
#######################################################
#                                                     #
#                        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   86 (   86),  selected   86 , name T0292TS393_4-D1
# Molecule2: number of CA atoms   77 (  591),  selected   77 , name T0292_D1.pdb
# PARAMETERS: T0292TS393_4-D1.T0292_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           #
LGA    R       2      R       2          2.516
LGA    A       3      A       3          3.658
LGA    E       4      E       4          2.695
LGA    D       5      D       5          3.576
LGA    Y       6      Y       6          5.790
LGA    E       7      E       7          2.211
LGA    V       8      V       8          0.923
LGA    L       9      L       9          1.591
LGA    Y      10      Y      10          1.299
LGA    T      11      T      11          1.205
LGA    I      12      I      12          0.845
LGA    G      13      G      13          1.067
LGA    T      14      T      14          3.640
LGA    G      15      G      15          2.895
LGA    S      16      S      16          2.907
LGA    Y      17      Y      17          1.846
LGA    G      18      G      18          2.586
LGA    R      19      R      19          0.913
LGA    C      20      C      20          0.728
LGA    Q      21      Q      21          0.631
LGA    K      22      K      22          0.890
LGA    I      23      I      23          1.012
LGA    R      24      R      24          0.588
LGA    R      25      R      25          1.203
LGA    K      26      K      26          1.006
LGA    S      27      S      27          1.762
LGA    D      28      D      28          0.565
LGA    G      29      G      29          1.119
LGA    K      30      K      30          1.894
LGA    I      31      I      31          1.277
LGA    L      32      L      32          1.154
LGA    V      33      V      33          0.773
LGA    W      34      W      34          1.842
LGA    K      35      K      35          2.026
LGA    E      36      E      36          0.797
LGA    L      37      L      37          0.741
LGA    D      38      D      38          1.234
LGA    Y      39      Y      39          2.010
LGA    G      40      G      40          2.086
LGA    S      41      S      41          2.409
LGA    M      42      M      42          2.280
LGA    T      43      -       -           -
LGA    E      44      T      43          2.706
LGA    A      45      -       -           -
LGA    E      46      -       -           -
LGA    K      47      -       -           -
LGA    Q      48      M      49          2.519
LGA    M      49      L      50          1.759
LGA    L      50      V      51          2.820
LGA    V      51      S      52          2.821
LGA    S      52      E      53          2.290
LGA    E      53      -       -           -
LGA    V      54      V      54          1.242
LGA    N      55      N      55          3.105
LGA    L      56      L      56          3.277
LGA    L      57      L      57          1.608
LGA    R      58      R      58          1.917
LGA    E      59      E      59          3.052
LGA    L      60      L      60          1.813
LGA    K      61      K      61          0.926
LGA    H      62      H      62          2.826
LGA    P      63      P      63          2.799
LGA    N      64      N      64          1.109
LGA    I      65      I      65          0.556
LGA    V      66      V      66          0.729
LGA    R      67      R      67          1.162
LGA    Y      68      Y      68          1.031
LGA    Y      69      Y      69          0.962
LGA    D      70      D      70          2.365
LGA    R      71      R      71          1.397
LGA    I      72      I      72          1.404
LGA    I      73      -       -           -
LGA    D      74      I      73          2.285
LGA    R      75      D      74          3.605
LGA    T      76      -       -           -
LGA    N      77      -       -           -
LGA    T      78      -       -           -
LGA    T      79      T      79          2.016
