
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms   90 (  685),  selected   90 , name T0340.pdb
# PARAMETERS: T0340TS168_4.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          3.022
LGA    L       3      L       3          1.166
LGA    R       4      R       4          0.298
LGA    P       5      P       5          2.632
LGA    R       6      R       6          2.162
LGA    L       7      L       7          1.814
LGA    C       8      C       8          1.550
LGA    H       9      H       9          1.458
LGA    L      10      L      10          1.271
LGA    R      11      R      11          1.554
LGA    K      12      K      12          1.050
LGA    G      13      G      13          2.897
LGA    P      14      P      14          2.259
LGA    Q      15      Q      15          1.979
LGA    G      16      G      16          0.464
LGA    Y      17      Y      17          1.382
LGA    G      18      G      18          1.581
LGA    F      19      F      19          1.967
LGA    N      20      N      20          1.871
LGA    L      21      L      21          1.713
LGA    H      22      H      22          1.266
LGA    S      23      S      23          1.545
LGA    D      24      D      24          3.924
LGA    K      25      K      25          1.299
LGA    S      26      S      26          3.288
LGA    R      27      R      27          4.558
LGA    P      28      P      28          1.876
LGA    G      29      G      29          1.063
LGA    Q      30      Q      30          1.737
LGA    Y      31      Y      31          1.670
LGA    I      32      I      32          1.036
LGA    R      33      R      33          0.841
LGA    S      34      S      34          0.500
LGA    V      35      V      35          1.002
LGA    D      36      D      36          1.287
LGA    P      37      P      37          2.937
LGA    G      38      G      38          1.582
LGA    S      39      S      39          1.487
LGA    P      40      P      40          1.379
LGA    A      41      A      41          1.167
LGA    A      42      A      42          1.957
LGA    R      43      R      43          2.265
LGA    S      44      S      44          3.136
LGA    G      45      G      45          1.627
LGA    L      46      L      46          0.634
LGA    R      47      R      47          0.321
LGA    A      48      A      48          1.410
LGA    Q      49      Q      49          3.166
LGA    D      50      D      50          2.260
LGA    R      51      R      51          1.746
LGA    L      52      L      52          1.242
LGA    I      53      I      53          0.969
LGA    E      54      E      54          2.470
LGA    V      55      V      55          0.770
LGA    N      56      N      56          0.789
LGA    G      57      G      57          0.828
LGA    Q      58      Q      58          1.594
LGA    N      59      N      59          3.260
LGA    V      60      V      60          1.317
LGA    E      61      E      61          1.653
LGA    G      62      G      62          2.598
LGA    L      63      L      63          2.118
LGA    R      64      R      64          2.809
LGA    H      65      H      65          1.128
LGA    A      66      A      66          0.140
LGA    E      67      E      67          0.894
LGA    V      68      V      68          1.522
LGA    V      69      V      69          1.202
LGA    A      70      A      70          0.370
LGA    S      71      S      71          1.141
LGA    I      72      I      72          1.794
LGA    K      73      K      73          1.398
LGA    A      74      A      74          0.622
LGA    R      75      R      75          1.792
LGA    E      76      E      76          2.532
LGA    D      77      D      77          3.517
LGA    E      78      E      78          3.530
LGA    A      79      A      79          0.963
LGA    R      80      R      80          1.250
LGA    L      81      L      81          0.910
LGA    L      82      L      82          0.718
LGA    V      83      V      83          1.242
LGA    V      84      V      84          1.282
LGA    G      85      G      85          1.189
LGA    P      86      P      86          1.336
