
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0358TS393_3-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS393_3-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    P      11      T      21           #
LGA    F      12      T      22          5.058
LGA    T      13      T      23          1.326
LGA    R      14      Y      24          1.647
LGA    R      15      S      25          1.872
LGA    Q      16      N      26          1.950
LGA    A      17      I      27          1.584
LGA    Q      18      T      28          2.955
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      L      29          2.889
LGA    T      22      E      30          1.948
LGA    T      23      -       -           -
LGA    Y      24      D      31          3.272
LGA    S      25      D      32           -
LGA    N      26      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    I      27      V      40          4.606
LGA    T      28      V      41           #
LGA    L      29      R      42           -
LGA    E      30      D      43           -
LGA    D      31      T      44           -
LGA    D      32      E      45           -
LGA    Q      33      G      46           -
LGA    G      34      R      47           -
LGA    S      35      M      48           -
LGA    H      36      -       -           -
LGA    F      37      -       -           -
LGA    R      38      -       -           -
LGA    L      39      V      49          1.300
LGA    V      40      -       -           -
LGA    V      41      -       -           -
LGA    R      42      -       -           -
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      -       -           -
LGA    M      48      -       -           -
LGA    V      49      -       -           -
LGA    W      50      -       -           -
LGA    R      51      -       -           -
LGA    A      52      W      50          4.020
LGA    W      53      R      51          1.772
LGA    N      54      A      52          1.607
LGA    F      55      W      53          4.810
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    E      56      E      56          2.672
LGA    P      57      P      57          3.987
LGA    D      58      -       -           -
LGA    A      59      D      58           #
LGA    G      60      A      59          3.475
LGA    E      61      G      60          2.767
LGA    G      62      E      61          2.473
LGA    L      63      G      62          2.361
LGA    N      64      L      63          2.103
LGA    R      65      N      64          0.449
LGA    Y      66      R      65          0.323
LGA    I      67      Y      66          0.718
LGA    R      68      I      67          1.700
LGA    T      69      R      68          1.825
LGA    S      70      -       -           -
LGA    G      71      -       -           -
LGA    I      72      T      69           #
LGA    R      73      S      70           -
LGA    T      74      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     28    2.71    10.71     28.704     0.997

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.954274 * X  +   0.054066 * Y  +   0.294005 * Z  +  -2.872855
  Y_new =   0.030396 * X  +  -0.960862 * Y  +   0.275355 * Z  +  -5.809504
  Z_new =   0.297386 * X  +   0.271701 * Y  +   0.915282 * Z  +   4.574940 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.288564   -2.853029  [ DEG:    16.5335   -163.4665 ]
  Theta =  -0.301953   -2.839639  [ DEG:   -17.3006   -162.6994 ]
  Phi   =   3.109751   -0.031842  [ DEG:   178.1756     -1.8244 ]
 
# 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: T0358TS393_3-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_3-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   65   65   5.0   28   2.71   10.71  28.704
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_3-D1
PFRMAT TS
TARGET T0358
MODEL 3
PARENT N/A
ATOM     10  CA  GLY    10      -3.753 -13.829  -8.043  1.00 25.00           C
ATOM     11  CA  PRO    11      -1.378 -10.831  -7.793  1.00 25.00           C
ATOM     12  CA  PHE    12       0.895 -11.463  -4.836  1.00 25.00           C
ATOM     13  CA  THR    13       2.818  -8.181  -5.046  1.00 25.00           C
ATOM     14  CA  ARG    14       0.423  -6.926  -2.336  1.00 25.00           C
ATOM     15  CA  ARG    15      -2.352  -6.401  -4.923  1.00 25.00           C
ATOM     16  CA  GLN    16      -4.711  -5.154  -2.176  1.00 25.00           C
ATOM     17  CA  ALA    17      -2.019  -2.731  -0.931  1.00 25.00           C
