
#######################################################
#                                                     #
#                        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   15 (  126),  selected   15 , name T0382TS009_2_3-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_2_3-D1.T0382_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    L      65      V      15          3.496
LGA    F      66      A      16          2.827
LGA    E      67      L      17          2.211
LGA    Y      68      F      18          2.105
LGA    P      69      A      19          1.431
LGA    N      70      K      20           #
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    -       -      F      37           -
LGA    -       -      N      38           -
LGA    -       -      R      39           -
LGA    -       -      L      40           -
LGA    -       -      F      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      A      45           -
LGA    -       -      E      46           -
LGA    -       -      I      47           -
LGA    -       -      A      48           -
LGA    -       -      D      49           -
LGA    -       -      E      50           -
LGA    -       -      L      51           -
LGA    -       -      K      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    M      71      L      65          3.045
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    Q      72      Y      68          2.192
LGA    -       -      P      69           -
LGA    V      73      N      70          3.319
LGA    -       -      M      71           -
LGA    R      74      Q      72          2.268
LGA    L      75      V      73          2.612
LGA    Q      76      R      74          1.359
LGA    A      77      L      75          0.690
LGA    A      78      Q      76           -
LGA    -       -      A      77           -
LGA    K      79      A      78          3.548
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  119    5.0     13    2.54     0.00      7.993     0.493

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.759490 * X  +   0.528593 * Y  +   0.379163 * Z  + -26.099838
  Y_new =  -0.597100 * X  +  -0.335152 * Y  +  -0.728797 * Z  +  36.258099
  Z_new =  -0.258159 * X  +  -0.779912 * Y  +   0.570167 * Z  +  21.607777 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.939524    2.202069  [ DEG:   -53.8308    126.1693 ]
  Theta =   0.261116    2.880476  [ DEG:    14.9609    165.0391 ]
  Phi   =  -2.475332    0.666261  [ DEG:  -141.8261     38.1739 ]
 
# 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: T0382TS009_2_3-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_3-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  119   5.0   13   2.54    0.00   7.993
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_3-D1
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                     
ATOM    500  N   LEU    65     -20.460  37.454  -4.627  1.00  0.00             
ATOM    501  CA  LEU    65     -19.677  37.208  -5.833  1.00  0.00             
ATOM    502  C   LEU    65     -18.254  36.784  -5.489  1.00  0.00             
ATOM    503  O   LEU    65     -17.979  35.602  -5.282  1.00  0.00             
ATOM    504  CB  LEU    65     -20.349  36.140  -6.699  1.00  0.00             
ATOM    505  CG  LEU    65     -20.948  36.619  -8.022  1.00  0.00             
ATOM    506  CD1 LEU    65     -21.549  35.454  -8.794  1.00  0.00             
ATOM    507  CD2 LEU    65     -19.900  37.338  -8.858  1.00  0.00             
ATOM    508  N   PHE    66     -17.349  37.757  -5.430  1.00  0.00             
ATOM    509  CA  PHE    66     -15.953  37.488  -5.112  1.00  0.00             
ATOM    510  C   PHE    66     -15.822  36.748  -3.784  1.00  0.00             
ATOM    511  O   PHE    66     -15.060  37.155  -2.909  1.00  0.00             
ATOM    512  CB  PHE    66     -15.294  36.679  -6.232  1.00  0.00             
ATOM    513  CG  PHE    66     -14.008  37.273  -6.732  1.00  0.00             
ATOM    514  CD1 PHE    66     -13.516  38.449  -6.194  1.00  0.00             
ATOM    515  CD2 PHE    66     -13.291  36.654  -7.740  1.00  0.00             
ATOM    516  CE1 PHE    66     -12.334  38.994  -6.655  1.00  0.00             
ATOM    517  CE2 PHE    66     -12.107  37.199  -8.201  1.00  0.00             
