
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0349TS677_1
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS677_1.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    R       2      R       2          1.734
LGA    E       3      E       3          1.681
LGA    L       4      L       4          1.220
LGA    L       5      L       5          1.158
LGA    R       6      R       6          1.848
LGA    T       7      T       7          2.709
LGA    N       8      N       8          3.954
LGA    D       9      D       9          1.278
LGA    A      10      A      10          1.810
LGA    V      11      V      11          1.364
LGA    L      12      L      12          0.472
LGA    L      13      L      13          1.295
LGA    S      14      S      14          1.341
LGA    A      15      A      15          0.590
LGA    V      16      V      16          0.409
LGA    G      17      G      17          1.129
LGA    A      18      A      18          0.696
LGA    L      19      L      19          0.588
LGA    L      20      L      20          1.161
LGA    D      21      D      21          1.403
LGA    G      22      G      22          0.864
LGA    A      23      A      23          1.859
LGA    D      24      D      24          2.663
LGA    I      25      I      25          1.092
LGA    G      26      G      26          1.755
LGA    H      27      H      27          1.301
LGA    L      28      L      28          1.655
LGA    V      29      V      29          1.446
LGA    L      30      L      30          1.817
LGA    D      31      D      31          3.952
LGA    Q      32      Q      32          4.468
LGA    G      42      N      33           -
LGA    -       -      M      34           -
LGA    -       -      S      35           -
LGA    -       -      I      36           -
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      G      42           -
LGA    V      43      V      43          3.491
LGA    I      44      I      44          0.915
LGA    P      45      P      45          1.167
LGA    R      46      R      46          1.433
LGA    R      47      R      47          1.000
LGA    V      48      V      48          1.171
LGA    L      49      L      49          1.162
LGA    V      50      V      50          0.856
LGA    H      51      H      51          0.937
LGA    E      52      E      52          1.583
LGA    D      53      D      53          2.005
LGA    D      54      D      54          1.261
LGA    L      55      L      55          0.754
LGA    A      56      A      56          0.082
LGA    G      57      G      57          0.094
LGA    A      58      A      58          0.522
LGA    R      59      R      59          0.442
LGA    R      60      R      60          0.190
LGA    L      61      L      61          0.144
LGA    L      62      L      62          0.329
LGA    T      63      T      63          0.349
LGA    D      64      D      64          0.939
LGA    A      65      A      65          2.636
LGA    -       -      G      66           -
LGA    G      66      L      67          1.544
LGA    L      67      A      68          3.217
LGA    A      68      H      69          3.522
LGA    H      69      E      70          6.494
LGA    E      70      L      71           -
LGA    L      71      R      72           -
LGA    R      72      S      73           -
LGA    S      73      D      74           -
LGA    D      74      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   75    5.0     58    1.94    93.10     70.193     2.840

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.703885 * X  +  -0.580283 * Y  +   0.409655 * Z  +   0.900212
  Y_new =   0.657611 * X  +   0.750371 * Y  +  -0.067020 * Z  + -64.188843
  Z_new =  -0.268502 * X  +   0.316568 * Y  +   0.909775 * Z  + -44.324352 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.334859   -2.806733  [ DEG:    19.1860   -160.8140 ]
  Theta =   0.271838    2.869755  [ DEG:    15.5752    164.4248 ]
  Phi   =   0.751424   -2.390169  [ DEG:    43.0534   -136.9466 ]
 
# 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: T0349TS677_1                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS677_1.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   64   75   5.0   58   1.94   93.10  70.193
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS677_1
PFRMAT TS