LGA    S      87      S      87          1.220
LGA    T      88      T      88          3.110
LGA    R      89      R      89          3.987
LGA    L      90      L      90          6.046

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     89    2.02   100.00     85.982     4.202

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.095706 * X  +   0.989809 * Y  +   0.105444 * Z  +  10.064091
  Y_new =  -0.978753 * X  +   0.112873 * Y  +  -0.171179 * Z  +  25.791508
  Z_new =  -0.181336 * X  +  -0.086821 * Y  +   0.979581 * Z  +   9.014772 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.088400    3.053193  [ DEG:    -5.0649    174.9351 ]
  Theta =   0.182345    2.959248  [ DEG:    10.4476    169.5524 ]
  Phi   =  -1.473323    1.668270  [ DEG:   -84.4152     95.5848 ]
 
# 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_4                                  
REMARK     2: T0340.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS168_4.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   89   2.02  100.00  85.982
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS168_4
PFRMAT TS
TARGET T0340
MODEL 4
PARENT N/A
ATOM      1  CA  SER     1      18.642  43.732   6.037  1.00 25.00           C
ATOM      2  CA  MET     2      15.315  45.120   7.115  1.00 25.00           C
ATOM      3  CA  LEU     3      13.338  42.293   5.449  1.00 25.00           C
ATOM      4  CA  ARG     4      14.842  40.239   8.335  1.00 25.00           C
ATOM      5  CA  PRO     5      11.833  38.131   9.208  1.00 25.00           C
ATOM      6  CA  ARG     6       8.654  36.768  10.919  1.00 25.00           C
ATOM      7  CA  LEU     7       9.045  33.419  12.748  1.00 25.00           C
ATOM      8  CA  CYS     8       5.658  32.070  13.620  1.00 25.00           C
ATOM      9  CA  HIS     9       5.315  31.571  17.418  1.00 25.00           C
ATOM     10  CA  LEU    10       4.213  27.932  17.484  1.00 25.00           C
ATOM     11  CA  ARG    11       2.879  24.761  19.110  1.00 25.00           C
ATOM     12  CA  LYS    12       1.717  21.205  18.921  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.662  22.395  20.146  1.00 25.00           C
ATOM     14  CA  PRO    14      -2.713  18.802  19.327  1.00 25.00           C
ATOM     15  CA  GLN    15      -1.913  16.581  16.322  1.00 25.00           C
ATOM     16  CA  GLY    16       1.079  18.353  14.643  1.00 25.00           C
ATOM     17  CA  TYR    17       2.992  21.322  13.208  1.00 25.00           C
ATOM     18  CA  GLY    18       1.423  20.334   9.884  1.00 25.00           C
ATOM     19  CA  PHE    19       4.665  21.293   8.190  1.00 25.00           C
ATOM     20  CA  ASN    20       6.849  19.398   5.696  1.00 25.00           C
ATOM     21  CA  LEU    21      10.540  19.783   4.930  1.00 25.00           C
ATOM     22  CA  HIS    22       9.958  19.415   1.171  1.00 25.00           C
ATOM     23  CA  SER    23      13.523  19.753  -0.249  1.00 25.00           C
ATOM     24  CA  ASP    24      16.435  17.353  -0.952  1.00 25.00           C
ATOM     25  CA  LYS    25      17.497  18.325  -4.485  1.00 25.00           C
ATOM     26  CA  SER    26      20.862  20.140  -4.864  1.00 25.00           C
ATOM     27  CA  ARG    27      21.077  20.712  -1.110  1.00 25.00           C
ATOM     28  CA  PRO    28      21.742  23.479   1.426  1.00 25.00           C
ATOM     29  CA  GLY    29      18.682  24.437   3.417  1.00 25.00           C
ATOM     30  CA  GLN    30      15.033  23.728   2.828  1.00 25.00           C
ATOM     31  CA  TYR    31      11.616  24.328   1.301  1.00 25.00           C
ATOM     32  CA  ILE    32       9.052  24.832   4.019  1.00 25.00           C
ATOM     33  CA  ARG    33       6.539  23.223   1.597  1.00 25.00           C
ATOM     34  CA  SER    34       2.719  23.597   1.601  1.00 25.00           C
ATOM     35  CA  VAL    35       1.275  23.991   5.098  1.00 25.00           C
ATOM     36  CA  ASP    36      -2.075  22.209   5.634  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.235  23.337   7.441  1.00 25.00           C
ATOM     38  CA  GLY    38      -6.059  25.523  10.406  1.00 25.00           C
