
#######################################################
#                                                     #
#                        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 T0340TS168_5
# Molecule2: number of CA atoms   90 (  685),  selected   90 , name T0340.pdb
# PARAMETERS: T0340TS168_5.T0340.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           #
LGA    M       2      M       2          1.723
LGA    L       3      L       3          0.914
LGA    R       4      R       4          1.128
LGA    P       5      P       5          1.848
LGA    R       6      R       6          2.386
LGA    L       7      L       7          2.158
LGA    C       8      C       8          1.341
LGA    H       9      H       9          0.692
LGA    L      10      L      10          0.428
LGA    R      11      R      11          1.964
LGA    K      12      K      12          1.070
LGA    G      13      G      13          2.165
LGA    P      14      P      14          2.551
LGA    Q      15      Q      15          1.493
LGA    G      16      G      16          0.626
LGA    Y      17      Y      17          1.011
LGA    G      18      G      18          0.969
LGA    F      19      F      19          2.082
LGA    N      20      N      20          1.658
LGA    L      21      L      21          1.290
LGA    H      22      H      22          1.430
LGA    S      23      S      23          1.569
LGA    D      24      D      24          2.952
LGA    K      25      K      25          4.392
LGA    S      26      S      26          6.635
LGA    R      27      R      27          2.898
LGA    P      28      P      28          2.001
LGA    G      29      G      29          1.070
LGA    Q      30      Q      30          0.939
LGA    Y      31      Y      31          0.434
LGA    I      32      I      32          0.607
LGA    R      33      R      33          1.114
LGA    S      34      S      34          1.400
LGA    V      35      V      35          1.542
LGA    D      36      D      36          1.406
LGA    P      37      P      37          1.339
LGA    G      38      G      38          1.906
LGA    S      39      S      39          1.232
LGA    P      40      P      40          1.473
LGA    A      41      A      41          1.061
LGA    A      42      A      42          1.059
LGA    R      43      R      43          1.576
LGA    S      44      S      44          2.440
LGA    G      45      G      45          1.051
LGA    L      46      L      46          0.502
LGA    R      47      R      47          0.983
LGA    A      48      A      48          0.777
LGA    Q      49      Q      49          2.155
LGA    D      50      D      50          1.435
LGA    R      51      R      51          1.293
LGA    L      52      L      52          1.518
LGA    I      53      I      53          1.786
LGA    E      54      E      54          1.949
LGA    V      55      V      55          1.735
LGA    N      56      N      56          2.069
LGA    G      57      G      57          1.902
LGA    Q      58      Q      58          2.030
LGA    N      59      N      59          2.885
LGA    V      60      V      60          1.099
LGA    E      61      E      61          1.622
LGA    G      62      G      62          1.699
LGA    L      63      L      63          2.463
LGA    R      64      R      64          3.134
LGA    H      65      H      65          2.379
LGA    A      66      A      66          1.862
LGA    E      67      E      67          1.983
LGA    V      68      V      68          2.257
LGA    V      69      V      69          1.676
LGA    A      70      A      70          1.393
LGA    S      71      S      71          1.842
LGA    I      72      I      72          1.788
LGA    K      73      K      73          1.169
LGA    A      74      A      74          1.744
LGA    R      75      R      75          3.461
LGA    E      76      E      76          3.339
LGA    D      77      D      77          1.711
LGA    E      78      E      78          2.452
LGA    A      79      A      79          1.541
LGA    R      80      R      80          0.926
LGA    L      81      L      81          1.730
LGA    L      82      L      82          1.739
LGA    V      83      V      83          1.266