TARGET T0349
MODEL  1
PARENT 1YJ7_A
ATOM     22  CA  ARG     2       3.470   8.490  -5.713  1.00 54.00
ATOM     23  CA  GLU     3       3.243   4.903  -4.488  1.00 54.00
ATOM     24  CA  LEU     4       4.312   4.364  -0.893  1.00 54.00
ATOM     25  CA  LEU     5       3.956   0.604  -0.416  1.00 57.00
ATOM     26  CA  ARG     6       2.539  -2.440  -2.225  1.00 68.00
ATOM     27  CA  THR     7       1.953  -6.002  -1.024  1.00 79.00
ATOM     28  CA  ASN     8       0.164  -4.953   2.170  1.00 91.00
ATOM     29  CA  ASP     9      -2.496  -6.956   4.016  1.00 99.00
ATOM     30  CA  ALA    10      -5.888  -5.323   4.259  1.00 99.00
ATOM     31  CA  VAL    11      -5.467  -4.873   8.045  1.00 94.00
ATOM     32  CA  LEU    12      -2.059  -3.180   7.849  1.00 92.00
ATOM     33  CA  LEU    13      -2.975  -0.974   4.865  1.00 92.00
ATOM     34  CA  SER    14      -5.985   0.129   6.921  1.00 56.00
ATOM     35  CA  ALA    15      -3.821   0.945   9.929  1.00 27.00
ATOM     36  CA  VAL    16      -1.406   2.937   7.742  1.00 46.00
ATOM     37  CA  GLY    17      -4.209   4.726   5.844  1.00 59.00
ATOM     38  CA  ALA    18      -5.991   5.714   9.049  1.00 41.00
ATOM     39  CA  LEU    19      -2.708   6.884  10.604  1.00 50.00
ATOM     40  CA  LEU    20      -1.941   9.130   7.614  1.00 50.00
ATOM     41  CA  ASP    21      -5.446  10.549   7.352  1.00 43.00
ATOM     42  CA  GLY    22      -5.537  11.302  11.080  1.00 32.00
ATOM     43  CA  ALA    23      -2.187  13.096  10.736  1.00 37.00
ATOM     44  CA  ASP    24      -3.527  15.283   7.909  1.00 25.00
ATOM     45  CA  ILE    25      -2.046  13.473   4.950  1.00 37.00
ATOM     46  CA  GLY    26      -4.348  12.420   2.114  1.00 60.00
ATOM     47  CA  HIS    27      -3.974   8.855   0.888  1.00 79.00
ATOM     48  CA  LEU    28      -5.375   6.653  -1.857  1.00 99.00
ATOM     49  CA  VAL    29      -5.642   2.874  -1.836  1.00 99.00
ATOM     50  CA  LEU    30      -6.009   0.158  -4.454  1.00 99.00
ATOM     51  CA  ASP    31      -5.997  -3.642  -4.553  1.00 99.00
ATOM     52  CA  GLN    32      -3.603  -5.266  -7.052  1.00 99.00
ATOM     53  CA  GLY    42      -4.214  -8.423  -9.108  1.00 99.00
ATOM     54  CA  VAL    43      -2.876 -10.691  -6.319  1.00 99.00
ATOM     55  CA  ILE    44      -5.317  -9.305  -3.736  1.00 86.00
ATOM     56  CA  PRO    45      -2.746  -7.178  -1.873  1.00 94.00
ATOM     57  CA  ARG    46      -3.117  -3.478  -1.042  1.00 58.00
ATOM     58  CA  ARG    47      -1.194  -0.491  -2.384  1.00 45.00
ATOM     59  CA  VAL    48      -1.133   2.919  -0.680  1.00 45.00
ATOM     60  CA  LEU    49      -0.194   6.114  -2.539  1.00 55.00
ATOM     61  CA  VAL    50      -0.047   9.828  -1.741  1.00 64.00
ATOM     62  CA  HIS    51       0.085  13.066  -3.699  1.00 79.00
ATOM     63  CA  GLU    52       3.743  13.472  -4.651  1.00 62.00
ATOM     64  CA  ASP    53       4.158  16.689  -2.659  1.00 70.00
ATOM     65  CA  ASP    54       3.154  14.807   0.489  1.00 71.00
ATOM     66  CA  LEU    55       5.691  11.998   0.118  1.00 55.00
ATOM     67  CA  ALA    56       8.222  13.195   2.729  1.00 49.00
ATOM     68  CA  GLY    57       5.523  14.003   5.333  1.00 55.00
ATOM     69  CA  ALA    58       3.934  10.595   4.726  1.00 69.00
ATOM     70  CA  ARG    59       7.128   8.559   5.044  1.00 85.00
ATOM     71  CA  ARG    60       7.996  10.576   8.183  1.00 86.00
ATOM     72  CA  LEU    61       4.680   9.686   9.830  1.00 94.00
ATOM     73  CA  LEU    62       4.949   6.033   8.803  1.00 89.00
ATOM     74  CA  THR    63       8.605   5.770   9.965  1.00 71.00
ATOM     75  CA  ASP    64       7.664   7.396  13.299  1.00 35.00
ATOM     76  CA  ALA    65       5.024   4.715  13.852  1.00 35.00
ATOM     77  CA  GLY    66       7.111   1.743  12.720  1.00 34.00
ATOM     78  CA  LEU    67       5.240   1.055   9.458  1.00 40.00
ATOM     79  CA  ALA    68       5.408  -1.102   7.547  1.00 49.00
ATOM     80  CA  HIS    69       5.626  -3.401  10.564  1.00 94.00
ATOM     81  CA  GLU    70       8.586  -5.640  11.113  1.00 99.00
ATOM     82  CA  LEU    71       7.983  -9.374  11.162  1.00 99.00
ATOM     83  CA  ARG    72       9.216 -11.791  13.820  1.00 99.00
ATOM     84  CA  SER    73      10.345 -15.400  13.716  1.00 99.00
ATOM     85  CA  ASP    74       7.693 -18.061  13.213  1.00 99.00
TER
END
