
#######################################################
#                                                     #
#                        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   18 (  178),  selected   18 , name T0386TS277_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS277_1-D2.T0386_D2.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    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    N     219      Y     258          4.472
LGA    P     220      R     259          2.637
LGA    E     221      G     260          1.299
LGA    K     222      A     261          2.090
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    I     223      F     266          1.717
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    R     224      G     277          3.686
LGA    -       -      N     278           -
LGA    L     225      I     279          2.646
LGA    L     226      D     280          1.987
LGA    K     227      H     281          1.657
LGA    E     228      L     282          1.450
LGA    F     229      P     283          3.461
LGA    M     230      P     284          1.899
LGA    H     231      E     285          2.431
LGA    T     232      Q     286          0.814
LGA    M     233      L     287          1.709
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    K     234      L     290          4.913
LGA    N     235      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    T     236      I     296          5.435
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18   81    5.0     17    2.91     0.00     16.103     0.565

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.588735 * X  +   0.534459 * Y  +  -0.606420 * Z  +   6.159568
  Y_new =  -0.802890 * X  +   0.299791 * Y  +  -0.515260 * Z  +  40.470470
  Z_new =  -0.093586 * X  +   0.790240 * Y  +   0.605609 * Z  +  53.188351 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.916906   -2.224687  [ DEG:    52.5348   -127.4652 ]
  Theta =   0.093723    3.047869  [ DEG:     5.3700    174.6301 ]
  Phi   =  -0.938089    2.203503  [ DEG:   -53.7486    126.2514 ]
 
# 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: T0386TS277_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS277_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   81   5.0   17   2.91    0.00  16.103
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS277_1-D2
PFRMAT TS 
TARGET T0386
MODEL 1
PARENT 2G03_A
ATOM   3847  H   ASN   219      25.122  67.986  84.969  1.00  0.00                              
ATOM   3849  N   ASN   219      25.834  67.568  85.423  1.00  0.00                              
ATOM   3851  CA  ASN   219      25.542  66.387  86.246  1.00  0.00                              
ATOM   3853  CB  ASN   219      26.025  66.518  87.699  1.00  0.00                              
ATOM   3855  C   ASN   219      24.070  65.976  86.135  1.00  0.00                              
ATOM   3857  O   ASN   219      23.380  66.429  85.221  1.00  0.00                              
ATOM   3859  CG  ASN   219      25.224  67.479  88.558  1.00  0.00                              
ATOM   3861  ND2 ASN   219      25.630  67.623  89.821  1.00  0.00                              
ATOM   3863 HD21 ASN   219      26.381  67.132  90.111  1.00  0.00                              
ATOM   3865 HD22 ASN   219      25.164  68.205  90.399  1.00  0.00                              
ATOM   3867  OD1 ASN   219      24.226  68.047  88.105  1.00  0.00                              
ATOM   3869  N   PRO   220      23.548  65.112  87.021  1.00  0.00                              
ATOM   3871  CA  PRO   220      22.141  64.682  86.958  1.00  0.00                              
ATOM   3873  CB  PRO   220      21.944  63.934  88.280  1.00  0.00                              
ATOM   3875  C   PRO   220      21.143  65.833  86.825  1.00  0.00                              
ATOM   3877  O   PRO   220      21.411  66.955  87.262  1.00  0.00                              
ATOM   3879  CG  PRO   220      23.297  63.351  88.549  1.00  0.00                              
ATOM   3881  CD  PRO   220      24.255  64.443  88.134  1.00  0.00                              
ATOM   3883  H   GLU   221      19.797  64.655  85.997  1.00  0.00                              
ATOM   3885  N   GLU   221      19.974  65.548  86.251  1.00  0.00                              
ATOM   3887  CA  GLU   221      18.951  66.569  86.036  1.00  0.00                              
ATOM   3889  CB  GLU   221      19.387  67.549  84.943  1.00  0.00                              
ATOM   3891  C   GLU   221      17.597  65.959  85.685  1.00  0.00                              
ATOM   3893  O   GLU   221      17.285  65.774  84.506  1.00  0.00                              
ATOM   3895  CG  GLU   221      18.510  68.789  84.845  1.00  0.00                              
ATOM   3897  CD  GLU   221      18.544  69.647  86.099  1.00  0.00                              
ATOM   3899  OE1 GLU   221      19.655  69.942  86.593  1.00  0.00                              
ATOM   3901  OE2 GLU   221      17.459  70.019  86.598  1.00  0.00                              
ATOM   3903  H   LYS   222      17.027  65.920  87.581  1.00  0.00                              
ATOM   3905  N   LYS   222      16.768  65.699  86.694  1.00  0.00                              
