S      39          2.305
LGA    P      40      P      40          2.383
LGA    A      41      A      41          0.906
LGA    A      42      A      42          0.785
LGA    R      43      R      43          0.844
LGA    S      44      S      44          1.704
LGA    G      45      G      45          0.565
LGA    L      46      L      46          1.117
LGA    R      47      R      47          1.420
LGA    A      48      A      48          1.103
LGA    Q      49      Q      49          1.129
LGA    D      50      D      50          1.178
LGA    R      51      R      51          1.605
LGA    L      52      L      52          1.702
LGA    I      53      I      53          0.837
LGA    E      54      E      54          0.994
LGA    V      55      V      55          0.892
LGA    N      56      N      56          0.495
LGA    G      57      G      57          3.990
LGA    Q      58      Q      58          3.166
LGA    N      59      N      59          1.816
LGA    V      60      V      60          0.660
LGA    E      61      E      61          0.927
LGA    G      62      G      62          1.262
LGA    L      63      L      63          2.640
LGA    R      64      R      64          2.914
LGA    H      65      H      65          1.798
LGA    A      66      A      66          1.584
LGA    E      67      E      67          1.554
LGA    V      68      V      68          1.466
LGA    V      69      V      69          1.222
LGA    A      70      A      70          1.201
LGA    S      71      S      71          1.111
LGA    I      72      I      72          1.142
LGA    K      73      K      73          1.118
LGA    A      74      A      74          0.960
LGA    R      75      R      75          1.368
LGA    E      76      E      76          1.615
LGA    D      77      D      77          2.050
LGA    E      78      E      78          1.820
LGA    A      79      A      79          0.130
LGA    R      80      R      80          1.603
LGA    L      81      L      81          1.720
LGA    L      82      L      82          0.973
LGA    V      83      V      83          1.663
LGA    V      84      V      84          0.479
LGA    G      85      G      85          0.580

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   82   82    5.0     82    1.75   100.00     91.319     4.443

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.522712 * X  +  -0.179180 * Y  +   0.833466 * Z  +  10.049665
  Y_new =  -0.339494 * X  +  -0.853046 * Y  +  -0.396305 * Z  +  25.974079
  Z_new =   0.781995 * X  +  -0.490110 * Y  +   0.385067 * Z  +   9.079885 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.904852    2.236741  [ DEG:   -51.8442    128.1558 ]
  Theta =  -0.897860   -2.243733  [ DEG:   -51.4436   -128.5564 ]
  Phi   =  -2.565580    0.576013  [ DEG:  -146.9969     33.0031 ]
 
