
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   77 (  602),  selected   77 , name T0303_D2.pdb
# PARAMETERS: T0303TS168_3-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          0.726
LGA    L      19      L      19          0.528
LGA    P      20      P      20          1.665
LGA    D      21      D      21          1.970
LGA    L      22      L      22          1.062
LGA    A      23      A      23          0.555
LGA    L      24      L      24          1.504
LGA    S      25      S      25          1.281
LGA    I      26      I      26          0.555
LGA    N      27      N      27          0.653
LGA    S      28      S      28          0.952
LGA    A      29      A      29          0.742
LGA    L      30      L      30          0.396
LGA    K      31      K      31          0.343
LGA    D      32      D      32          1.023
LGA    V      33      V      33          4.927
LGA    N      34      N      34           -
LGA    L      35      L      35           -
LGA    P      36      P      36           -
LGA    Q      37      Q      37           -
LGA    A      38      A      38           -
LGA    S      39      S      39           -
LGA    E      40      E      40           -
LGA    N      41      N      41           -
LGA    L      42      L      42           -
LGA    V      43      V      43           -
LGA    M      44      M      44           -
LGA    T      45      T      45           -
LGA    W      46      W      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      N      49           -
LGA    I      47      G      50          4.501
LGA    G      48      A      51          3.054
LGA    N      49      -       -           -
LGA    G      50      D      52           #
LGA    A      51      V      53          0.722
LGA    D      52      L      54           #
LGA    V      53      S      55           -
LGA    L      54      Q      56          4.673
LGA    S      55      R      57           -
LGA    Q      56      A      58           -
LGA    R      57      V      59           -
LGA    A      58      D      60           -
LGA    V      59      W      61           -
LGA    D      60      A      62           -
LGA    W      61      C      63           -
LGA    A      62      T      64           -
LGA    C      63      Q      65           -
LGA    T      64      A      66           -
LGA    Q      65      E      67           -
LGA    A      66      K      68           -
LGA    E      67      -       -           -
LGA    K      68      -       -           -
LGA    E      69      -       -           -
LGA    L      70      E      69          7.010
LGA    T      71      L      70          1.698
LGA    E      72      T      71          3.075
LGA    D      73      E      72          2.711
LGA    -       -      D      73           -
LGA    E      74      E      74          2.172
LGA    F      75      F      75          2.236
LGA    K      76      K      76          2.164
LGA    Y      77      Y      77          1.574
LGA    F      78      F      78          1.380
LGA    K      79      K      79          1.587
LGA    R      80      R      80          1.481
LGA    Q      81      Q      81          1.005
LGA    F      82      F      82          0.715
LGA    G      83      G      83          0.721
LGA    F      84      F      84          0.734
LGA    Y      85      Y      85          0.769
LGA    Y      86      Y      86          1.166
LGA    G      87      G      87          1.206
LGA    E      88      E      88          1.151
LGA    N      89      N      89          1.709
LGA    L      90      L      90          3.170
LGA    C      91      -       -           -
LGA    N      92      -       -           -
LGA    I      93      C      91          2.476
LGA    S      94      N      92          1.084
LGA    -       -      I      93           -
LGA    -       -      S      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77   77    5.0     43    2.22    76.74     42.980     1.851

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.567615 * X  +  -0.175107 * Y  +  -0.804457 * Z  + -13.629307
  Y_new =  -0.108398 * X  +   0.984508 * Y  +  -0.137815 * Z  +  82.691887
  Z_new =   0.816127 * X  +   0.008976 * Y  +  -0.577803 * Z  +  18.059305 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.126060   -0.015533  [ DEG:   179.1100     -0.8900 ]
  Theta =  -0.954677   -2.186916  [ DEG:   -54.6990   -125.3010 ]
  Phi   =  -2.952894    0.188699  [ DEG:  -169.1884     10.8116 ]
 
# 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_3-D2                               
REMARK     2: T0303_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS168_3-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   43   2.22   76.74  42.980
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS168_3-D2
PFRMAT TS
TARGET T0303
MODEL 3
PARENT N/A
ATOM     18  CA  SER    18     -12.142  83.620  21.309  1.00 25.00           C
ATOM     19  CA  LEU    19     -11.194  86.909  19.691  1.00 25.00           C
ATOM     20  CA  PRO    20     -12.151  90.572  20.273  1.00 25.00           C
ATOM     21  CA  ASP    21     -11.843  90.076  24.058  1.00 25.00           C
ATOM     22  CA  LEU    22      -8.393  88.480  23.592  1.00 25.00           C
ATOM     23  CA  ALA    23      -7.298  91.424  21.401  1.00 25.00           C
ATOM     24  CA  LEU    24      -8.529  93.892  24.059  1.00 25.00           C
ATOM     25  CA  SER    25      -6.595  91.984  26.759  1.00 25.00           C
