
#######################################################
#                                                     #
#                        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   58 (   58),  selected   58 , name T0356TS464_4-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS464_4-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      10      -       -           -
LGA    D      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    T      14      N       7           #
LGA    L      15      D       8           -
LGA    -       -      L       9           -
LGA    L      16      R      10           #
LGA    E      17      D      11          3.348
LGA    Q      18      F      12          5.203
LGA    Q      19      L      13          3.363
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    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    E      34      I      35          1.900
LGA    I      35      T      36          2.035
LGA    T      36      E      37          1.606
LGA    E      37      I      38          1.475
LGA    I      38      A      39          2.228
LGA    A      39      D      40          2.178
LGA    D      40      R      41          0.982
LGA    R      41      T      42          1.154
LGA    T      42      L      43          1.465
LGA    L      43      R      44          0.739
LGA    R      44      A      45          1.764
LGA    A      45      G      46          1.976
LGA    G      46      G      47           -
LGA    G      47      P      48           -
LGA    P      48      -       -           -
LGA    A      49      -       -           -
LGA    L      50      -       -           -
LGA    L      51      -       -           -
LGA    F      52      -       -           -
LGA    V      62      -       -           -
LGA    L      63      -       -           -
LGA    C      64      -       -           -
LGA    N      65      -       -           -
LGA    L      66      -       -           -
LGA    M      77      -       -           -
LGA    G      78      A      49          3.795
LGA    Q      79      L      50          3.101
LGA    E      80      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    D      81      N      65           #
LGA    V      82      L      66          2.235
LGA    -       -      F      67           -
LGA    S      83      G      68          4.906
LGA    A      84      T      69          6.523
LGA    L      85      P      70          5.930
LGA    R      86      K      71          3.802
LGA    E      87      R      72          3.572
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    V      88      M      75          3.276
LGA    G      89      G      76           #
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    K      90      V      82          1.925
LGA    L      91      S      83          3.599
LGA    L      92      A      84          2.943
LGA    A      93      L      85          2.762
LGA    A     315      R      86           -
LGA    I     316      E      87           -
LGA    Y     317      V      88           -
LGA    H     318      G      89           -
LGA    S     319      K      90           -
LGA    T     320      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    Y     321      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    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      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)   58  124    5.0     28    3.19     0.00     15.298     0.850

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.454637 * X  +   0.799968 * Y  +   0.391608 * Z  +  29.699223
  Y_new =   0.808037 * X  +   0.185494 * Y  +   0.559167 * Z  +  60.409584
  Z_new =   0.374674 * X  +   0.570652 * Y  +  -0.730736 * Z  +  54.687965 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.478590   -0.663003  [ DEG:   142.0127    -37.9873 ]
  Theta =  -0.384046   -2.757547  [ DEG:   -22.0042   -157.9958 ]
  Phi   =   2.083295   -1.058298  [ DEG:   119.3640    -60.6360 ]
 
