
#######################################################
#                                                     #
#                        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   66 (   66),  selected   66 , name T0356TS464_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS464_2-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N       7      N       7           #
LGA    D       8      D       8          1.683
LGA    L       9      L       9          1.252
LGA    R      10      R      10          1.606
LGA    D      11      D      11          0.699
LGA    F      12      F      12          0.466
LGA    L      13      L      13          0.559
LGA    T      14      T      14          0.445
LGA    L      15      L      15          0.646
LGA    L      16      L      16          0.682
LGA    E      17      E      17          0.591
LGA    Q      18      Q      18          0.601
LGA    Q      19      Q      19          0.995
LGA    G      20      G      20          1.084
LGA    E      21      E      21          1.362
LGA    L      22      L      22          0.843
LGA    K      23      K      23          2.087
LGA    R      24      R      24          2.708
LGA    E      34      I      25           -
LGA    I      35      T      26           -
LGA    T      36      L      27           -
LGA    E      37      P      28           -
LGA    I      38      V      29           -
LGA    A      39      D      30           -
LGA    D      40      P      31           -
LGA    R      41      H      32           -
LGA    T      42      L      33           -
LGA    L      43      E      34           -
LGA    R      44      I      35           -
LGA    A      45      T      36           -
LGA    G      46      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    G      47      G      47           #
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    P      48      L      66          4.782
LGA    A      49      F      67          2.840
LGA    L      50      G      68           -
LGA    L      51      T      69           -
LGA    F      52      -       -           -
LGA    V      62      P      70          1.977
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    L      63      V      73          1.189
LGA    C      64      A      74          2.396
LGA    N      65      M      75           #
LGA    -       -      G      76           -
LGA    L      66      M      77          3.384
LGA    M      77      G      78           -
LGA    G      78      Q      79           -
LGA    -       -      E      80           -
LGA    Q      79      D      81          5.652
LGA    E      80      -       -           -
LGA    D      81      -       -           -
LGA    V      82      V      82          3.584
LGA    S      83      S      83          3.506
LGA    A      84      A      84           -
LGA    L      85      L      85           #
LGA    R      86      R      86           -
LGA    E      87      E      87           -
LGA    V      88      V      88           -
LGA    G      89      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    K      90      L     332           #
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    L      91      A     335          1.270
LGA    L      92      L     336          3.180
LGA    D     314      N     337           -
LGA    A     315      E     338           -
LGA    I     316      V     339           -
LGA    Y     317      F     340           -
LGA    H     318      V     341           -
LGA    S     319      P     342           -
LGA    T     320      I     343           -
LGA    Y     321      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   66  124    5.0     28    2.30    71.43     17.020     1.165

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.418537 * X  +  -0.528492 * Y  +   0.738595 * Z  +  81.331940
  Y_new =   0.740546 * X  +   0.669382 * Y  +   0.059325 * Z  +  39.716358
  Z_new =  -0.525755 * X  +   0.522134 * Y  +   0.671534 * Z  +  60.535858 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.660885   -2.480708  [ DEG:    37.8659   -142.1341 ]
  Theta =   0.553602    2.587990  [ DEG:    31.7191    148.2809 ]
  Phi   =   1.056378   -2.085215  [ DEG:    60.5260   -119.4740 ]
 
# 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: T0356TS464_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_2-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   66  124   5.0   28   2.30   71.43  17.020
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_2-D1
