
#######################################################
#                                                     #
#                        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 T0356TS464_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS464_3-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    R      10      P      31           #
LGA    D      11      H      32          0.997
LGA    F      12      L      33          4.715
LGA    L      13      -       -           -
LGA    T      14      E      34          2.579
LGA    L      15      I      35          0.974
LGA    L      16      T      36          1.452
LGA    E      17      E      37          1.419
LGA    Q      18      I      38          2.290
LGA    Q      19      A      39          2.611
LGA    G      20      D      40          1.949
LGA    E      21      R      41          5.517
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    L      22      R      44           #
LGA    K      23      A      45           -
LGA    R      24      G      46           -
LGA    I      25      G      47           -
LGA    T      26      P      48           -
LGA    E      37      A      49          3.628
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    I      38      N      65          4.801
LGA    A      39      L      66          2.127
LGA    D      40      F      67          3.284
LGA    R      41      G      68          3.677
LGA    T      42      T      69          3.836
LGA    L      43      P      70          2.817
LGA    R      44      -       -           -
LGA    A      45      -       -           -
LGA    G      46      K      71          2.688
LGA    G      47      R      72          3.843
LGA    -       -      V      73           -
LGA    P      48      A      74          2.091
LGA    A      49      M      75          4.133
LGA    L      50      G      76          0.598
LGA    L      51      M      77          5.220
LGA    F      52      G      78           -
LGA    S      59      Q      79           -
LGA    M      60      E      80           -
LGA    P      61      D      81           -
LGA    V      62      V      82           -
LGA    L      63      S      83           -
LGA    C      64      A      84           -
LGA    K      71      L      85           -
LGA    R      72      R      86           -
LGA    V      73      E      87           -
LGA    A      74      V      88           -
LGA    M      75      G      89           -
LGA    G      76      K      90           -
LGA    M      77      L      91           -
LGA    G      78      L      92           -
LGA    Q      79      A      93           -
LGA    E      80      F      94           -
LGA    D      81      L      95           -
LGA    V      82      K      96           -
LGA    S      83      D     314          2.876
LGA    A      84      -       -           -
LGA    L      85      -       -           -
LGA    R      86      -       -           -
LGA    E      87      A     315          1.079
LGA    V      88      I     316          2.481
LGA    G      89      -       -           -
LGA    K      90      -       -           -
LGA    L      91      Y     317          1.413
LGA    L      92      H     318          3.172
LGA    A      93      -       -           -
LGA    F      94      -       -           -
LGA    L      95      S     319          1.657
LGA    K      96      T     320          1.947
LGA    A     315      Y     321           -
LGA    I     316      -       -           -
LGA    Y     317      T     322          4.240
LGA    H     318      G     323          2.354
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    S     319      D     327          1.211
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    T     320      V     331           #
LGA    Y     321      L     332           -
LGA    V     339      G     333           -
LGA    F     340      V     334           -
LGA    V     341      A     335           -
LGA    P     342      L     336           -
LGA    I     343      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77  124    5.0     33    3.01     6.06     15.729     1.061

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.227469 * X  +   0.791102 * Y  +  -0.567817 * Z  +  -4.341831
  Y_new =  -0.786673 * X  +   0.492960 * Y  +   0.371666 * Z  + 117.359802
  Z_new =   0.573937 * X  +   0.362144 * Y  +   0.734472 * Z  +  21.447191 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.458086   -2.683507  [ DEG:    26.2464   -153.7536 ]
  Theta =  -0.611305   -2.530288  [ DEG:   -35.0252   -144.9748 ]
  Phi   =  -1.289321    1.852272  [ DEG:   -73.8726    106.1274 ]
 
# 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_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_3-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   77  124   5.0   33   3.01    6.06  15.729
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_3-D1
PFRMAT TS
TARGET T0356
MODEL 3
PARENT N/A
ATOM      1  CA  ARG    10      61.449  57.019  95.374  1.00  0.00
ATOM      2  CA  ASP    11      61.311  60.320  97.296  1.00  0.00
