
#######################################################
#                                                     #
#                        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   77 (   77),  selected   77 , name T0303TS168_4-D2
# Molecule2: number of CA atoms   77 (  602),  selected   77 , name T0303_D2.pdb
# PARAMETERS: T0303TS168_4-D2.T0303_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      18      S      18          1.006
LGA    L      19      L      19          3.296
LGA    P      20      P      20          2.486
LGA    D      21      D      21          2.996
LGA    L      22      L      22          2.969
LGA    A      23      A      23          2.515
LGA    L      24      L      24          2.261
LGA    S      25      S      25          2.307
LGA    I      26      I      26          2.569
LGA    N      27      N      27          2.542
LGA    S      28      S      28          2.108
LGA    A      29      A      29          2.178
LGA    L      30      L      30          2.285
LGA    K      31      K      31          2.192
LGA    D      32      D      32          2.216
LGA    V      33      V      33          2.310
LGA    N      34      N      34          3.471
LGA    L      35      -       -           -
LGA    P      36      L      35           #
LGA    Q      37      P      36          3.481
LGA    A      38      Q      37          1.142
LGA    S      39      A      38          1.663
LGA    E      40      S      39          4.026
LGA    -       -      E      40           -
LGA    -       -      N      41           -
LGA    N      41      L      42          4.343
LGA    L      42      V      43          4.027
LGA    V      43      M      44          4.213
LGA    M      44      T      45          3.388
LGA    T      45      W      46          3.380
LGA    W      46      -       -           -
LGA    I      47      I      47          1.933
LGA    G      48      G      48          2.989
LGA    N      49      N      49          2.033
LGA    G      50      G      50          3.445
LGA    A      51      A      51          3.463
LGA    D      52      D      52          3.746
LGA    V      53      V      53          3.418
LGA    L      54      L      54          3.780
LGA    -       -      S      55           -
LGA    S      55      Q      56          1.562
LGA    Q      56      R      57          6.292
LGA    -       -      A      58           -
LGA    -       -      V      59           -
LGA    R      57      D      60           #
LGA    A      58      -       -           -
LGA    V      59      -       -           -
LGA    D      60      -       -           -
LGA    W      61      W      61          5.508
LGA    A      62      A      62           #
LGA    C      63      C      63          5.190
LGA    T      64      T      64          4.361
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    Q      65      E      67          1.950
LGA    A      66      K      68          2.502
LGA    E      67      E      69          1.286
LGA    K      68      L      70          5.312
LGA    E      69      T      71          2.700
LGA    L      70      -       -           -
LGA    T      71      -       -           -
LGA    E      72      E      72          3.266
LGA    D      73      D      73          3.034
LGA    E      74      E      74          3.257
LGA    F      75      F      75          2.842
LGA    K      76      K      76          2.058
LGA    Y      77      Y      77          2.136
LGA    F      78      F      78          2.162
LGA    K      79      K      79          1.633
LGA    R      80      R      80          1.274
LGA    Q      81      Q      81          1.644
LGA    F      82      F      82          1.403
LGA    G      83      G      83          0.440
LGA    F      84      F      84          0.601