LGA    V      84      V      84          1.551
LGA    G      85      G      85          2.251
LGA    P      86      P      86          1.844
LGA    S      87      S      87          2.425
LGA    T      88      T      88          2.761
LGA    R      89      R      89          2.934
LGA    L      90      L      90           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     88    1.98   100.00     86.301     4.225

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.209487 * X  +   0.977110 * Y  +  -0.037029 * Z  +  10.048062
  Y_new =  -0.487550 * X  +   0.071552 * Y  +  -0.870158 * Z  +  25.823341
  Z_new =  -0.847591 * X  +   0.200340 * Y  +   0.491380 * Z  +   9.051276 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.387135   -2.754458  [ DEG:    22.1812   -157.8188 ]
  Theta =   1.011428    2.130164  [ DEG:    57.9506    122.0494 ]
  Phi   =  -1.164975    1.976618  [ DEG:   -66.7481    113.2519 ]
 
# 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: T0340TS168_5                                  
REMARK     2: T0340.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS168_5.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   88   1.98  100.00  86.301
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS168_5
PFRMAT TS
TARGET T0340
MODEL 5
PARENT N/A
ATOM      1  CA  SER     1      15.401  45.491   3.146  1.00 25.00           C
ATOM      2  CA  MET     2      14.103  44.971   6.656  1.00 25.00           C
ATOM      3  CA  LEU     3      14.182  41.326   5.674  1.00 25.00           C
ATOM      4  CA  ARG     4      14.492  40.578   9.448  1.00 25.00           C
ATOM      5  CA  PRO     5      12.493  37.334   9.888  1.00 25.00           C
ATOM      6  CA  ARG     6       8.833  36.636   9.490  1.00 25.00           C
ATOM      7  CA  LEU     7       8.646  34.402  12.616  1.00 25.00           C
ATOM      8  CA  CYS     8       5.895  32.137  13.944  1.00 25.00           C
ATOM      9  CA  HIS     9       5.311  30.157  17.140  1.00 25.00           C
ATOM     10  CA  LEU    10       3.727  26.878  16.259  1.00 25.00           C
ATOM     11  CA  ARG    11       0.376  25.972  17.768  1.00 25.00           C
ATOM     12  CA  LYS    12       2.033  22.674  18.796  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.129  20.737  19.719  1.00 25.00           C
ATOM     14  CA  PRO    14      -1.457  16.934  19.135  1.00 25.00           C
ATOM     15  CA  GLN    15      -1.651  15.864  15.481  1.00 25.00           C
ATOM     16  CA  GLY    16       0.699  18.771  14.767  1.00 25.00           C
ATOM     17  CA  TYR    17       1.151  22.305  13.492  1.00 25.00           C
ATOM     18  CA  GLY    18       1.011  21.216   9.835  1.00 25.00           C
ATOM     19  CA  PHE    19       4.546  21.946   8.681  1.00 25.00           C
ATOM     20  CA  ASN    20       6.071  19.351   6.328  1.00 25.00           C
ATOM     21  CA  LEU    21       9.776  20.400   6.235  1.00 25.00           C
ATOM     22  CA  HIS    22      11.596  18.956   3.179  1.00 25.00           C
ATOM     23  CA  SER    23      13.290  19.341  -0.216  1.00 25.00           C
ATOM     24  CA  ASP    24      16.670  18.299  -1.719  1.00 25.00           C
ATOM     25  CA  LYS    25      20.036  17.078  -3.003  1.00 25.00           C
ATOM     26  CA  SER    26      23.055  19.294  -2.296  1.00 25.00           C
ATOM     27  CA  ARG    27      21.339  22.645  -2.017  1.00 25.00           C
ATOM     28  CA  PRO    28      21.666  23.810   1.546  1.00 25.00           C
ATOM     29  CA  GLY    29      17.995  23.001   2.042  1.00 25.00           C
ATOM     30  CA  GLN    30      14.977  23.613   4.216  1.00 25.00           C
ATOM     31  CA  TYR    31      11.356  24.298   3.123  1.00 25.00           C
ATOM     32  CA  ILE    32       7.717  24.721   4.265  1.00 25.00           C
ATOM     33  CA  ARG    33       6.561  22.274   1.591  1.00 25.00           C
ATOM     34  CA  SER    34       2.838  22.291   2.505  1.00 25.00           C
ATOM     35  CA  VAL    35       0.358  23.412   5.169  1.00 25.00           C
ATOM     36  CA  ASP    36      -3.078  22.083   5.998  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.618  24.862   6.816  1.00 25.00           C