ATOM     18  CA  GLN    18      -1.497  -1.438  -4.499  1.00 25.00           C
ATOM     19  CA  ALA    19      -5.272  -0.929  -4.893  1.00 25.00           C
ATOM     20  CA  VAL    20      -5.384   0.983  -1.576  1.00 25.00           C
ATOM     21  CA  THR    21      -2.472   3.191  -2.721  1.00 25.00           C
ATOM     22  CA  THR    22      -4.272   3.894  -6.029  1.00 25.00           C
ATOM     23  CA  THR    23      -7.461   4.823  -4.123  1.00 25.00           C
ATOM     24  CA  TYR    24      -5.456   7.179  -1.866  1.00 25.00           C
ATOM     25  CA  SER    25      -8.160   8.191   0.603  1.00 25.00           C
ATOM     26  CA  ASN    26     -11.315   6.085   0.000  1.00 25.00           C
ATOM     27  CA  ILE    27      -9.006   3.252   1.102  1.00 25.00           C
ATOM     28  CA  THR    28      -8.068   3.550   4.773  1.00 25.00           C
ATOM     29  CA  LEU    29      -8.198   4.112   8.485  1.00 25.00           C
ATOM     30  CA  GLU    30      -8.035   3.347  12.170  1.00 25.00           C
ATOM     31  CA  ASP    31     -10.392   6.317  12.499  1.00 25.00           C
ATOM     32  CA  ASP    32     -11.141   5.884  16.204  1.00 25.00           C
ATOM     33  CA  GLN    33      -9.050   7.114  19.072  1.00 25.00           C
ATOM     34  CA  GLY    34      -6.969   8.720  16.264  1.00 25.00           C
ATOM     35  CA  SER    35      -5.213   7.628  13.040  1.00 25.00           C
ATOM     36  CA  HIS    36      -3.583   5.362  10.392  1.00 25.00           C
ATOM     37  CA  PHE    37      -3.575   2.118   8.461  1.00 25.00           C
ATOM     38  CA  ARG    38      -4.194  -1.679   8.776  1.00 25.00           C
ATOM     39  CA  LEU    39      -7.614  -0.812   7.271  1.00 25.00           C
ATOM     40  CA  VAL    40     -10.963  -0.846   5.589  1.00 25.00           C
ATOM     41  CA  VAL    41     -12.597  -0.300   2.149  1.00 25.00           C
ATOM     42  CA  ARG    42     -14.284  -1.041  -1.176  1.00 25.00           C
ATOM     43  CA  ASP    43     -15.733   0.460  -4.358  1.00 25.00           C
ATOM     44  CA  THR    44     -19.412   0.941  -4.878  1.00 25.00           C
ATOM     45  CA  GLU    45     -19.979  -2.210  -6.897  1.00 25.00           C
ATOM     46  CA  GLY    46     -19.986  -4.072  -3.548  1.00 25.00           C
ATOM     47  CA  ARG    47     -16.458  -5.445  -3.032  1.00 25.00           C
ATOM     48  CA  MET    48     -13.191  -5.979  -1.044  1.00 25.00           C
ATOM     49  CA  VAL    49     -10.075  -3.914  -0.295  1.00 25.00           C
ATOM     50  CA  TRP    50      -7.673  -1.914   1.877  1.00 25.00           C
ATOM     51  CA  ARG    51      -4.634  -2.955   3.872  1.00 25.00           C
ATOM     52  CA  ALA    52      -2.635   0.269   3.429  1.00 25.00           C
ATOM     53  CA  TRP    53      -2.950   4.002   2.858  1.00 25.00           C
ATOM     54  CA  ASN    54      -0.664   6.633   4.425  1.00 25.00           C
ATOM     55  CA  PHE    55       0.363   9.991   6.006  1.00 25.00           C
ATOM     56  CA  GLU    56       3.810   8.319   6.258  1.00 25.00           C
ATOM     57  CA  PRO    57       5.840  10.123   3.581  1.00 25.00           C
ATOM     58  CA  ASP    58       3.472   9.470   0.627  1.00 25.00           C
ATOM     59  CA  ALA    59       3.894   5.844   1.700  1.00 25.00           C
ATOM     60  CA  GLY    60       6.945   3.782   2.679  1.00 25.00           C
ATOM     61  CA  GLU    61       4.499   0.939   3.118  1.00 25.00           C
ATOM     62  CA  GLY    62       4.880   1.064   6.926  1.00 25.00           C
ATOM     63  CA  LEU    63       1.194   0.113   7.351  1.00 25.00           C
ATOM     64  CA  ASN    64       1.646  -2.818   4.928  1.00 25.00           C
ATOM     65  CA  ARG    65       4.727  -3.987   6.879  1.00 25.00           C
ATOM     66  CA  TYR    66       2.757  -3.787  10.158  1.00 25.00           C
ATOM     67  CA  ILE    67      -0.088  -5.825   8.601  1.00 25.00           C
ATOM     68  CA  ARG    68       2.422  -8.455   7.397  1.00 25.00           C
ATOM     69  CA  THR    69       3.947  -8.642  10.905  1.00 25.00           C
ATOM     70  CA  SER    70       4.390  -7.098  14.308  1.00 25.00           C
ATOM     71  CA  GLY    71       4.822 -10.567  15.769  1.00 25.00           C
ATOM     72  CA  ILE    72       3.020 -13.370  14.004  1.00 25.00           C
ATOM     73  CA  ARG    73       5.134 -15.573  16.339  1.00 25.00           C
ATOM     74  CA  THR    74       8.078 -15.687  13.880  1.00 25.00           C
TER
END