ATOM    518  CZ  PHE    66     -11.628  38.365  -7.662  1.00  0.00             
ATOM    519  N   GLU    67     -16.572  35.660  -3.644  1.00  0.00             
ATOM    520  CA  GLU    67     -16.541  34.862  -2.424  1.00  0.00             
ATOM    521  C   GLU    67     -16.276  35.733  -1.201  1.00  0.00             
ATOM    522  O   GLU    67     -17.049  35.726  -0.243  1.00  0.00             
ATOM    523  CB  GLU    67     -17.856  34.098  -2.250  1.00  0.00             
ATOM    524  CG  GLU    67     -17.840  32.693  -2.831  1.00  0.00             
ATOM    525  CD  GLU    67     -19.046  31.876  -2.412  1.00  0.00             
ATOM    526  OE1 GLU    67     -20.136  32.093  -2.981  1.00  0.00             
ATOM    527  OE2 GLU    67     -18.901  31.018  -1.516  1.00  0.00             
ATOM    528  N   TYR    68     -15.179  36.482  -1.241  1.00  0.00             
ATOM    529  CA  TYR    68     -14.809  37.360  -0.137  1.00  0.00             
ATOM    530  C   TYR    68     -16.043  37.969   0.519  1.00  0.00             
ATOM    531  O   TYR    68     -16.356  39.142   0.318  1.00  0.00             
ATOM    532  CB  TYR    68     -13.983  36.597   0.901  1.00  0.00             
ATOM    533  CG  TYR    68     -12.542  37.044   0.986  1.00  0.00             
ATOM    534  CD1 TYR    68     -12.169  38.320   0.583  1.00  0.00             
ATOM    535  CD2 TYR    68     -11.559  36.191   1.471  1.00  0.00             
ATOM    536  CE1 TYR    68     -10.854  38.739   0.658  1.00  0.00             
ATOM    537  CE2 TYR    68     -10.239  36.593   1.552  1.00  0.00             
ATOM    538  CZ  TYR    68      -9.893  37.878   1.141  1.00  0.00             
ATOM    539  OH  TYR    68      -8.581  38.288   1.219  1.00  0.00             
ATOM    540  N   PRO    69     -16.762  37.169   1.319  1.00  0.00             
ATOM    541  CA  PRO    69     -17.971  37.625   2.013  1.00  0.00             
ATOM    542  C   PRO    69     -18.794  38.575   1.150  1.00  0.00             
ATOM    543  O   PRO    69     -19.842  39.063   1.574  1.00  0.00             
ATOM    544  CB  PRO    69     -18.743  36.326   2.249  1.00  0.00             
ATOM    545  CG  PRO    69     -18.504  35.520   1.016  1.00  0.00             
ATOM    546  CD  PRO    69     -16.450  35.758   1.606  1.00  0.00             
ATOM    547  N   ASN    70     -18.313  38.835  -0.061  1.00  0.00             
ATOM    548  CA  ASN    70     -19.002  39.728  -0.985  1.00  0.00             
ATOM    549  C   ASN    70     -19.686  40.871  -0.240  1.00  0.00             
ATOM    550  O   ASN    70     -20.892  41.076  -0.372  1.00  0.00             
ATOM    551  CB  ASN    70     -18.026  40.285  -2.022  1.00  0.00             
ATOM    552  CG  ASN    70     -18.098  39.548  -3.345  1.00  0.00             
ATOM    553  OD1 ASN    70     -17.658  40.058  -4.375  1.00  0.00             
ATOM    554  ND2 ASN    70     -18.657  38.344  -3.320  1.00  0.00             
ATOM    555  N   MET    71     -18.906  41.611   0.540  1.00  0.00             
ATOM    556  CA  MET    71     -19.434  42.733   1.306  1.00  0.00             
ATOM    557  C   MET    71     -20.427  42.262   2.362  1.00  0.00             
ATOM    558  O   MET    71     -20.512  42.834   3.449  1.00  0.00             
ATOM    559  CB  MET    71     -18.296  43.514   1.966  1.00  0.00             
ATOM    560  CG  MET    71     -17.982  44.841   1.294  1.00  0.00             
ATOM    561  SD  MET    71     -16.345  45.467   1.719  1.00  0.00             
ATOM    562  CE  MET    71     -16.537  47.205   1.336  1.00  0.00             
ATOM    563  N   GLN    72     -21.179  41.217   2.035  1.00  0.00             
ATOM    564  CA  GLN    72     -22.169  40.667   2.955  1.00  0.00             
ATOM    565  C   GLN    72     -21.559  40.401   4.326  1.00  0.00             
ATOM    566  O   GLN    72     -22.047  40.900   5.341  1.00  0.00             
ATOM    567  CB  GLN    72     -23.364  41.613   3.084  1.00  0.00             
ATOM    568  CG  GLN    72     -24.687  41.007   2.645  1.00  0.00             
ATOM    569  CD  GLN    72     -25.883  41.747   3.208  1.00  0.00             
ATOM    570  OE1 GLN    72     -27.006  41.587   2.729  1.00  0.00             
ATOM    571  NE2 GLN    72     -25.647  42.563   4.228  1.00  0.00             