ATOM     38  CA  GLY    38      -7.154  25.291  10.263  1.00 25.00           C
ATOM     39  CA  SER    39      -3.865  23.874  11.558  1.00 25.00           C
ATOM     40  CA  PRO    40      -2.077  26.746  13.405  1.00 25.00           C
ATOM     41  CA  ALA    41       0.860  27.259  11.002  1.00 25.00           C
ATOM     42  CA  ALA    42      -1.368  29.338   8.682  1.00 25.00           C
ATOM     43  CA  ARG    43      -2.515  31.466  11.652  1.00 25.00           C
ATOM     44  CA  SER    44       0.813  33.006  12.688  1.00 25.00           C
ATOM     45  CA  GLY    45       2.479  32.779   9.294  1.00 25.00           C
ATOM     46  CA  LEU    46       4.445  29.838   7.936  1.00 25.00           C
ATOM     47  CA  ARG    47       3.900  31.178   4.431  1.00 25.00           C
ATOM     48  CA  ALA    48       4.889  28.506   1.945  1.00 25.00           C
ATOM     49  CA  GLN    49       8.008  30.380   0.807  1.00 25.00           C
ATOM     50  CA  ASP    50       9.342  30.624   4.332  1.00 25.00           C
ATOM     51  CA  ARG    51      12.727  29.190   3.178  1.00 25.00           C
ATOM     52  CA  LEU    52      13.030  27.601   6.606  1.00 25.00           C
ATOM     53  CA  ILE    53      15.898  27.538   9.162  1.00 25.00           C
ATOM     54  CA  GLU    54      15.664  26.353  12.812  1.00 25.00           C
ATOM     55  CA  VAL    55      15.665  24.727  16.214  1.00 25.00           C
ATOM     56  CA  ASN    56      15.375  28.068  18.068  1.00 25.00           C
ATOM     57  CA  GLY    57      18.732  29.781  17.934  1.00 25.00           C
ATOM     58  CA  GLN    58      20.833  27.568  15.692  1.00 25.00           C
ATOM     59  CA  ASN    59      20.443  24.168  13.993  1.00 25.00           C
ATOM     60  CA  VAL    60      20.036  23.960  10.185  1.00 25.00           C
ATOM     61  CA  GLU    61      21.555  23.877   6.671  1.00 25.00           C
ATOM     62  CA  GLY    62      23.398  20.697   7.667  1.00 25.00           C
ATOM     63  CA  LEU    63      20.969  17.796   7.143  1.00 25.00           C
ATOM     64  CA  ARG    64      18.195  16.826   4.638  1.00 25.00           C
ATOM     65  CA  HIS    65      14.762  15.245   5.184  1.00 25.00           C
ATOM     66  CA  ALA    66      14.556  12.881   8.190  1.00 25.00           C
ATOM     67  CA  GLU    67      16.846  15.199  10.201  1.00 25.00           C
ATOM     68  CA  VAL    68      14.656  18.203   9.279  1.00 25.00           C
ATOM     69  CA  VAL    69      11.526  16.286  10.372  1.00 25.00           C
ATOM     70  CA  ALA    70      13.203  15.393  13.697  1.00 25.00           C
ATOM     71  CA  SER    71      14.150  19.065  14.233  1.00 25.00           C
ATOM     72  CA  ILE    72      10.544  20.128  13.506  1.00 25.00           C
ATOM     73  CA  LYS    73       9.248  17.533  16.006  1.00 25.00           C
ATOM     74  CA  ALA    74      11.703  18.816  18.649  1.00 25.00           C
ATOM     75  CA  ARG    75      11.389  22.059  20.648  1.00 25.00           C
ATOM     76  CA  GLU    76       8.811  20.151  22.694  1.00 25.00           C
ATOM     77  CA  ASP    77       5.688  22.318  22.824  1.00 25.00           C
ATOM     78  CA  GLU    78       4.979  25.897  21.862  1.00 25.00           C
ATOM     79  CA  ALA    79       7.491  25.227  19.146  1.00 25.00           C
ATOM     80  CA  ARG    80       9.813  28.103  18.065  1.00 25.00           C
ATOM     81  CA  LEU    81       9.896  27.309  14.389  1.00 25.00           C
ATOM     82  CA  LEU    82      11.911  29.972  12.575  1.00 25.00           C
ATOM     83  CA  VAL    83      13.101  31.774   9.426  1.00 25.00           C
ATOM     84  CA  VAL    84      14.027  33.936   6.523  1.00 25.00           C
ATOM     85  CA  GLY    85      13.021  34.490   2.923  1.00 25.00           C
ATOM     86  CA  PRO    86      13.389  34.099  -0.821  1.00 25.00           C
ATOM     87  CA  SER    87      13.869  35.494  -4.360  1.00 25.00           C
ATOM     88  CA  THR    88      16.911  36.497  -6.391  1.00 25.00           C
ATOM     89  CA  ARG    89      20.517  37.129  -5.359  1.00 25.00           C
ATOM     90  CA  LEU    90      22.871  36.818  -2.420  1.00 25.00           C
TER
END
