
#######################################################
#                                                     #
#                        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   67 (   67),  selected   67 , name T0379TS168_4-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS168_4-D2.T0379_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          1.605
LGA    R      18      R      18          1.930
LGA    E      19      E      19          2.825
LGA    E      20      E      20          1.628
LGA    S      21      S      21          1.184
LGA    I      22      I      22          2.079
LGA    R      23      R      23          1.394
LGA    R      24      R      24          1.308
LGA    F      25      F      25          2.379
LGA    K      26      K      26          2.032
LGA    A      27      A      27          0.686
LGA    I      28      I      28          1.964
LGA    G      29      G      29          3.789
LGA    V      30      V      30          4.291
LGA    A      31      A      31          1.700
LGA    D      32      D      32          3.480
LGA    I      33      I      33          3.306
LGA    E      34      E      34          3.376
LGA    E      35      E      35          4.115
LGA    M      36      M      36          3.377
LGA    L      37      L      37          2.791
LGA    D      38      D      38          4.169
LGA    -       -      P      39           -
LGA    P      39      K      43          4.216
LGA    Y      40      G      44          1.331
LGA    L      41      L      45          1.447
LGA    Q      42      F      46          3.231
LGA    K      43      L      47          3.023
LGA    G      44      D      48          1.314
LGA    L      45      L      49          2.482
LGA    F      46      E      50          4.123
LGA    L      47      S      51          3.664
LGA    D      48      G      52          1.389
LGA    L      49      R      53           #
LGA    E      50      -       -           -
LGA    S      51      K      54           #
LGA    G      52      -       -           -
LGA    R      53      -       -           -
LGA    K      54      -       -           -
LGA    S      55      -       -           -
LGA    E      56      -       -           -
LGA    E      57      -       -           -
LGA    E      58      S      55          3.034
LGA    F      59      E      56          3.027
LGA    R      60      -       -           -
LGA    T      61      E      57          2.096
LGA    E      62      E      58          3.151
LGA    L      63      F      59          2.594
LGA    S      64      R      60          1.171
LGA    R      65      T      61          2.682
LGA    Y      66      E      62          2.946
LGA    I      67      L      63          1.364
LGA    G      68      S      64          1.253
LGA    K      69      R      65          3.813
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      G      68           -
LGA    -       -      K      69           -
LGA    E      70      E      70          1.276
LGA    L      71      L      71          2.036
LGA    T      72      T      72          2.064
LGA    Y      73      Y      73          2.069
LGA    Q      74      Q      74          1.310
LGA    Q      75      Q      75          0.873
LGA    V      76      V      76          0.623
LGA    Y      77      Y      77          0.450
LGA    D      78      D      78          0.487
LGA    A      79      A      79          1.008
LGA    L      80      L      80          1.915
LGA    L      81      L      81          2.077
LGA    G      82      G      82          2.099
LGA    F      83      F      83          1.553

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   67   64    5.0     57    2.49    68.42     60.240     2.200

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.047600 * X  +   0.990149 * Y  +  -0.131680 * Z  +  63.353195
  Y_new =   0.534135 * X  +  -0.136630 * Y  +  -0.834286 * Z  +   5.276527
  Z_new =  -0.844058 * X  +  -0.030623 * Y  +  -0.535376 * Z  +   7.638996 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.084456    0.057136  [ DEG:  -176.7263      3.2737 ]
  Theta =   1.004807    2.136786  [ DEG:    57.5712    122.4288 ]
  Phi   =   1.481915   -1.659678  [ DEG:    84.9074    -95.0926 ]
 
