
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS599_3.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      I       3           -
LGA    M       1      H       4          2.945
LGA    Q       2      V       5          2.951
LGA    -       -      Y       6           -
LGA    I       3      D       7          3.848
LGA    H       4      T       8           #
LGA    V       5      Y       9           -
LGA    Y       6      V      10           #
LGA    D       7      K      11           -
LGA    T       8      -       -           -
LGA    Y       9      A      12          4.995
LGA    V      10      K      13          5.200
LGA    K      11      D      14          2.543
LGA    A      12      G      15          4.032
LGA    K      13      -       -           -
LGA    D      14      -       -           -
LGA    G      15      -       -           -
LGA    H      16      -       -           -
LGA    V      17      H      16           #
LGA    M      18      V      17          2.860
LGA    H      19      M      18          2.473
LGA    F      20      H      19          3.883
LGA    D      21      F      20          4.037
LGA    V      22      D      21          2.248
LGA    F      23      V      22          2.566
LGA    T      24      F      23          1.767
LGA    D      25      -       -           -
LGA    V      26      -       -           -
LGA    R      27      -       -           -
LGA    D      28      T      24          3.233
LGA    D      29      D      25          3.766
LGA    K      30      -       -           -
LGA    K      31      V      26          4.045
LGA    A      32      R      27          1.681
LGA    I      33      -       -           -
LGA    E      34      -       -           -
LGA    F      35      -       -           -
LGA    A      36      -       -           -
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      D      28          4.178
LGA    H      59      D      29          2.052
LGA    S      60      K      30          2.770
LGA    Q      61      K      31          5.475
LGA    K      62      A      32           #
LGA    A      63      I      33          4.177
LGA    P      64      E      34          4.458
LGA    D      65      F      35          2.205
LGA    E      66      A      36          4.733
LGA    V      67      K      37          2.126
LGA    I      68      Q      38          4.490
LGA    E      69      W      39          2.490
LGA    -       -      L      40           -
LGA    A      70      S      41          3.408
LGA    I      71      S      42           #
LGA    K      72      I      43          2.389
LGA    Q      73      G      44          1.724
LGA    N      74      E      45          1.753
LGA    G      75      E      46           #
LGA    Y      76      G      47           -
LGA    F      77      A      48           -
LGA    I      78      T      49           -
LGA    Y      79      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           -
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    K      80      Y      79          3.404
LGA    M      81      K      80           -
LGA    E      82      M      81           -
LGA    G      83      E      82           -
LGA    C      84      G      83           -
LGA    N      85      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   85    5.0     34    3.43     2.94     22.195     0.962

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.172562 * X  +  -0.265923 * Y  +  -0.948424 * Z  +  -1.484799
  Y_new =  -0.192769 * X  +   0.953366 * Y  +  -0.232236 * Z  +   4.175886
  Z_new =   0.965952 * X  +   0.142751 * Y  +  -0.215776 * Z  +   0.029773 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.557126   -0.584466  [ DEG:   146.5125    -33.4875 ]
  Theta =  -1.309097   -1.832496  [ DEG:   -75.0057   -104.9943 ]
  Phi   =  -2.300940    0.840653  [ DEG:  -131.8341     48.1659 ]
 
# 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_3                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_3.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   34   3.43    2.94  22.195
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_3
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       5.337   3.494  -1.374  1.00  0.00              
ATOM      2  CA  GLN     2       5.407   3.010   2.356  1.00  0.00              
ATOM      3  CA  ILE     3       2.343   1.577   4.092  1.00  0.00              
ATOM      4  CA  HIS     4       1.855   1.978   7.681  1.00  0.00              
ATOM      5  CA  VAL     5      -0.244  -1.051   9.481  1.00  0.00              
ATOM      6  CA  TYR     6      -2.035  -0.505  12.629  1.00  0.00              
ATOM      7  CA  ASP     7      -3.170  -3.492  14.545  1.00  0.00              
ATOM      8  CA  THR     8      -4.284  -1.948  17.818  1.00  0.00              
ATOM      9  CA  TYR     9      -6.247   0.587  15.736  1.00  0.00              
ATOM     10  CA  VAL    10      -8.324  -2.107  14.041  1.00  0.00              
ATOM     11  CA  LYS    11      -9.588  -3.177  17.431  1.00  0.00              
ATOM     12  CA  ALA    12      -7.804  -1.349  20.181  1.00  0.00              
ATOM     13  CA  LYS    13      -8.965  -1.704  23.743  1.00  0.00              
ATOM     14  CA  ASP    14     -10.763   1.700  23.602  1.00  0.00              
ATOM     15  CA  GLY    15     -12.559   0.910  20.406  1.00  0.00              
ATOM     16  CA  HIS    16     -10.847   3.140  17.958  1.00  0.00              
ATOM     17  CA  VAL    17     -10.485   1.396  14.646  1.00  0.00              