ATOM   3907  CA  LYS   222      15.484  65.040  86.468  1.00  0.00                              
ATOM   3909  CB  LYS   222      14.567  65.930  85.624  1.00  0.00                              
ATOM   3911  C   LYS   222      15.689  63.701  85.768  1.00  0.00                              
ATOM   3913  O   LYS   222      16.704  63.034  85.989  1.00  0.00                              
ATOM   3915  CG  LYS   222      13.950  67.085  86.398  1.00  0.00                              
ATOM   3917  CD  LYS   222      12.961  67.865  85.542  1.00  0.00                              
ATOM   3919  CE  LYS   222      13.656  68.581  84.392  1.00  0.00                              
ATOM   3921  NZ  LYS   222      14.874  69.312  84.847  1.00  0.00                              
ATOM   3923  H   ILE   223      13.921  63.774  84.894  1.00  0.00                              
ATOM   3925  N   ILE   223      14.721  63.283  84.959  1.00  0.00                              
ATOM   3927  CA  ILE   223      14.866  62.052  84.187  1.00  0.00                              
ATOM   3929  CB  ILE   223      16.337  61.850  83.748  1.00  0.00                              
ATOM   3931  C   ILE   223      14.361  60.832  84.961  1.00  0.00                              
ATOM   3933  O   ILE   223      13.299  60.292  84.639  1.00  0.00                              
ATOM   3935  CG1 ILE   223      16.798  63.016  82.863  1.00  0.00                              
ATOM   3937  CD1 ILE   223      18.221  62.886  82.341  1.00  0.00                              
ATOM   3939  CG2 ILE   223      16.515  60.511  83.033  1.00  0.00                              
ATOM   3941  H   ARG   224      15.934  60.816  86.165  1.00  0.00                              
ATOM   3943  N   ARG   224      15.131  60.357  85.939  1.00  0.00                              
ATOM   3945  CA  ARG   224      14.776  59.136  86.663  1.00  0.00                              
ATOM   3947  CB  ARG   224      15.983  58.199  86.797  1.00  0.00                              
ATOM   3949  C   ARG   224      14.140  59.407  88.027  1.00  0.00                              
ATOM   3951  O   ARG   224      14.114  58.517  88.885  1.00  0.00                              
ATOM   3953  CG  ARG   224      16.350  57.488  85.500  1.00  0.00                              
ATOM   3955  CD  ARG   224      17.612  56.638  85.616  1.00  0.00                              
ATOM   3957  NE  ARG   224      17.402  55.428  86.409  1.00  0.00                              
ATOM   3959  HE  ARG   224      16.551  55.313  86.814  1.00  0.00                              
ATOM   3961  CZ  ARG   224      18.308  54.477  86.611  1.00  0.00                              
ATOM   3963  NH1 ARG   224      19.497  54.545  86.020  1.00  0.00                              
ATOM   3965  NH2 ARG   224      18.045  53.480  87.451  1.00  0.00                              
ATOM   3967  H   LEU   225      13.589  61.229  87.500  1.00  0.00                              
ATOM   3969  N   LEU   225      13.568  60.603  88.207  1.00  0.00                              
ATOM   3971  CA  LEU   225      12.936  60.991  89.473  1.00  0.00                              
ATOM   3973  CB  LEU   225      12.748  62.515  89.556  1.00  0.00                              
ATOM   3975  C   LEU   225      11.621  60.249  89.735  1.00  0.00                              
ATOM   3977  O   LEU   225      11.454  59.119  89.285  1.00  0.00                              
ATOM   3979  CG  LEU   225      11.607  63.159  88.754  1.00  0.00                              
ATOM   3981  CD1 LEU   225      11.362  64.578  89.249  1.00  0.00                              
ATOM   3983  CD2 LEU   225      11.933  63.170  87.267  1.00  0.00                              
ATOM   3985  H   LEU   226      10.934  61.683  90.902  1.00  0.00                              
ATOM   3987  N   LEU   226      10.716  60.853  90.508  1.00  0.00                              
ATOM   3989  CA  LEU   226       9.393  60.275  90.784  1.00  0.00                              
ATOM   3991  CB  LEU   226       8.510  60.311  89.532  1.00  0.00                              
ATOM   3993  C   LEU   226       9.420  58.868  91.397  1.00  0.00                              
ATOM   3995  O   LEU   226       8.929  58.682  92.514  1.00  0.00                              
ATOM   3997  CG  LEU   226       8.250  61.698  88.937  1.00  0.00                              
ATOM   3999  CD1 LEU   226       7.412  61.586  87.671  1.00  0.00                              
ATOM   4001  CD2 LEU   226       7.561  62.590  89.961  1.00  0.00                              
ATOM   4003  H   LYS   227      10.345  58.116  89.826  1.00  0.00                              
ATOM   4005  N   LYS   227       9.959  57.885  90.663  1.00  0.00                              
ATOM   4007  CA  LYS   227      10.010  56.482  91.091  1.00  0.00                              
ATOM   4009  CB  LYS   227      10.249  55.546  89.891  1.00  0.00                              
ATOM   4011  C   LYS   227      11.045  56.239  92.193  1.00  0.00                              
ATOM   4013  O   LYS   227      10.710  55.664  93.232  1.00  0.00                              