PFRMAT TS
TARGET T0356
MODEL 2
PARENT N/A
ATOM      4  CA  ASN     7      76.596  80.887  87.997  1.00  0.00
ATOM      5  CA  ASP     8      74.930  79.547  84.863  1.00  0.00
ATOM      6  CA  LEU     9      72.222  77.393  86.377  1.00  0.00
ATOM      7  CA  ARG    10      71.656  80.085  88.930  1.00  0.00
ATOM      8  CA  ASP    11      72.578  82.765  86.334  1.00  0.00
ATOM      9  CA  PHE    12      69.842  80.871  84.516  1.00  0.00
ATOM     10  CA  LEU    13      68.121  80.144  87.825  1.00  0.00
ATOM     11  CA  THR    14      68.544  83.804  88.738  1.00  0.00
ATOM     12  CA  LEU    15      66.838  84.633  85.442  1.00  0.00
ATOM     13  CA  LEU    16      63.917  82.252  86.030  1.00  0.00
ATOM     14  CA  GLU    17      63.581  83.379  89.655  1.00  0.00
ATOM     15  CA  GLN    18      63.402  86.945  88.399  1.00  0.00
ATOM     16  CA  GLN    19      60.466  85.889  86.234  1.00  0.00
ATOM     17  CA  GLY    20      58.710  84.200  89.141  1.00  0.00
ATOM     18  CA  GLU    21      58.950  80.769  87.520  1.00  0.00
ATOM     19  CA  LEU    22      61.344  79.279  90.035  1.00  0.00
ATOM     20  CA  LYS    23      61.782  79.678  93.772  1.00  0.00
ATOM     21  CA  ARG    24      64.559  78.655  96.132  1.00  0.00
ATOM     22  CA  GLU    34      73.407  86.006  76.293  1.00  0.00
ATOM     23  CA  ILE    35      71.646  85.688  79.676  1.00  0.00
ATOM     24  CA  THR    36      69.389  88.710  79.239  1.00  0.00
ATOM     25  CA  GLU    37      68.499  88.064  75.588  1.00  0.00
ATOM     26  CA  ILE    38      67.486  84.583  76.834  1.00  0.00
ATOM     27  CA  ALA    39      65.273  85.976  79.597  1.00  0.00
ATOM     28  CA  ASP    40      63.701  88.443  77.160  1.00  0.00
ATOM     29  CA  ARG    41      62.794  85.581  74.838  1.00  0.00
ATOM     30  CA  THR    42      61.081  83.710  77.685  1.00  0.00
ATOM     31  CA  LEU    43      61.822  82.998  81.484  1.00  0.00
ATOM     32  CA  ARG    44      59.560  85.906  80.507  1.00  0.00
ATOM     33  CA  ALA    45      57.418  83.578  78.402  1.00  0.00
ATOM     34  CA  GLY    46      56.858  81.349  81.429  1.00  0.00
ATOM     35  CA  GLY    47      59.375  78.471  81.220  1.00  0.00
ATOM     36  CA  PRO    48      60.594  77.300  84.640  1.00  0.00
ATOM     37  CA  ALA    49      62.489  74.074  83.841  1.00  0.00
ATOM     38  CA  LEU    50      65.617  74.806  81.807  1.00  0.00
ATOM     39  CA  LEU    51      67.529  72.163  79.878  1.00  0.00
ATOM     40  CA  PHE    52      70.921  73.430  78.715  1.00  0.00
ATOM     41  CA  VAL    62      58.872  74.334  75.304  1.00  0.00
ATOM     42  CA  LEU    63      62.508  75.316  75.931  1.00  0.00
ATOM     43  CA  CYS    64      64.600  77.305  73.481  1.00  0.00
ATOM     44  CA  ASN    65      68.044  75.690  73.433  1.00  0.00
ATOM     45  CA  LEU    66      71.039  77.768  72.338  1.00  0.00
ATOM     46  CA  MET    77      63.380  79.101  61.926  1.00  0.00
ATOM     47  CA  GLY    78      62.105  82.297  63.608  1.00  0.00
ATOM     48  CA  GLN    79      60.373  83.456  66.793  1.00  0.00
ATOM     49  CA  GLU    80      57.036  83.167  65.014  1.00  0.00
ATOM     50  CA  ASP    81      57.699  79.491  64.400  1.00  0.00
ATOM     51  CA  VAL    82      58.145  78.952  68.116  1.00  0.00
ATOM     52  CA  SER    83      54.878  80.790  68.818  1.00  0.00
ATOM     53  CA  ALA    84      53.143  78.480  66.391  1.00  0.00
ATOM     54  CA  LEU    85      54.766  75.454  68.024  1.00  0.00
ATOM     55  CA  ARG    86      53.217  76.482  71.382  1.00  0.00
ATOM     56  CA  GLU    87      49.777  76.103  69.821  1.00  0.00
ATOM     57  CA  VAL    88      50.747  72.985  68.199  1.00  0.00
ATOM     58  CA  GLY    89      51.492  71.654  71.664  1.00  0.00
ATOM     59  CA  LYS    90      55.102  70.780  70.956  1.00  0.00
ATOM     60  CA  LEU    91      58.599  71.701  72.084  1.00  0.00
ATOM     61  CA  LEU    92      61.611  73.668  70.949  1.00  0.00
ATOM     99  CA  ASP   314      72.279  73.989 100.173  1.00  0.00
ATOM    100  CA  ALA   315      69.086  75.331  98.574  1.00  0.00
ATOM    101  CA  ILE   316      65.592  74.096  97.886  1.00  0.00
ATOM    102  CA  TYR   317      64.166  75.356  94.587  1.00  0.00
ATOM    103  CA  HIS   318      60.388  75.375  94.036  1.00  0.00
ATOM    104  CA  SER   319      58.261  76.060  90.925  1.00  0.00
ATOM    105  CA  THR   320      55.299  77.997  92.294  1.00  0.00
ATOM    106  CA  TYR   321      52.232  78.737  90.251  1.00  0.00
TER
END