LGA    Y      85      Y      85          0.971
LGA    Y      86      Y      86          1.303
LGA    G      87      G      87          1.520
LGA    E      88      E      88          1.124
LGA    N      89      N      89          1.253
LGA    L      90      L      90          3.774
LGA    C      91      -       -           -
LGA    N      92      -       -           -
LGA    I      93      C      91          2.789
LGA    S      94      N      92          0.459
LGA    -       -      I      93           -
LGA    -       -      S      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77   77    5.0     65    2.92    73.85     54.642     2.154

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.724541 * X  +  -0.054555 * Y  +  -0.687069 * Z  + -14.851584
  Y_new =   0.687684 * X  +   0.009538 * Y  +  -0.725947 * Z  +  81.925224
  Z_new =   0.046158 * X  +  -0.998465 * Y  +   0.030606 * Z  +  18.801012 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.540153    1.601439  [ DEG:   -88.2443     91.7557 ]
  Theta =  -0.046174   -3.095419  [ DEG:    -2.6456   -177.3544 ]
  Phi   =   2.382287   -0.759305  [ DEG:   136.4950    -43.5050 ]
 
# 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: T0303TS168_4-D2                               
REMARK     2: T0303_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS168_4-D2.T0303_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   77   77   5.0   65   2.92   73.85  54.642
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS168_4-D2
PFRMAT TS
TARGET T0303
MODEL 4
PARENT N/A
ATOM     18  CA  SER    18     -12.909  83.758  21.982  1.00 25.00           C
ATOM     19  CA  LEU    19     -13.960  87.131  20.584  1.00 25.00           C
ATOM     20  CA  PRO    20     -14.989  90.489  22.111  1.00 25.00           C
ATOM     21  CA  ASP    21     -13.783  89.320  25.554  1.00 25.00           C
ATOM     22  CA  LEU    22     -10.440  88.229  24.039  1.00 25.00           C
ATOM     23  CA  ALA    23     -10.072  91.637  22.331  1.00 25.00           C
ATOM     24  CA  LEU    24     -10.809  93.406  25.646  1.00 25.00           C
ATOM     25  CA  SER    25      -8.187  91.244  27.412  1.00 25.00           C
ATOM     26  CA  ILE    26      -5.626  92.087  24.691  1.00 25.00           C
ATOM     27  CA  ASN    27      -6.404  95.816  25.079  1.00 25.00           C
ATOM     28  CA  SER    28      -5.961  95.539  28.873  1.00 25.00           C
ATOM     29  CA  ALA    29      -2.603  93.766  28.375  1.00 25.00           C
ATOM     30  CA  LEU    30      -1.479  96.520  25.963  1.00 25.00           C
ATOM     31  CA  LYS    31      -2.493  99.198  28.506  1.00 25.00           C
ATOM     32  CA  ASP    32      -0.531  97.375  31.244  1.00 25.00           C
ATOM     33  CA  VAL    33       2.632  98.486  29.369  1.00 25.00           C
ATOM     34  CA  ASN    34       1.759 102.150  29.994  1.00 25.00           C
ATOM     35  CA  LEU    35       0.740 102.945  26.420  1.00 25.00           C
ATOM     36  CA  PRO    36      -0.658 104.953  23.569  1.00 25.00           C
ATOM     37  CA  GLN    37      -2.788 102.846  21.284  1.00 25.00           C
ATOM     38  CA  ALA    38      -2.659  99.235  20.090  1.00 25.00           C
ATOM     39  CA  SER    39      -3.416  97.762  16.664  1.00 25.00           C
ATOM     40  CA  GLU    40      -4.503  94.762  14.685  1.00 25.00           C
ATOM     41  CA  ASN    41      -0.972  93.357  15.171  1.00 25.00           C
ATOM     42  CA  LEU    42      -1.788  92.503  18.814  1.00 25.00           C
ATOM     43  CA  VAL    43      -5.004  90.742  17.707  1.00 25.00           C
ATOM     44  CA  MET    44      -3.040  88.747  15.094  1.00 25.00           C
ATOM     45  CA  THR    45      -0.476  87.740  17.755  1.00 25.00           C
ATOM     46  CA  TRP    46      -3.299  86.624  20.090  1.00 25.00           C