ATOM    572  N   VAL    73     -20.489  39.613   4.351  1.00  0.00             
ATOM    573  CA  VAL    73     -19.795  39.272   5.625  1.00  0.00             
ATOM    574  C   VAL    73     -19.073  40.486   6.202  1.00  0.00             
ATOM    575  O   VAL    73     -19.704  41.473   6.582  1.00  0.00             
ATOM    576  CB  VAL    73     -20.781  38.727   6.676  1.00  0.00             
ATOM    577  CG1 VAL    73     -20.461  37.276   7.003  1.00  0.00             
ATOM    578  CG2 VAL    73     -22.213  38.867   6.185  1.00  0.00             
ATOM    579  N   ARG    74     -17.748  40.405   6.265  1.00  0.00             
ATOM    580  CA  ARG    74     -16.939  41.496   6.794  1.00  0.00             
ATOM    581  C   ARG    74     -17.358  42.835   6.196  1.00  0.00             
ATOM    582  O   ARG    74     -17.352  43.860   6.878  1.00  0.00             
ATOM    583  CB  ARG    74     -17.041  41.547   8.320  1.00  0.00             
ATOM    584  CG  ARG    74     -15.699  41.625   9.031  1.00  0.00             
ATOM    585  CD  ARG    74     -15.843  41.339  10.516  1.00  0.00             
ATOM    586  NE  ARG    74     -14.646  41.712  11.264  1.00  0.00             
ATOM    587  CZ  ARG    74     -14.343  42.958  11.614  1.00  0.00             
ATOM    588  NH1 ARG    74     -15.153  43.955  11.284  1.00  0.00             
ATOM    589  NH2 ARG    74     -13.232  43.204  12.294  1.00  0.00             
ATOM    590  N   LEU    75     -17.719  42.818   4.917  1.00  0.00             
ATOM    591  CA  LEU    75     -18.141  44.030   4.224  1.00  0.00             
ATOM    592  C   LEU    75     -18.817  45.005   5.182  1.00  0.00             
ATOM    593  O   LEU    75     -18.572  46.211   5.131  1.00  0.00             
ATOM    594  CB  LEU    75     -16.946  44.703   3.546  1.00  0.00             
ATOM    595  CG  LEU    75     -17.086  44.986   2.049  1.00  0.00             
ATOM    596  CD1 LEU    75     -16.611  46.393   1.721  1.00  0.00             
ATOM    597  CD2 LEU    75     -18.524  44.782   1.597  1.00  0.00             
ATOM    598  N   GLN    76     -19.670  44.476   6.053  1.00  0.00             
ATOM    599  CA  GLN    76     -20.383  45.297   7.023  1.00  0.00             
ATOM    600  C   GLN    76     -19.474  46.369   7.614  1.00  0.00             
ATOM    601  O   GLN    76     -19.945  47.348   8.193  1.00  0.00             
ATOM    602  CB  GLN    76     -21.609  45.946   6.376  1.00  0.00             
ATOM    603  CG  GLN    76     -22.925  45.269   6.723  1.00  0.00             
ATOM    604  CD  GLN    76     -24.096  45.841   5.948  1.00  0.00             
ATOM    605  OE1 GLN    76     -25.253  45.546   6.247  1.00  0.00             
ATOM    606  NE2 GLN    76     -23.798  46.663   4.949  1.00  0.00             
ATOM    607  N   ALA    77     -18.167  46.177   7.463  1.00  0.00             
ATOM    608  CA  ALA    77     -17.189  47.126   7.981  1.00  0.00             
ATOM    609  C   ALA    77     -17.838  48.468   8.300  1.00  0.00             
ATOM    610  O   ALA    77     -17.290  49.524   7.984  1.00  0.00             
ATOM    611  CB  ALA    77     -16.510  46.565   9.221  1.00  0.00             
ATOM    612  N   ALA    78     -19.008  48.419   8.928  1.00  0.00             
ATOM    613  CA  ALA    78     -19.734  49.631   9.291  1.00  0.00             
ATOM    614  C   ALA    78     -20.176  50.402   8.051  1.00  0.00             
ATOM    615  O   ALA    78     -21.366  50.638   7.847  1.00  0.00             
ATOM    616  CB  ALA    78     -20.939  49.289  10.153  1.00  0.00             
ATOM    617  N   LYS    79     -19.209  50.791   7.228  1.00  0.00             
ATOM    618  CA  LYS    79     -19.496  51.535   6.007  1.00  0.00             
ATOM    619  C   LYS    79     -20.968  51.422   5.625  1.00  0.00             
ATOM    620  O   LYS    79     -21.565  52.377   5.128  1.00  0.00             
ATOM    621  CB  LYS    79     -19.107  53.006   6.172  1.00  0.00             
ATOM    622  CG  LYS    79     -18.062  53.487   5.179  1.00  0.00             
ATOM    623  CD  LYS    79     -18.130  54.994   4.991  1.00  0.00             
ATOM    624  CE  LYS    79     -17.298  55.440   3.799  1.00  0.00             
ATOM    625  NZ  LYS    79     -17.422  56.903   3.553  1.00  0.00             
TER
END