ATOM     26  CA  ILE    26      -3.437  92.072  24.595  1.00 25.00           C
ATOM     27  CA  ASN    27      -3.867  95.843  24.078  1.00 25.00           C
ATOM     28  CA  SER    28      -4.276  96.339  27.853  1.00 25.00           C
ATOM     29  CA  ALA    29      -1.104  94.290  28.490  1.00 25.00           C
ATOM     30  CA  LEU    30       0.803  96.400  25.926  1.00 25.00           C
ATOM     31  CA  LYS    31      -0.431  99.609  27.611  1.00 25.00           C
ATOM     32  CA  ASP    32       0.691  98.280  31.022  1.00 25.00           C
ATOM     33  CA  VAL    33       3.078  95.821  32.672  1.00 25.00           C
ATOM     34  CA  ASN    34       1.357  96.791  35.882  1.00 25.00           C
ATOM     35  CA  LEU    35       1.137  93.137  36.853  1.00 25.00           C
ATOM     36  CA  PRO    36       1.427  91.169  40.062  1.00 25.00           C
ATOM     37  CA  GLN    37      -0.065  87.725  40.866  1.00 25.00           C
ATOM     38  CA  ALA    38       0.671  85.732  37.643  1.00 25.00           C
ATOM     39  CA  SER    39       0.223  82.198  36.201  1.00 25.00           C
ATOM     40  CA  GLU    40      -0.390  80.480  32.829  1.00 25.00           C
ATOM     41  CA  ASN    41       0.245  77.264  30.850  1.00 25.00           C
ATOM     42  CA  LEU    42      -3.292  77.434  29.393  1.00 25.00           C
ATOM     43  CA  VAL    43      -2.732  81.087  28.393  1.00 25.00           C
ATOM     44  CA  MET    44       0.578  80.146  26.711  1.00 25.00           C
ATOM     45  CA  THR    45      -1.166  77.314  24.810  1.00 25.00           C
ATOM     46  CA  TRP    46      -3.902  79.736  23.666  1.00 25.00           C
ATOM     47  CA  ILE    47      -1.242  82.222  22.479  1.00 25.00           C
ATOM     48  CA  GLY    48       0.322  80.259  19.649  1.00 25.00           C
ATOM     49  CA  ASN    49       0.658  81.411  16.033  1.00 25.00           C
ATOM     50  CA  GLY    50       0.608  85.044  17.240  1.00 25.00           C
ATOM     51  CA  ALA    51       4.323  84.278  17.460  1.00 25.00           C
ATOM     52  CA  ASP    52       5.580  80.667  17.666  1.00 25.00           C
ATOM     53  CA  VAL    53       9.203  81.889  17.440  1.00 25.00           C
ATOM     54  CA  LEU    54       8.547  84.427  20.231  1.00 25.00           C
ATOM     55  CA  SER    55       7.011  81.674  22.407  1.00 25.00           C
ATOM     56  CA  GLN    56      10.060  79.443  21.778  1.00 25.00           C
ATOM     57  CA  ARG    57      12.396  82.322  22.740  1.00 25.00           C
ATOM     58  CA  ALA    58      10.395  82.905  25.953  1.00 25.00           C
ATOM     59  CA  VAL    59      10.613  79.175  26.795  1.00 25.00           C
ATOM     60  CA  ASP    60      14.398  79.239  26.208  1.00 25.00           C
ATOM     61  CA  TRP    61      14.724  82.298  28.489  1.00 25.00           C
ATOM     62  CA  ALA    62      12.686  80.522  31.203  1.00 25.00           C
ATOM     63  CA  CYS    63      11.462  83.827  32.729  1.00 25.00           C
ATOM     64  CA  THR    64      15.071  84.885  33.384  1.00 25.00           C
ATOM     65  CA  GLN    65      18.087  86.957  32.359  1.00 25.00           C
ATOM     66  CA  ALA    66      15.704  89.820  32.845  1.00 25.00           C
ATOM     67  CA  GLU    67      17.790  92.768  31.776  1.00 25.00           C
ATOM     68  CA  LYS    68      19.381  91.730  28.478  1.00 25.00           C
ATOM     69  CA  GLU    69      18.578  94.402  25.891  1.00 25.00           C
ATOM     70  CA  LEU    70      15.733  96.512  27.140  1.00 25.00           C
ATOM     71  CA  THR    71      13.305  96.189  24.196  1.00 25.00           C
ATOM     72  CA  GLU    72      13.415  92.372  24.492  1.00 25.00           C
ATOM     73  CA  ASP    73      12.708  92.619  28.248  1.00 25.00           C
ATOM     74  CA  GLU    74       9.746  94.948  27.562  1.00 25.00           C
ATOM     75  CA  PHE    75       8.384  92.489  24.959  1.00 25.00           C
ATOM     76  CA  LYS    76       8.722  89.613  27.463  1.00 25.00           C
ATOM     77  CA  TYR    77       6.868  91.667  30.111  1.00 25.00           C
ATOM     78  CA  PHE    78       4.077  92.429  27.602  1.00 25.00           C
ATOM     79  CA  LYS    79       3.803  88.707  26.740  1.00 25.00           C
ATOM     80  CA  ARG    80       3.592  87.836  30.464  1.00 25.00           C
ATOM     81  CA  GLN    81       0.843  90.457  30.947  1.00 25.00           C
ATOM     82  CA  PHE    82      -1.089  89.016  27.970  1.00 25.00           C
ATOM     83  CA  GLY    83      -0.766  85.492  29.436  1.00 25.00           C
ATOM     84  CA  PHE    84      -2.044  86.755  32.819  1.00 25.00           C
ATOM     85  CA  TYR    85      -5.021  88.437  31.093  1.00 25.00           C
ATOM     86  CA  TYR    86      -5.806  85.187  29.225  1.00 25.00           C
ATOM     87  CA  GLY    87      -5.654  83.231  32.514  1.00 25.00           C
ATOM     88  CA  GLU    88      -8.019  85.758  34.155  1.00 25.00           C
ATOM     89  CA  ASN    89     -10.447  85.435  31.210  1.00 25.00           C
ATOM     90  CA  LEU    90     -10.336  81.617  31.507  1.00 25.00           C
ATOM     91  CA  CYS    91     -11.044  81.864  35.262  1.00 25.00           C
ATOM     92  CA  ASN    92     -14.791  82.661  34.920  1.00 25.00           C
ATOM     93  CA  ILE    93     -15.614  83.772  31.349  1.00 25.00           C
ATOM     94  CA  SER    94     -15.623  86.462  28.597  1.00 25.00           C
TER
END
