
#######################################################
#                                                     #
#                        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   85 (   85),  selected   85 , name T0353TS599_2
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS599_2.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.667
LGA    Q       2      Q       2          2.964
LGA    I       3      I       3          2.883
LGA    H       4      H       4          0.924
LGA    V       5      V       5          1.053
LGA    Y       6      Y       6          1.349
LGA    D       7      D       7          1.649
LGA    T       8      T       8          1.721
LGA    Y       9      Y       9          1.571
LGA    V      10      V      10          1.639
LGA    K      11      K      11          0.646
LGA    A      12      A      12          0.723
LGA    K      13      K      13          1.666
LGA    D      14      D      14          3.370
LGA    G      15      G      15           #
LGA    H      16      H      16          3.131
LGA    V      17      V      17          1.385
LGA    M      18      M      18          1.768
LGA    H      19      H      19          1.084
LGA    F      20      F      20          0.978
LGA    D      21      D      21          1.299
LGA    V      22      V      22          1.617
LGA    F      23      F      23          1.533
LGA    T      24      T      24          2.177
LGA    D      25      D      25          4.201
LGA    V      26      V      26           #
LGA    R      27      -       -           -
LGA    D      28      -       -           -
LGA    D      29      -       -           -
LGA    K      30      R      27           #
LGA    K      31      D      28           -
LGA    A      32      D      29           -
LGA    I      33      K      30           -
LGA    E      34      K      31           -
LGA    F      35      A      32           -
LGA    A      36      I      33           -
LGA    K      37      -       -           -
LGA    Q      38      -       -           -
LGA    W      39      -       -           -
LGA    L      40      -       -           -
LGA    S      41      -       -           -
LGA    S      42      -       -           -
LGA    I      43      -       -           -
LGA    G      44      -       -           -
LGA    E      45      -       -           -
LGA    E      46      -       -           -
LGA    G      47      -       -           -
LGA    A      48      -       -           -
LGA    T      49      -       -           -
LGA    V      50      -       -           -
LGA    T      51      -       -           -
LGA    S      52      -       -           -
LGA    E      53      -       -           -
LGA    E      54      -       -           -
LGA    C      55      -       -           -
LGA    R      56      -       -           -
LGA    F      57      -       -           -
LGA    C      58      -       -           -
LGA    H      59      -       -           -
LGA    S      60      -       -           -
LGA    Q      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      E      34           #
LGA    P      64      F      35          1.281
LGA    -       -      A      36           -
LGA    D      65      K      37          4.171
LGA    E      66      Q      38          1.699
LGA    V      67      W      39          2.257
LGA    I      68      L      40          4.186
LGA    E      69      S      41          2.859
LGA    -       -      S      42           -
LGA    A      70      I      43          5.254
LGA    I      71      G      44           #
LGA    K      72      E      45           #
LGA    Q      73      E      46          4.380
LGA    N      74      -       -           -
LGA    G      75      G      47          2.927
LGA    Y      76      A      48          3.371
LGA    F      77      T      49          3.765
LGA    I      78      V      50          3.798
LGA    Y      79      T      51           #
LGA    -       -      S      52           -
LGA    -       -      E      53           -
LGA    K      80      E      54          3.930
LGA    M      81      C      55          2.316
LGA    E      82      R      56          3.139
LGA    G      83      F      57          1.009