ATOM     39  CA  SER    39      -2.976  24.650  12.547  1.00 25.00           C
ATOM     40  CA  PRO    40       0.083  26.614  13.645  1.00 25.00           C
ATOM     41  CA  ALA    41       2.008  27.143  10.376  1.00 25.00           C
ATOM     42  CA  ALA    42      -1.290  27.356   8.440  1.00 25.00           C
ATOM     43  CA  ARG    43      -2.626  29.921  10.950  1.00 25.00           C
ATOM     44  CA  SER    44      -0.156  32.616  12.015  1.00 25.00           C
ATOM     45  CA  GLY    45       2.085  32.666   8.878  1.00 25.00           C
ATOM     46  CA  LEU    46       5.176  30.504   8.341  1.00 25.00           C
ATOM     47  CA  ARG    47       4.296  30.155   4.674  1.00 25.00           C
ATOM     48  CA  ALA    48       3.531  28.463   1.370  1.00 25.00           C
ATOM     49  CA  GLN    49       5.956  30.256  -0.930  1.00 25.00           C
ATOM     50  CA  ASP    50       8.786  29.216   1.352  1.00 25.00           C
ATOM     51  CA  ARG    51      11.759  29.197   3.741  1.00 25.00           C
ATOM     52  CA  LEU    52      13.592  27.329   6.464  1.00 25.00           C
ATOM     53  CA  ILE    53      16.592  28.258   8.694  1.00 25.00           C
ATOM     54  CA  GLU    54      15.763  26.104  11.700  1.00 25.00           C
ATOM     55  CA  VAL    55      15.008  24.924  15.278  1.00 25.00           C
ATOM     56  CA  ASN    56      13.796  26.914  18.336  1.00 25.00           C
ATOM     57  CA  GLY    57      17.375  28.088  18.512  1.00 25.00           C
ATOM     58  CA  GLN    58      19.572  27.287  15.475  1.00 25.00           C
ATOM     59  CA  ASN    59      19.820  23.885  13.867  1.00 25.00           C
ATOM     60  CA  VAL    60      19.558  23.192  10.154  1.00 25.00           C
ATOM     61  CA  GLU    61      22.472  23.717   7.739  1.00 25.00           C
ATOM     62  CA  GLY    62      23.486  20.182   6.651  1.00 25.00           C
ATOM     63  CA  LEU    63      20.505  18.031   7.726  1.00 25.00           C
ATOM     64  CA  ARG    64      18.575  16.666   4.741  1.00 25.00           C
ATOM     65  CA  HIS    65      15.222  16.197   6.509  1.00 25.00           C
ATOM     66  CA  ALA    66      15.659  13.646   9.333  1.00 25.00           C
ATOM     67  CA  GLU    67      17.243  16.337  11.551  1.00 25.00           C
ATOM     68  CA  VAL    68      14.327  18.704  10.806  1.00 25.00           C
ATOM     69  CA  VAL    69      11.826  15.944  11.694  1.00 25.00           C
ATOM     70  CA  ALA    70      13.681  15.287  14.979  1.00 25.00           C
ATOM     71  CA  SER    71      13.609  19.027  15.798  1.00 25.00           C
ATOM     72  CA  ILE    72       9.849  19.137  15.076  1.00 25.00           C
ATOM     73  CA  LYS    73       9.298  16.110  17.357  1.00 25.00           C
ATOM     74  CA  ALA    74      11.320  17.804  20.134  1.00 25.00           C
ATOM     75  CA  ARG    75       9.073  20.830  20.966  1.00 25.00           C
ATOM     76  CA  GLU    76       5.867  20.968  23.038  1.00 25.00           C
ATOM     77  CA  ASP    77       5.856  24.787  23.231  1.00 25.00           C
ATOM     78  CA  GLU    78       8.383  26.252  20.794  1.00 25.00           C
ATOM     79  CA  ALA    79       9.118  24.799  17.357  1.00 25.00           C
ATOM     80  CA  ARG    80       9.174  28.396  16.219  1.00 25.00           C
ATOM     81  CA  LEU    81      10.717  27.749  12.850  1.00 25.00           C
ATOM     82  CA  LEU    82      13.308  30.500  12.104  1.00 25.00           C
ATOM     83  CA  VAL    83      12.564  32.535   9.030  1.00 25.00           C
ATOM     84  CA  VAL    84      14.185  33.744   5.812  1.00 25.00           C
ATOM     85  CA  GLY    85      11.496  34.424   3.187  1.00 25.00           C
ATOM     86  CA  PRO    86      12.511  33.789  -0.352  1.00 25.00           C
ATOM     87  CA  SER    87      14.420  34.915  -3.414  1.00 25.00           C
ATOM     88  CA  THR    88      16.073  36.707  -6.304  1.00 25.00           C
ATOM     89  CA  ARG    89      19.313  38.708  -6.753  1.00 25.00           C
ATOM     90  CA  LEU    90      22.746  37.973  -5.434  1.00 25.00           C
TER
END