LGA    L      80      L      80          1.371
LGA    Y      81      Y      81          1.865
LGA    I      82      I      82          1.345
LGA    V      83      V      83          2.054
LGA    M      84      M      84          2.155
LGA    E      85      E      85          0.781
LGA    Y      86      Y      86          0.503

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   86   77    5.0     76    2.06    89.47     83.411     3.511

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.003157 * X  +   0.600652 * Y  +   0.799504 * Z  +   6.172729
  Y_new =   0.954664 * X  +  -0.239801 * Y  +   0.176388 * Z  +  14.519479
  Z_new =   0.297670 * X  +   0.762701 * Y  +  -0.574178 * Z  +  16.753960 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.216101   -0.925491  [ DEG:   126.9733    -53.0267 ]
  Theta =  -0.302251   -2.839342  [ DEG:   -17.3177   -162.6823 ]
  Phi   =   1.567489   -1.574104  [ DEG:    89.8105    -90.1895 ]
 
# 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: T0292TS393_4-D1                               
REMARK     2: T0292_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0292TS393_4-D1.T0292_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   86   77   5.0   76   2.06   89.47  83.411
REMARK  ---------------------------------------------------------- 
MOLECULE T0292TS393_4-D1
PFRMAT TS
TARGET T0292
MODEL 4
PARENT N/A
ATOM      1  CA  SER     1     -13.428  -6.334   3.819  1.00 25.00           C
ATOM      2  CA  ARG     2     -10.652  -8.778   4.558  1.00 25.00           C
ATOM      3  CA  ALA     3     -10.477  -7.708   8.205  1.00 25.00           C
ATOM      4  CA  GLU     4     -13.293  -9.111  10.344  1.00 25.00           C
ATOM      5  CA  ASP     5     -14.356  -6.364  12.675  1.00 25.00           C
ATOM      6  CA  TYR     6     -16.764  -6.481  15.670  1.00 25.00           C
ATOM      7  CA  GLU     7     -16.612  -2.654  15.712  1.00 25.00           C
ATOM      8  CA  VAL     8     -15.019   0.575  14.356  1.00 25.00           C
ATOM      9  CA  LEU     9     -15.643   2.781  17.356  1.00 25.00           C
ATOM     10  CA  TYR    10     -15.599   6.637  17.186  1.00 25.00           C
ATOM     11  CA  THR    11     -13.834   9.585  15.482  1.00 25.00           C
ATOM     12  CA  ILE    12     -10.901  10.755  17.499  1.00 25.00           C
ATOM     13  CA  GLY    13      -9.308  13.733  15.657  1.00 25.00           C
ATOM     14  CA  THR    14      -8.892  16.836  13.498  1.00 25.00           C
ATOM     15  CA  GLY    15      -6.889  14.494  11.267  1.00 25.00           C
ATOM     16  CA  SER    16      -6.351  16.616   8.228  1.00 25.00           C
ATOM     17  CA  TYR    17      -4.582  13.880   6.300  1.00 25.00           C
ATOM     18  CA  GLY    18      -6.569  10.829   7.492  1.00 25.00           C
ATOM     19  CA  ARG    19      -9.182   9.545   9.967  1.00 25.00           C
ATOM     20  CA  CYS    20      -8.272   8.097  13.429  1.00 25.00           C
ATOM     21  CA  GLN    21     -10.637   5.617  15.100  1.00 25.00           C
ATOM     22  CA  LYS    22     -10.528   3.882  18.486  1.00 25.00           C
ATOM     23  CA  ILE    23     -11.166   0.238  17.702  1.00 25.00           C
ATOM     24  CA  ARG    24     -10.837  -3.509  18.364  1.00 25.00           C
ATOM     25  CA  ARG    25     -10.103  -6.794  16.624  1.00 25.00           C
ATOM     26  CA  LYS    26     -12.191  -9.878  17.475  1.00 25.00           C
ATOM     27  CA  SER    27      -9.745 -12.680  18.473  1.00 25.00           C
ATOM     28  CA  ASP    28      -8.368 -10.679  21.446  1.00 25.00           C
ATOM     29  CA  GLY    29     -10.841  -7.827  21.986  1.00 25.00           C
ATOM     30  CA  LYS    30      -8.226  -5.038  22.376  1.00 25.00           C
ATOM     31  CA  ILE    31      -6.480  -2.154  20.616  1.00 25.00           C
ATOM     32  CA  LEU    32      -6.117   0.087  17.555  1.00 25.00           C
ATOM     33  CA  VAL    33      -6.095   3.578  16.119  1.00 25.00           C
ATOM     34  CA  TRP    34      -7.512   1.872  13.078  1.00 25.00           C