LGA    C      84      C      58          2.823
LGA    -       -      H      59           -
LGA    -       -      S      60           -
LGA    -       -      Q      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    -       -      I      78           -
LGA    -       -      Y      79           -
LGA    -       -      K      80           -
LGA    N      85      M      81           #
LGA    -       -      E      82           -
LGA    -       -      G      83           -
LGA    -       -      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   85    5.0     41    2.72    63.41     32.465     1.456

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.295134 * X  +  -0.672453 * Y  +   0.678751 * Z  +  -3.200438
  Y_new =   0.096643 * X  +   0.727762 * Y  +   0.678987 * Z  +  -4.835636
  Z_new =  -0.950556 * X  +  -0.134796 * Y  +   0.279775 * Z  +  -1.389802 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.448982    2.692611  [ DEG:   -25.7247    154.2753 ]
  Theta =   1.255020    1.886573  [ DEG:    71.9073    108.0927 ]
  Phi   =   0.316450   -2.825142  [ DEG:    18.1313   -161.8687 ]
 
# 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: T0353TS599_2                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_2.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   85   5.0   41   2.72   63.41  32.465
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_2
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      14.245   4.176 -10.388  1.00  0.00              
ATOM      2  CA  GLN     2      10.811   4.697  -9.439  1.00  0.00              
ATOM      3  CA  ILE     3       9.770   4.065  -5.935  1.00  0.00              
ATOM      4  CA  HIS     4       6.190   4.529  -4.901  1.00  0.00              
ATOM      5  CA  VAL     5       5.159   4.401  -1.286  1.00  0.00              
ATOM      6  CA  TYR     6       1.649   3.595  -0.377  1.00  0.00              
ATOM      7  CA  ASP     7       0.483   4.160   3.064  1.00  0.00              
ATOM      8  CA  THR     8      -2.429   2.363   4.161  1.00  0.00              
ATOM      9  CA  TYR     9      -3.925   3.375   7.306  1.00  0.00              
ATOM     10  CA  VAL    10      -6.327   1.099   8.865  1.00  0.00              
ATOM     11  CA  LYS    11      -8.695   2.397  11.330  1.00  0.00              
ATOM     12  CA  ALA    12     -10.543  -0.086  13.461  1.00  0.00              
ATOM     13  CA  LYS    13     -13.996   0.839  14.864  1.00  0.00              
ATOM     14  CA  ASP    14     -12.522   1.414  18.307  1.00  0.00              
ATOM     15  CA  GLY    15      -9.942   3.912  17.148  1.00  0.00              
ATOM     16  CA  HIS    16      -6.909   1.711  16.943  1.00  0.00              
ATOM     17  CA  VAL    17      -4.789   2.803  14.215  1.00  0.00              
ATOM     18  CA  MET    18      -3.046   0.220  12.108  1.00  0.00              
ATOM     19  CA  HIS    19      -0.298   1.275   9.755  1.00  0.00              
ATOM     20  CA  PHE    20       0.303  -0.649   6.591  1.00  0.00              
ATOM     21  CA  ASP    21       3.102   0.251   4.379  1.00  0.00              
ATOM     22  CA  VAL    22       3.090  -0.835   0.812  1.00  0.00              
ATOM     23  CA  PHE    23       6.085  -0.186  -1.293  1.00  0.00              
ATOM     24  CA  THR    24       5.800  -0.150  -4.958  1.00  0.00              
ATOM     25  CA  ASP    25       8.849  -0.480  -7.116  1.00  0.00              
ATOM     26  CA  VAL    26       8.340   0.119 -10.771  1.00  0.00              
ATOM     27  CA  ARG    27      10.218  -2.724 -12.344  1.00  0.00              
ATOM     28  CA  ASP    28       9.125  -5.092  -9.546  1.00  0.00              
ATOM     29  CA  ASP    29       5.499  -3.943  -9.338  1.00  0.00              
ATOM     30  CA  LYS    30       4.766  -4.825 -12.947  1.00  0.00              
ATOM     31  CA  LYS    31       6.251  -8.272 -12.473  1.00  0.00              
ATOM     32  CA  ALA    32       4.261  -8.985  -9.332  1.00  0.00              
ATOM     33  CA  ILE    33       1.031  -7.942 -11.013  1.00  0.00              
ATOM     34  CA  GLU    34       1.694 -10.185 -13.996  1.00  0.00              