ATOM     47  CA  ILE    47      -4.852  84.557  17.263  1.00 25.00           C
ATOM     48  CA  GLY    48      -2.193  83.742  14.607  1.00 25.00           C
ATOM     49  CA  ASN    49       0.687  81.663  16.041  1.00 25.00           C
ATOM     50  CA  GLY    50       0.448  83.159  19.578  1.00 25.00           C
ATOM     51  CA  ALA    51       3.948  82.220  20.643  1.00 25.00           C
ATOM     52  CA  ASP    52       7.632  82.273  19.601  1.00 25.00           C
ATOM     53  CA  VAL    53       6.612  82.383  15.911  1.00 25.00           C
ATOM     54  CA  LEU    54       4.218  85.284  16.633  1.00 25.00           C
ATOM     55  CA  SER    55       7.007  87.159  18.471  1.00 25.00           C
ATOM     56  CA  GLN    56       9.369  86.600  15.509  1.00 25.00           C
ATOM     57  CA  ARG    57       6.698  87.911  13.099  1.00 25.00           C
ATOM     58  CA  ALA    58       6.200  91.008  15.297  1.00 25.00           C
ATOM     59  CA  VAL    59       9.981  91.614  15.342  1.00 25.00           C
ATOM     60  CA  ASP    60      10.103  91.299  11.528  1.00 25.00           C
ATOM     61  CA  TRP    61       7.216  93.795  11.205  1.00 25.00           C
ATOM     62  CA  ALA    62       9.035  96.235  13.530  1.00 25.00           C
ATOM     63  CA  CYS    63      11.576  96.432  16.429  1.00 25.00           C
ATOM     64  CA  THR    64      11.812 100.206  15.787  1.00 25.00           C
ATOM     65  CA  GLN    65       9.955 102.028  18.485  1.00 25.00           C
ATOM     66  CA  ALA    66       9.567  99.889  21.660  1.00 25.00           C
ATOM     67  CA  GLU    67      13.264  99.058  21.979  1.00 25.00           C
ATOM     68  CA  LYS    68      15.641  99.762  24.867  1.00 25.00           C
ATOM     69  CA  GLU    69      14.713  97.099  27.334  1.00 25.00           C
ATOM     70  CA  LEU    70      15.912  93.998  25.524  1.00 25.00           C
ATOM     71  CA  THR    71      13.512  93.091  22.681  1.00 25.00           C
ATOM     72  CA  GLU    72      13.339  89.480  23.946  1.00 25.00           C
ATOM     73  CA  ASP    73      12.594  90.731  27.489  1.00 25.00           C
ATOM     74  CA  GLU    74       9.821  92.997  26.132  1.00 25.00           C
ATOM     75  CA  PHE    75       8.324  90.049  24.199  1.00 25.00           C
ATOM     76  CA  LYS    76       8.413  87.897  27.366  1.00 25.00           C
ATOM     77  CA  TYR    77       6.674  90.682  29.337  1.00 25.00           C
ATOM     78  CA  PHE    78       3.984  90.957  26.625  1.00 25.00           C
ATOM     79  CA  LYS    79       3.452  87.165  26.734  1.00 25.00           C
ATOM     80  CA  ARG    80       3.122  87.297  30.547  1.00 25.00           C
ATOM     81  CA  GLN    81       0.563  90.132  30.252  1.00 25.00           C
ATOM     82  CA  PHE    82      -1.423  88.105  27.679  1.00 25.00           C
ATOM     83  CA  GLY    83      -1.380  85.064  30.006  1.00 25.00           C
ATOM     84  CA  PHE    84      -2.614  87.236  32.909  1.00 25.00           C
ATOM     85  CA  TYR    85      -5.433  88.613  30.712  1.00 25.00           C
ATOM     86  CA  TYR    86      -6.425  85.053  29.711  1.00 25.00           C
ATOM     87  CA  GLY    87      -6.466  84.002  33.394  1.00 25.00           C
ATOM     88  CA  GLU    88      -8.665  87.017  34.255  1.00 25.00           C
ATOM     89  CA  ASN    89     -11.065  86.109  31.411  1.00 25.00           C
ATOM     90  CA  LEU    90     -11.238  82.499  32.677  1.00 25.00           C
ATOM     91  CA  CYS    91     -11.984  83.750  36.219  1.00 25.00           C
ATOM     92  CA  ASN    92     -14.897  85.652  34.617  1.00 25.00           C
ATOM     93  CA  ILE    93     -16.150  83.838  31.495  1.00 25.00           C
ATOM     94  CA  SER    94     -16.092  87.243  29.676  1.00 25.00           C
TER
END