# 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: T0379TS168_4-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS168_4-D2.T0379_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   67   64   5.0   57   2.49   68.42  60.240
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS168_4-D2
PFRMAT TS
TARGET T0379
MODEL 4
PARENT N/A
ATOM     17  CA  ASN    17      69.871   7.001  12.772  1.00 25.00           C
ATOM     18  CA  ARG    18      67.981   4.667  15.059  1.00 25.00           C
ATOM     19  CA  GLU    19      71.224   4.630  17.095  1.00 25.00           C
ATOM     20  CA  GLU    20      70.060   7.711  19.049  1.00 25.00           C
ATOM     21  CA  SER    21      66.695   6.024  19.754  1.00 25.00           C
ATOM     22  CA  ILE    22      68.502   2.875  20.974  1.00 25.00           C
ATOM     23  CA  ARG    23      70.714   5.003  23.265  1.00 25.00           C
ATOM     24  CA  ARG    24      67.613   6.759  24.668  1.00 25.00           C
ATOM     25  CA  PHE    25      65.952   3.369  25.309  1.00 25.00           C
ATOM     26  CA  LYS    26      69.104   2.136  27.104  1.00 25.00           C
ATOM     27  CA  ALA    27      69.144   5.302  29.258  1.00 25.00           C
ATOM     28  CA  ILE    28      66.945   4.985  32.415  1.00 25.00           C
ATOM     29  CA  GLY    29      68.165   1.354  32.220  1.00 25.00           C
ATOM     30  CA  VAL    30      65.438  -0.330  30.279  1.00 25.00           C
ATOM     31  CA  ALA    31      62.975  -2.065  27.885  1.00 25.00           C
ATOM     32  CA  ASP    32      59.784  -0.362  29.142  1.00 25.00           C
ATOM     33  CA  ILE    33      60.377   2.571  26.753  1.00 25.00           C
ATOM     34  CA  GLU    34      60.880   0.132  23.844  1.00 25.00           C
ATOM     35  CA  GLU    35      57.631  -1.674  24.764  1.00 25.00           C
ATOM     36  CA  MET    36      55.773   1.674  24.871  1.00 25.00           C
ATOM     37  CA  LEU    37      57.186   2.597  21.434  1.00 25.00           C
ATOM     38  CA  ASP    38      55.318  -0.355  19.932  1.00 25.00           C
ATOM     39  CA  PRO    39      51.826   1.149  20.067  1.00 25.00           C
ATOM     40  CA  TYR    40      49.423   2.605  22.669  1.00 25.00           C
ATOM     41  CA  LEU    41      51.610   5.735  22.974  1.00 25.00           C
ATOM     42  CA  GLN    42      51.635   6.118  19.162  1.00 25.00           C
ATOM     43  CA  LYS    43      47.821   5.782  19.079  1.00 25.00           C
ATOM     44  CA  GLY    44      47.502   8.441  21.817  1.00 25.00           C
ATOM     45  CA  LEU    45      49.807  10.780  19.846  1.00 25.00           C
ATOM     46  CA  PHE    46      47.708  10.234  16.692  1.00 25.00           C
ATOM     47  CA  LEU    47      44.512  11.011  18.654  1.00 25.00           C
ATOM     48  CA  ASP    48      46.103  14.212  20.025  1.00 25.00           C
ATOM     49  CA  LEU    49      47.128  15.249  16.484  1.00 25.00           C
ATOM     50  CA  GLU    50      43.562  14.613  15.240  1.00 25.00           C
ATOM     51  CA  SER    51      41.641  16.802  17.597  1.00 25.00           C
ATOM     52  CA  GLY    52      43.050  18.607  20.612  1.00 25.00           C
ATOM     53  CA  ARG    53      45.024  21.533  19.124  1.00 25.00           C
ATOM     54  CA  LYS    54      47.842  20.200  21.336  1.00 25.00           C
ATOM     55  CA  SER    55      51.409  20.271  19.861  1.00 25.00           C
ATOM     56  CA  GLU    56      54.467  18.563  21.366  1.00 25.00           C
ATOM     57  CA  GLU    57      54.348  19.138  25.151  1.00 25.00           C
ATOM     58  CA  GLU    58      50.945  17.391  25.333  1.00 25.00           C
ATOM     59  CA  PHE    59      52.331  14.430  23.339  1.00 25.00           C
ATOM     60  CA  ARG    60      55.336  14.212  25.702  1.00 25.00           C
ATOM     61  CA  THR    61      52.990  14.256  28.729  1.00 25.00           C
ATOM     62  CA  GLU    62      50.884  11.465  27.167  1.00 25.00           C
ATOM     63  CA  LEU    63      54.045   9.398  26.536  1.00 25.00           C
ATOM     64  CA  SER    64      55.138   9.914  30.170  1.00 25.00           C
ATOM     65  CA  ARG    65      51.681   8.810  31.393  1.00 25.00           C
ATOM     66  CA  TYR    66      51.873   5.685  29.187  1.00 25.00           C
ATOM     67  CA  ILE    67      55.347   4.882  30.584  1.00 25.00           C
ATOM     68  CA  GLY    68      55.462   6.355  34.092  1.00 25.00           C
ATOM     69  CA  LYS    69      55.451   7.358  37.738  1.00 25.00           C
ATOM     70  CA  GLU    70      58.254   9.802  36.873  1.00 25.00           C
ATOM     71  CA  LEU    71      60.392   9.012  33.846  1.00 25.00           C
ATOM     72  CA  THR    72      61.074  12.728  33.279  1.00 25.00           C
ATOM     73  CA  TYR    73      59.675  14.572  30.200  1.00 25.00           C
ATOM     74  CA  GLN    74      63.146  16.178  29.980  1.00 25.00           C
ATOM     75  CA  GLN    75      64.715  12.749  29.307  1.00 25.00           C
ATOM     76  CA  VAL    76      62.135  12.081  26.556  1.00 25.00           C
ATOM     77  CA  TYR    77      62.898  15.486  24.980  1.00 25.00           C
ATOM     78  CA  ASP    78      66.649  14.718  25.074  1.00 25.00           C
ATOM     79  CA  ALA    79      66.020  11.325  23.412  1.00 25.00           C
ATOM     80  CA  LEU    80      63.923  13.017  20.691  1.00 25.00           C
ATOM     81  CA  LEU    81      66.716  15.569  20.093  1.00 25.00           C
ATOM     82  CA  GLY    82      69.279  12.735  19.817  1.00 25.00           C
ATOM     83  CA  PHE    83      67.032  10.914  17.307  1.00 25.00           C
TER
END