ATOM     35  CA  PHE    35       2.510 -13.232 -11.853  1.00  0.00              
ATOM     36  CA  ALA    36      -0.650 -12.662  -9.779  1.00  0.00              
ATOM     37  CA  LYS    37      -2.833 -12.329 -12.883  1.00  0.00              
ATOM     38  CA  GLN    38      -1.433 -15.543 -14.388  1.00  0.00              
ATOM     39  CA  TRP    39      -2.027 -17.501 -11.161  1.00  0.00              
ATOM     40  CA  LEU    40      -5.545 -16.238 -10.698  1.00  0.00              
ATOM     41  CA  SER    41      -6.466 -17.117 -14.285  1.00  0.00              
ATOM     42  CA  SER    42      -5.088 -20.609 -14.101  1.00  0.00              
ATOM     43  CA  ILE    43      -7.080 -21.334 -10.904  1.00  0.00              
ATOM     44  CA  GLY    44     -10.335 -19.981 -12.334  1.00  0.00              
ATOM     45  CA  GLU    45     -10.349 -16.700 -10.519  1.00  0.00              
ATOM     46  CA  GLU    46     -11.187 -13.516 -12.395  1.00  0.00              
ATOM     47  CA  GLY    47      -8.924 -10.746 -11.083  1.00  0.00              
ATOM     48  CA  ALA    48     -11.825  -8.861  -9.453  1.00  0.00              
ATOM     49  CA  THR    49     -13.039 -11.847  -7.508  1.00  0.00              
ATOM     50  CA  VAL    50      -9.754 -13.239  -6.294  1.00  0.00              
ATOM     51  CA  THR    51      -9.985 -15.607  -3.367  1.00  0.00              
ATOM     52  CA  SER    52      -7.718 -15.045  -0.376  1.00  0.00              
ATOM     53  CA  GLU    53      -5.689 -18.202  -1.056  1.00  0.00              
ATOM     54  CA  GLU    54      -5.091 -17.420  -4.704  1.00  0.00              
ATOM     55  CA  CYS    55      -3.924 -13.905  -4.099  1.00  0.00              
ATOM     56  CA  ARG    56      -1.688 -14.145  -1.060  1.00  0.00              
ATOM     57  CA  PHE    57       0.902 -16.292  -2.733  1.00  0.00              
ATOM     58  CA  CYS    58       2.056 -13.368  -4.969  1.00  0.00              
ATOM     59  CA  HIS    59       0.482 -10.413  -3.289  1.00  0.00              
ATOM     60  CA  SER    60       2.286 -10.040  -0.030  1.00  0.00              
ATOM     61  CA  GLN    61       1.425  -6.281   0.145  1.00  0.00              
ATOM     62  CA  LYS    62      -2.336  -6.811  -0.323  1.00  0.00              
ATOM     63  CA  ALA    63      -3.729  -5.079  -3.333  1.00  0.00              
ATOM     64  CA  PRO    64      -6.060  -2.186  -2.835  1.00  0.00              
ATOM     65  CA  ASP    65      -9.321  -3.772  -3.871  1.00  0.00              
ATOM     66  CA  GLU    66      -8.836  -6.776  -1.678  1.00  0.00              
ATOM     67  CA  VAL    67      -7.812  -4.832   1.350  1.00  0.00              
ATOM     68  CA  ILE    68     -10.750  -2.485   1.121  1.00  0.00              
ATOM     69  CA  GLU    69     -13.220  -5.324   0.822  1.00  0.00              
ATOM     70  CA  ALA    70     -11.709  -7.151   3.846  1.00  0.00              
ATOM     71  CA  ILE    71     -11.674  -4.073   6.011  1.00  0.00              
ATOM     72  CA  LYS    72     -15.236  -3.181   5.264  1.00  0.00              
ATOM     73  CA  GLN    73     -16.451  -6.665   5.985  1.00  0.00              
ATOM     74  CA  ASN    74     -14.601  -6.678   9.276  1.00  0.00              
ATOM     75  CA  GLY    75     -15.680  -3.201  10.515  1.00  0.00              
ATOM     76  CA  TYR    76     -12.315  -1.629   9.597  1.00  0.00              
ATOM     77  CA  PHE    77     -11.968   1.724   7.889  1.00  0.00              
ATOM     78  CA  ILE    78      -9.260   2.067   5.287  1.00  0.00              
ATOM     79  CA  TYR    79      -7.452   5.245   4.887  1.00  0.00              
ATOM     80  CA  LYS    80      -5.037   5.506   2.037  1.00  0.00              
ATOM     81  CA  MET    81      -2.185   7.973   2.124  1.00  0.00              
ATOM     82  CA  GLU    82      -0.438   8.632  -1.116  1.00  0.00              
ATOM     83  CA  GLY    83       2.889   9.800  -0.518  1.00  0.00              
ATOM     84  CA  CYS    84       3.511   7.921   3.165  1.00  0.00              
ATOM     85  CA  ASN    85       5.297   5.068   5.682  1.00  0.00              
TER                                                                             
END