ATOM      3  CA  PHE    12      62.592  62.486  94.459  1.00  0.00
ATOM      4  CA  LEU    13      59.620  61.474  92.317  1.00  0.00
ATOM      5  CA  THR    14      57.363  62.192  95.284  1.00  0.00
ATOM      6  CA  LEU    15      58.964  65.635  95.434  1.00  0.00
ATOM      7  CA  LEU    16      58.640  65.626  91.639  1.00  0.00
ATOM      8  CA  GLU    17      55.224  63.956  92.047  1.00  0.00
ATOM      9  CA  GLN    18      54.136  66.413  94.757  1.00  0.00
ATOM     10  CA  GLN    19      55.105  69.294  92.423  1.00  0.00
ATOM     11  CA  GLY    20      52.866  67.763  89.770  1.00  0.00
ATOM     12  CA  GLU    21      55.799  67.307  87.356  1.00  0.00
ATOM     13  CA  LEU    22      55.453  63.541  87.225  1.00  0.00
ATOM     14  CA  LYS    23      52.403  61.321  87.307  1.00  0.00
ATOM     15  CA  ARG    24      51.736  57.586  87.224  1.00  0.00
ATOM     16  CA  ILE    25      49.685  55.920  84.537  1.00  0.00
ATOM     17  CA  THR    26      49.780  52.282  85.559  1.00  0.00
ATOM     18  CA  GLU    37      62.080  72.131  87.830  1.00  0.00
ATOM     19  CA  ILE    38      62.707  75.534  86.248  1.00  0.00
ATOM     20  CA  ALA    39      62.944  73.987  82.807  1.00  0.00
ATOM     21  CA  ASP    40      59.512  72.363  83.181  1.00  0.00
ATOM     22  CA  ARG    41      57.534  75.585  83.798  1.00  0.00
ATOM     23  CA  THR    42      59.722  77.636  81.258  1.00  0.00
ATOM     24  CA  LEU    43      58.908  74.849  78.786  1.00  0.00
ATOM     25  CA  ARG    44      55.269  74.788  79.928  1.00  0.00
ATOM     26  CA  ALA    45      55.297  78.600  79.649  1.00  0.00
ATOM     27  CA  GLY    46      56.233  78.457  75.972  1.00  0.00
ATOM     28  CA  GLY    47      59.994  79.061  76.046  1.00  0.00
ATOM     29  CA  PRO    48      61.659  78.153  72.744  1.00  0.00
ATOM     30  CA  ALA    49      65.059  77.593  74.363  1.00  0.00
ATOM     31  CA  LEU    50      66.756  77.553  77.766  1.00  0.00
ATOM     32  CA  LEU    51      70.061  79.078  78.879  1.00  0.00
ATOM     33  CA  PHE    52      71.806  78.281  82.171  1.00  0.00
ATOM     34  CA  SER    59      64.906  70.405  90.993  1.00  0.00
ATOM     35  CA  MET    60      65.654  72.686  93.938  1.00  0.00
ATOM     36  CA  PRO    61      66.139  76.357  94.781  1.00  0.00
ATOM     37  CA  VAL    62      68.677  77.937  97.128  1.00  0.00
ATOM     38  CA  LEU    63      67.110  79.821 100.024  1.00  0.00
ATOM     39  CA  CYS    64      69.001  82.450 102.002  1.00  0.00
ATOM     40  CA  LYS    71      79.308  70.475 105.547  1.00  0.00
ATOM     41  CA  ARG    72      80.942  67.824 103.396  1.00  0.00
ATOM     42  CA  VAL    73      80.725  70.017 100.269  1.00  0.00
ATOM     43  CA  ALA    74      82.703  72.847 101.952  1.00  0.00
ATOM     44  CA  MET    75      85.279  70.278 103.065  1.00  0.00
ATOM     45  CA  GLY    76      85.960  68.430  99.819  1.00  0.00
ATOM     46  CA  MET    77      85.848  71.620  97.687  1.00  0.00
ATOM     47  CA  GLY    78      86.761  74.372 100.132  1.00  0.00
ATOM     48  CA  GLN    79      83.582  76.357  99.461  1.00  0.00
ATOM     49  CA  GLU    80      81.592  78.990 101.343  1.00  0.00
ATOM     50  CA  ASP    81      78.412  77.642 102.960  1.00  0.00
ATOM     51  CA  VAL    82      76.318  79.493 100.319  1.00  0.00
ATOM     52  CA  SER    83      78.152  77.997  97.268  1.00  0.00
ATOM     53  CA  ALA    84      77.531  74.551  98.827  1.00  0.00
ATOM     54  CA  LEU    85      73.744  75.215  98.960  1.00  0.00
ATOM     55  CA  ARG    86      73.378  76.682  95.480  1.00  0.00
ATOM     56  CA  GLU    87      75.371  73.779  93.973  1.00  0.00
ATOM     57  CA  VAL    88      72.905  71.358  95.587  1.00  0.00
ATOM     58  CA  GLY    89      69.894  72.783  93.776  1.00  0.00
ATOM     59  CA  LYS    90      71.761  72.511  90.490  1.00  0.00
ATOM     60  CA  LEU    91      72.010  68.707  90.681  1.00  0.00
ATOM     61  CA  LEU    92      68.327  68.277  91.536  1.00  0.00
ATOM     62  CA  ALA    93      67.475  70.267  88.424  1.00  0.00
ATOM     63  CA  PHE    94      69.799  68.136  86.294  1.00  0.00
ATOM     64  CA  LEU    95      67.483  65.169  87.235  1.00  0.00
ATOM     65  CA  LYS    96      64.352  63.846  85.575  1.00  0.00
ATOM    130  CA  ALA   315      53.611  52.571  87.403  1.00  0.00
ATOM    131  CA  ILE   316      54.534  54.675  84.391  1.00  0.00
ATOM    132  CA  TYR   317      56.134  58.108  84.667  1.00  0.00
ATOM    133  CA  HIS   318      55.174  61.050  82.481  1.00  0.00
ATOM    134  CA  SER   319      55.862  64.777  82.472  1.00  0.00
ATOM    135  CA  THR   320      52.916  67.097  83.066  1.00  0.00
ATOM    136  CA  TYR   321      52.751  70.057  80.700  1.00  0.00
ATOM    137  CA  VAL   339      70.205  95.518  96.445  1.00  0.00
ATOM    138  CA  PHE   340      68.910  94.038  93.190  1.00  0.00
ATOM    139  CA  VAL   341      68.155  90.739  94.982  1.00  0.00
ATOM    140  CA  PRO   342      64.891  90.845  97.015  1.00  0.00
ATOM    141  CA  ILE   343      64.891  91.244 100.789  1.00  0.00
TER
END