ATOM     35  CA  LYS    35      -6.842   4.343  10.282  1.00 25.00           C
ATOM     36  CA  GLU    36      -7.833   5.776   6.938  1.00 25.00           C
ATOM     37  CA  LEU    37      -7.730   7.599   3.556  1.00 25.00           C
ATOM     38  CA  ASP    38     -10.407   7.935   0.826  1.00 25.00           C
ATOM     39  CA  TYR    39      -7.871   8.800  -1.875  1.00 25.00           C
ATOM     40  CA  GLY    40     -10.628   9.054  -4.525  1.00 25.00           C
ATOM     41  CA  SER    41      -9.012   9.937  -7.861  1.00 25.00           C
ATOM     42  CA  MET    42      -5.950   8.203  -6.492  1.00 25.00           C
ATOM     43  CA  THR    43      -5.083   5.482  -9.078  1.00 25.00           C
ATOM     44  CA  GLU    44      -2.340   7.843 -10.229  1.00 25.00           C
ATOM     45  CA  ALA    45       0.900   6.692  -8.594  1.00 25.00           C
ATOM     46  CA  GLU    46      -0.435   7.443  -5.057  1.00 25.00           C
ATOM     47  CA  LYS    47       0.094   3.691  -4.504  1.00 25.00           C
ATOM     48  CA  GLN    48       3.889   4.175  -4.675  1.00 25.00           C
ATOM     49  CA  MET    49       3.664   7.028  -2.129  1.00 25.00           C
ATOM     50  CA  LEU    50       1.569   4.821   0.195  1.00 25.00           C
ATOM     51  CA  VAL    51       4.143   2.004  -0.118  1.00 25.00           C
ATOM     52  CA  SER    52       6.966   4.457   0.704  1.00 25.00           C
ATOM     53  CA  GLU    53       5.033   5.692   3.771  1.00 25.00           C
ATOM     54  CA  VAL    54       4.503   2.078   4.922  1.00 25.00           C
ATOM     55  CA  ASN    55       8.242   1.368   4.494  1.00 25.00           C
ATOM     56  CA  LEU    56       9.095   4.497   6.529  1.00 25.00           C
ATOM     57  CA  LEU    57       6.681   3.389   9.289  1.00 25.00           C
ATOM     58  CA  ARG    58       8.287  -0.087   9.333  1.00 25.00           C
ATOM     59  CA  GLU    59      11.765   1.498   9.597  1.00 25.00           C
ATOM     60  CA  LEU    60      12.168  -0.904  12.529  1.00 25.00           C
ATOM     61  CA  LYS    61      10.103  -1.716  15.596  1.00 25.00           C
ATOM     62  CA  HIS    62      11.935   1.267  17.047  1.00 25.00           C
ATOM     63  CA  PRO    63      10.619   0.395  20.494  1.00 25.00           C
ATOM     64  CA  ASN    64       9.702   3.912  21.535  1.00 25.00           C
ATOM     65  CA  ILE    65       7.838   5.015  18.396  1.00 25.00           C
ATOM     66  CA  VAL    66       4.400   4.044  17.172  1.00 25.00           C
ATOM     67  CA  ARG    67       4.606   0.203  17.387  1.00 25.00           C
ATOM     68  CA  TYR    68       3.238   0.379  13.857  1.00 25.00           C
ATOM     69  CA  TYR    69       0.649  -2.391  13.234  1.00 25.00           C
ATOM     70  CA  ASP    70       1.059  -3.825   9.691  1.00 25.00           C
ATOM     71  CA  ARG    71      -1.100  -2.729   6.799  1.00 25.00           C
ATOM     72  CA  ILE    72      -4.588  -3.386   5.353  1.00 25.00           C
ATOM     73  CA  ILE    73      -5.686  -2.740   1.805  1.00 25.00           C
ATOM     74  CA  ASP    74      -9.409  -2.286   1.284  1.00 25.00           C
ATOM     75  CA  ARG    75      -9.943  -1.679  -2.449  1.00 25.00           C
ATOM     76  CA  THR    76     -13.650  -1.443  -1.492  1.00 25.00           C
ATOM     77  CA  ASN    77     -14.678   1.999  -2.821  1.00 25.00           C
ATOM     78  CA  THR    78     -11.320   3.476  -1.799  1.00 25.00           C
ATOM     79  CA  THR    79      -8.276   2.802   0.411  1.00 25.00           C
ATOM     80  CA  LEU    80      -5.228   2.493   2.759  1.00 25.00           C
ATOM     81  CA  TYR    81      -4.511   1.567   6.395  1.00 25.00           C
ATOM     82  CA  ILE    82      -1.751   2.323   8.930  1.00 25.00           C
ATOM     83  CA  VAL    83      -2.216   1.738  12.659  1.00 25.00           C
ATOM     84  CA  MET    84      -0.936   3.442  15.809  1.00 25.00           C
ATOM     85  CA  GLU    85      -0.849   0.778  18.482  1.00 25.00           C
ATOM     86  CA  TYR    86      -3.150   2.817  20.646  1.00 25.00           C
TER
END