ATOM     18  CA  MET    18      -7.798   2.554  12.314  1.00  0.00              
ATOM     19  CA  HIS    19      -6.298   0.224   9.783  1.00  0.00              
ATOM     20  CA  PHE    20      -3.854   1.320   7.175  1.00  0.00              
ATOM     21  CA  ASP    21      -2.540  -1.144   4.813  1.00  0.00              
ATOM     22  CA  VAL    22       1.068  -0.350   3.402  1.00  0.00              
ATOM     23  CA  PHE    23       2.601  -2.425   0.836  1.00  0.00              
ATOM     24  CA  THR    24       5.932  -1.277  -0.551  1.00  0.00              
ATOM     25  CA  ASP    25       7.502  -3.195  -3.446  1.00  0.00              
ATOM     26  CA  VAL    26      10.240  -1.140  -5.089  1.00  0.00              
ATOM     27  CA  ARG    27       9.191  -1.598  -8.735  1.00  0.00              
ATOM     28  CA  ASP    28       5.632  -0.519  -7.918  1.00  0.00              
ATOM     29  CA  ASP    29       6.712   2.511  -5.908  1.00  0.00              
ATOM     30  CA  LYS    30       8.607   3.970  -8.894  1.00  0.00              
ATOM     31  CA  LYS    31       5.558   3.506 -11.145  1.00  0.00              
ATOM     32  CA  ALA    32       3.160   5.191  -8.678  1.00  0.00              
ATOM     33  CA  ILE    33       5.494   8.148  -8.326  1.00  0.00              
ATOM     34  CA  GLU    34       5.768   8.476 -12.129  1.00  0.00              
ATOM     35  CA  PHE    35       2.011   8.378 -12.658  1.00  0.00              
ATOM     36  CA  ALA    36       1.507  11.033 -10.020  1.00  0.00              
ATOM     37  CA  LYS    37       4.168  13.241 -11.591  1.00  0.00              
ATOM     38  CA  GLN    38       2.688  13.002 -15.078  1.00  0.00              
ATOM     39  CA  TRP    39      -0.825  13.822 -13.920  1.00  0.00              
ATOM     40  CA  LEU    40       0.355  16.684 -11.779  1.00  0.00              
ATOM     41  CA  SER    41       2.234  18.291 -14.641  1.00  0.00              
ATOM     42  CA  SER    42      -0.696  18.073 -16.993  1.00  0.00              
ATOM     43  CA  ILE    43      -3.107  19.664 -14.469  1.00  0.00              
ATOM     44  CA  GLY    44      -0.780  22.494 -13.489  1.00  0.00              
ATOM     45  CA  GLU    45       0.349  21.085 -10.121  1.00  0.00              
ATOM     46  CA  GLU    46       4.053  21.219  -9.504  1.00  0.00              
ATOM     47  CA  GLY    47       5.127  17.920  -7.849  1.00  0.00              
ATOM     48  CA  ALA    48       5.947  19.718  -4.654  1.00  0.00              
ATOM     49  CA  THR    49       2.665  21.419  -4.126  1.00  0.00              
ATOM     50  CA  VAL    50       0.249  18.680  -5.010  1.00  0.00              
ATOM     51  CA  THR    51      -3.257  19.936  -4.624  1.00  0.00              
ATOM     52  CA  SER    52      -5.980  17.749  -3.169  1.00  0.00              
ATOM     53  CA  GLU    53      -7.849  17.562  -6.516  1.00  0.00              
ATOM     54  CA  GLU    54      -4.764  16.600  -8.527  1.00  0.00              
ATOM     55  CA  CYS    55      -3.660  13.589  -6.403  1.00  0.00              
ATOM     56  CA  ARG    56      -7.022  12.112  -5.390  1.00  0.00              
ATOM     57  CA  PHE    57      -7.937  11.476  -9.036  1.00  0.00              
ATOM     58  CA  CYS    58      -5.289   8.732  -9.241  1.00  0.00              
ATOM     59  CA  HIS    59      -5.280   7.495  -5.666  1.00  0.00              
ATOM     60  CA  SER    60      -9.010   6.825  -5.249  1.00  0.00              
ATOM     61  CA  GLN    61      -9.403   5.359  -8.716  1.00  0.00              
ATOM     62  CA  LYS    62      -6.366   3.016  -8.740  1.00  0.00              
ATOM     63  CA  ALA    63      -6.537   0.966  -5.704  1.00  0.00              
ATOM     64  CA  PRO    64      -3.758  -0.685  -3.813  1.00  0.00              
ATOM     65  CA  ASP    65      -5.364  -4.084  -4.306  1.00  0.00              
ATOM     66  CA  GLU    66      -8.742  -2.762  -3.172  1.00  0.00              
ATOM     67  CA  VAL    67      -7.256  -1.323   0.036  1.00  0.00              
ATOM     68  CA  ILE    68      -5.554  -4.623   0.832  1.00  0.00              
ATOM     69  CA  GLU    69      -8.785  -6.521   0.342  1.00  0.00              
ATOM     70  CA  ALA    70     -10.769  -4.110   2.575  1.00  0.00              
ATOM     71  CA  ILE    71      -8.159  -4.207   5.287  1.00  0.00              
ATOM     72  CA  LYS    72      -8.024  -8.049   5.295  1.00  0.00              
ATOM     73  CA  GLN    73     -11.787  -8.261   5.535  1.00  0.00              
ATOM     74  CA  ASN    74     -12.005  -5.804   8.466  1.00  0.00              
ATOM     75  CA  GLY    75      -9.199  -7.312  10.468  1.00  0.00              
ATOM     76  CA  TYR    76      -6.672  -4.515   9.895  1.00  0.00              
ATOM     77  CA  PHE    77      -3.105  -5.455   9.110  1.00  0.00              
ATOM     78  CA  ILE    78      -0.490  -2.964   8.690  1.00  0.00              
ATOM     79  CA  TYR    79       2.607  -3.944   6.452  1.00  0.00              
ATOM     80  CA  LYS    80       5.323  -1.497   6.276  1.00  0.00              
ATOM     81  CA  MET    81       7.632  -1.451   3.333  1.00  0.00              
ATOM     82  CA  GLU    82      10.930   0.288   3.726  1.00  0.00              
ATOM     83  CA  GLY    83      13.717  -1.000   1.856  1.00  0.00              
ATOM     84  CA  CYS    84      11.401  -3.056  -0.972  1.00  0.00              
ATOM     85  CA  ASN    85      11.655  -6.567  -2.968  1.00  0.00              
TER                                                                             
END