# 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_2-D1                               
REMARK     2: T0340_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS393_2-D1.T0340_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   82   82   5.0   82   1.75  100.00  91.319
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS393_2-D1
PFRMAT TS
TARGET T0340
MODEL 2
PARENT N/A
ATOM      4  CA  ARG     4      16.001  39.593   9.428  1.00 25.00           C
ATOM      5  CA  PRO     5      13.321  37.609  11.138  1.00 25.00           C
ATOM      6  CA  ARG     6       9.760  37.461   9.863  1.00 25.00           C
ATOM      7  CA  LEU     7       8.982  34.759  12.465  1.00 25.00           C
ATOM      8  CA  CYS     8       7.056  31.784  13.894  1.00 25.00           C
ATOM      9  CA  HIS     9       5.964  30.820  17.470  1.00 25.00           C
ATOM     10  CA  LEU    10       3.706  27.992  16.271  1.00 25.00           C
ATOM     11  CA  ARG    11       1.631  26.600  19.142  1.00 25.00           C
ATOM     12  CA  LYS    12       1.550  22.826  18.893  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.846  21.136  19.334  1.00 25.00           C
ATOM     14  CA  PRO    14      -2.339  17.425  19.920  1.00 25.00           C
ATOM     15  CA  GLN    15      -2.148  16.228  16.298  1.00 25.00           C
ATOM     16  CA  GLY    16       0.790  17.313  14.056  1.00 25.00           C
ATOM     17  CA  TYR    17       2.428  20.785  14.101  1.00 25.00           C
ATOM     18  CA  GLY    18       1.042  21.518  10.624  1.00 25.00           C
ATOM     19  CA  PHE    19       3.775  21.163   7.948  1.00 25.00           C
ATOM     20  CA  ASN    20       5.497  18.536   5.802  1.00 25.00           C
ATOM     21  CA  LEU    21       8.829  20.315   5.292  1.00 25.00           C
ATOM     22  CA  HIS    22      10.863  19.919   2.136  1.00 25.00           C
ATOM     23  CA  SER    23      13.747  20.980  -0.035  1.00 25.00           C
ATOM     24  CA  ASP    24      17.047  19.244  -0.711  1.00 25.00           C
ATOM     25  CA  LYS    25      18.944  17.695  -3.580  1.00 25.00           C
ATOM     26  CA  SER    26      22.097  19.791  -2.919  1.00 25.00           C
ATOM     27  CA  ARG    27      20.875  23.281  -1.885  1.00 25.00           C
ATOM     28  CA  PRO    28      21.867  23.778   1.753  1.00 25.00           C
ATOM     29  CA  GLY    29      18.200  24.600   2.504  1.00 25.00           C
ATOM     30  CA  GLN    30      16.126  23.160   5.358  1.00 25.00           C
ATOM     31  CA  TYR    31      12.969  24.409   3.708  1.00 25.00           C
ATOM     32  CA  ILE    32       9.363  25.409   4.629  1.00 25.00           C
ATOM     33  CA  ARG    33       6.795  23.819   2.328  1.00 25.00           C
ATOM     34  CA  SER    34       3.145  23.770   3.414  1.00 25.00           C
ATOM     35  CA  VAL    35       0.867  25.667   5.877  1.00 25.00           C
ATOM     36  CA  ASP    36      -2.050  23.221   6.055  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.702  24.143   6.448  1.00 25.00           C
ATOM     38  CA  GLY    38      -6.991  24.324  10.006  1.00 25.00           C
ATOM     39  CA  SER    39      -3.836  22.674  11.312  1.00 25.00           C
ATOM     40  CA  PRO    40      -2.923  26.133  12.539  1.00 25.00           C
ATOM     41  CA  ALA    41       0.639  26.615  11.216  1.00 25.00           C
ATOM     42  CA  ALA    42      -0.495  29.672   9.208  1.00 25.00           C
ATOM     43  CA  ARG    43      -2.179  31.126  12.326  1.00 25.00           C
ATOM     44  CA  SER    44       1.230  32.519  13.316  1.00 25.00           C
ATOM     45  CA  GLY    45       3.457  32.761  10.277  1.00 25.00           C
ATOM     46  CA  LEU    46       4.429  30.678   7.185  1.00 25.00           C
ATOM     47  CA  ARG    47       3.815  31.261   3.489  1.00 25.00           C
ATOM     48  CA  ALA    48       3.825  28.217   1.146  1.00 25.00           C
ATOM     49  CA  GLN    49       7.326  28.776  -0.340  1.00 25.00           C
ATOM     50  CA  ASP    50       8.765  30.108   2.881  1.00 25.00           C
ATOM     51  CA  ARG    51      12.525  29.383   3.017  1.00 25.00           C
ATOM     52  CA  LEU    52      13.678  28.506   6.499  1.00 25.00           C
ATOM     53  CA  ILE    53      16.869  28.963   8.488  1.00 25.00           C
ATOM     54  CA  GLU    54      16.275  27.887  12.105  1.00 25.00           C
ATOM     55  CA  VAL    55      15.481  25.866  15.267  1.00 25.00           C
ATOM     56  CA  ASN    56      14.328  26.946  18.755  1.00 25.00           C
ATOM     57  CA  GLY    57      17.466  25.148  19.944  1.00 25.00           C
ATOM     58  CA  GLN    58      19.394  23.351  17.180  1.00 25.00           C
ATOM     59  CA  ASN    59      20.827  25.390  14.231  1.00 25.00           C
ATOM     60  CA  VAL    60      19.726  24.326  10.732  1.00 25.00           C
ATOM     61  CA  GLU    61      21.110  25.593   7.402  1.00 25.00           C
ATOM     62  CA  GLY    62      23.144  22.379   7.326  1.00 25.00           C
ATOM     63  CA  LEU    63      21.038  19.337   6.443  1.00 25.00           C
ATOM     64  CA  ARG    64      18.495  17.109   4.765  1.00 25.00           C
ATOM     65  CA  HIS    65      14.868  16.624   5.627  1.00 25.00           C
ATOM     66  CA  ALA    66      14.790  13.705   8.105  1.00 25.00           C
ATOM     67  CA  GLU    67      16.979  15.686  10.545  1.00 25.00           C
ATOM     68  CA  VAL    68      14.644  18.705  10.227  1.00 25.00           C
ATOM     69  CA  VAL    69      11.614  16.464  10.905  1.00 25.00           C
ATOM     70  CA  ALA    70      13.349  15.011  13.995  1.00 25.00           C
ATOM     71  CA  SER    71      14.124  18.545  15.251  1.00 25.00           C
ATOM     72  CA  ILE    72      10.467  19.558  14.732  1.00 25.00           C
ATOM     73  CA  LYS    73       9.310  16.460  16.663  1.00 25.00           C
ATOM     74  CA  ALA    74      11.716  17.310  19.519  1.00 25.00           C
ATOM     75  CA  ARG    75       9.967  20.284  21.234  1.00 25.00           C
ATOM     76  CA  GLU    76       6.373  19.703  22.180  1.00 25.00           C
ATOM     77  CA  ASP    77       5.503  23.037  23.780  1.00 25.00           C
ATOM     78  CA  GLU    78       6.610  25.461  21.044  1.00 25.00           C
ATOM     79  CA  ALA    79       8.398  24.824  17.826  1.00 25.00           C
ATOM     80  CA  ARG    80      10.115  27.446  15.714  1.00 25.00           C
ATOM     81  CA  LEU    81      10.841  27.498  12.003  1.00 25.00           C
ATOM     82  CA  LEU    82      12.311  31.014  11.575  1.00 25.00           C
ATOM     83  CA  VAL    83      11.380  32.802   8.363  1.00 25.00           C
ATOM     84  CA  VAL    84      13.403  33.764   5.289  1.00 25.00           C
ATOM     85  CA  GLY    85      11.393  34.325   2.175  1.00 25.00           C
TER
END