# 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_4-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_4-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   58  124   5.0   28   3.19    0.00  15.298
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_4-D1
PFRMAT TS
TARGET T0356
MODEL 4
PARENT N/A
ATOM      1  CA  ARG    10      67.548  86.879  74.177  1.00  0.00
ATOM      2  CA  ASP    11      65.819  88.451  77.147  1.00  0.00
ATOM      3  CA  PHE    12      64.612  85.146  78.561  1.00  0.00
ATOM      4  CA  LEU    13      68.051  83.630  78.002  1.00  0.00
ATOM      5  CA  THR    14      69.566  86.716  79.612  1.00  0.00
ATOM      6  CA  LEU    15      67.271  86.071  82.574  1.00  0.00
ATOM      7  CA  LEU    16      68.230  82.392  82.878  1.00  0.00
ATOM      8  CA  GLU    17      71.923  83.196  82.389  1.00  0.00
ATOM      9  CA  GLN    18      71.617  85.715  85.199  1.00  0.00
ATOM     10  CA  GLN    19      70.343  82.896  87.402  1.00  0.00
ATOM     11  CA  GLU    34      59.088  64.703  93.499  1.00  0.00
ATOM     12  CA  ILE    35      56.937  63.022  90.840  1.00  0.00
ATOM     13  CA  THR    36      53.668  63.494  92.746  1.00  0.00
ATOM     14  CA  GLU    37      54.278  67.272  93.143  1.00  0.00
ATOM     15  CA  ILE    38      55.359  67.180  89.500  1.00  0.00
ATOM     16  CA  ALA    39      52.019  66.173  87.976  1.00  0.00
ATOM     17  CA  ASP    40      50.376  68.563  90.459  1.00  0.00
ATOM     18  CA  ARG    41      53.091  71.228  90.152  1.00  0.00
ATOM     19  CA  THR    42      53.954  69.866  86.689  1.00  0.00
ATOM     20  CA  LEU    43      50.302  70.240  85.629  1.00  0.00
ATOM     21  CA  ARG    44      47.987  73.186  86.531  1.00  0.00
ATOM     22  CA  ALA    45      50.410  74.453  83.890  1.00  0.00
ATOM     23  CA  GLY    46      48.666  73.098  80.794  1.00  0.00
ATOM     24  CA  GLY    47      50.328  69.682  80.599  1.00  0.00
ATOM     25  CA  PRO    48      48.536  66.578  79.385  1.00  0.00
ATOM     26  CA  ALA    49      51.273  63.937  79.637  1.00  0.00
ATOM     27  CA  LEU    50      54.443  63.085  81.531  1.00  0.00
ATOM     28  CA  LEU    51      57.150  60.436  81.502  1.00  0.00
ATOM     29  CA  PHE    52      59.281  59.161  84.385  1.00  0.00
ATOM     30  CA  VAL    62      58.337  68.595  77.711  1.00  0.00
ATOM     31  CA  LEU    63      58.275  65.719  80.223  1.00  0.00
ATOM     32  CA  CYS    64      59.671  65.963  83.732  1.00  0.00
ATOM     33  CA  ASN    65      61.524  62.707  84.393  1.00  0.00
ATOM     34  CA  LEU    66      62.044  61.577  87.990  1.00  0.00
ATOM     35  CA  MET    77      67.474  73.373  88.466  1.00  0.00
ATOM     36  CA  GLY    78      64.040  74.611  89.623  1.00  0.00
ATOM     37  CA  GLN    79      60.487  75.655  88.669  1.00  0.00
ATOM     38  CA  GLU    80      61.789  78.839  87.077  1.00  0.00
ATOM     39  CA  ASP    81      64.227  76.843  84.896  1.00  0.00
ATOM     40  CA  VAL    82      61.620  74.302  83.836  1.00  0.00
ATOM     41  CA  SER    83      59.315  77.164  82.822  1.00  0.00
ATOM     42  CA  ALA    84      62.182  79.072  81.124  1.00  0.00
ATOM     43  CA  LEU    85      62.977  75.963  79.105  1.00  0.00
ATOM     44  CA  ARG    86      59.303  75.585  78.056  1.00  0.00
ATOM     45  CA  GLU    87      59.216  79.200  76.860  1.00  0.00
ATOM     46  CA  VAL    88      62.574  78.999  75.052  1.00  0.00
ATOM     47  CA  GLY    89      61.488  75.950  73.064  1.00  0.00
ATOM     48  CA  LYS    90      58.248  77.648  72.063  1.00  0.00
ATOM     49  CA  LEU    91      59.948  80.974  71.171  1.00  0.00
ATOM     50  CA  LEU    92      62.707  79.203  69.238  1.00  0.00
ATOM     51  CA  ALA    93      60.025  77.328  67.308  1.00  0.00
ATOM    114  CA  ALA   315      76.556  81.133  70.188  1.00  0.00
ATOM    115  CA  ILE   316      75.738  77.716  71.604  1.00  0.00
ATOM    116  CA  TYR   317      73.424  77.195  74.572  1.00  0.00
ATOM    117  CA  HIS   318      74.098  74.705  77.345  1.00  0.00
ATOM    118  CA  SER   319      72.651  73.982  80.773  1.00  0.00
ATOM    119  CA  THR   320      74.894  74.577  83.777  1.00  0.00
ATOM    120  CA  TYR   321      74.831  71.799  86.357  1.00  0.00
TER
END