ATOM   4015  CG  LYS   227      10.401  54.068  90.230  1.00  0.00                              
ATOM   4017  CD  LYS   227      10.532  53.224  88.970  1.00  0.00                              
ATOM   4019  CE  LYS   227      10.661  51.740  89.293  1.00  0.00                              
ATOM   4021  NZ  LYS   227      10.729  50.908  88.056  1.00  0.00                              
ATOM   4023  H   GLU   228      12.559  56.948  91.125  1.00  0.00                              
ATOM   4025  N   GLU   228      12.304  56.625  91.978  1.00  0.00                              
ATOM   4027  CA  GLU   228      13.324  56.489  93.017  1.00  0.00                              
ATOM   4029  CB  GLU   228      14.719  56.741  92.435  1.00  0.00                              
ATOM   4031  C   GLU   228      13.070  57.415  94.207  1.00  0.00                              
ATOM   4033  O   GLU   228      13.761  57.332  95.230  1.00  0.00                              
ATOM   4035  CG  GLU   228      15.155  55.706  91.408  1.00  0.00                              
ATOM   4037  CD  GLU   228      16.518  56.002  90.803  1.00  0.00                              
ATOM   4039  OE1 GLU   228      17.201  56.924  91.305  1.00  0.00                              
ATOM   4041  OE2 GLU   228      16.909  55.312  89.832  1.00  0.00                              
ATOM   4043  H   PHE   229      11.707  58.461  93.220  1.00  0.00                              
ATOM   4045  N   PHE   229      12.126  58.342  94.067  1.00  0.00                              
ATOM   4047  CA  PHE   229      11.770  59.219  95.179  1.00  0.00                              
ATOM   4049  CB  PHE   229      10.582  60.112  94.803  1.00  0.00                              
ATOM   4051  C   PHE   229      11.455  58.394  96.422  1.00  0.00                              
ATOM   4053  O   PHE   229      11.037  57.237  96.322  1.00  0.00                              
ATOM   4055  CG  PHE   229      10.090  61.047  95.884  1.00  0.00                              
ATOM   4057  CD1 PHE   229      10.433  62.398  95.862  1.00  0.00                              
ATOM   4059  CE1 PHE   229       9.900  63.282  96.798  1.00  0.00                              
ATOM   4061  CZ  PHE   229       9.064  62.805  97.802  1.00  0.00                              
ATOM   4063  CD2 PHE   229       9.237  60.587  96.884  1.00  0.00                              
ATOM   4065  CE2 PHE   229       8.744  61.456  97.854  1.00  0.00                              
ATOM   4067  H   MET   230      11.962  59.883  97.619  1.00  0.00                              
ATOM   4069  N   MET   230      11.690  58.978  97.592  1.00  0.00                              
ATOM   4071  CA  MET   230      11.510  58.271  98.845  1.00  0.00                              
ATOM   4073  CB  MET   230      10.586  57.072  98.644  1.00  0.00                              
ATOM   4075  C   MET   230      12.870  57.815  99.357  1.00  0.00                              
ATOM   4077  O   MET   230      13.077  57.678 100.566  1.00  0.00                              
ATOM   4079  CG  MET   230      10.143  56.447  99.952  1.00  0.00                              
ATOM   4081  SD  MET   230       9.567  57.677 101.147  1.00  0.00                              
ATOM   4083  CE  MET   230       7.854  57.828 100.666  1.00  0.00                              
ATOM   4085  H   HIS   231      13.553  57.621  97.515  1.00  0.00                              
ATOM   4087  N   HIS   231      13.797  57.583  98.429  1.00  0.00                              
ATOM   4089  CA  HIS   231      15.169  57.254  98.798  1.00  0.00                              
ATOM   4091  CB  HIS   231      15.569  55.860  98.301  1.00  0.00                              
ATOM   4093  C   HIS   231      16.124  58.298  98.225  1.00  0.00                              
ATOM   4095  O   HIS   231      16.799  59.003  98.978  1.00  0.00                              
ATOM   4097  CG  HIS   231      16.963  55.468  98.691  1.00  0.00                              
ATOM   4099  ND1 HIS   231      17.349  55.283 100.002  1.00  0.00                              
ATOM   4101  HD1 HIS   231      16.804  55.421 100.769  1.00  0.00                              
ATOM   4103  CE1 HIS   231      18.638  54.984 100.037  1.00  0.00                              
ATOM   4105  NE2 HIS   231      19.097  54.959  98.798  1.00  0.00                              
ATOM   4107  HE2 HIS   231      20.004  54.807  98.559  1.00  0.00                              
ATOM   4109  CD2 HIS   231      18.079  55.292  97.938  1.00  0.00                              
ATOM   4111  H   THR   232      15.575  57.894  96.370  1.00  0.00                              
ATOM   4113  N   THR   232      16.135  58.428  96.898  1.00  0.00                              
ATOM   4115  CA  THR   232      17.005  59.394  96.225  1.00  0.00                              
ATOM   4117  CB  THR   232      18.337  58.743  95.797  1.00  0.00                              
ATOM   4119  C   THR   232      16.337  59.978  94.982  1.00  0.00                              
ATOM   4121  O   THR   232      16.182  59.289  93.969  1.00  0.00                              
ATOM   4123  CG2 THR   232      18.197  58.089  94.427  1.00  0.00                              
ATOM   4125  OG1 THR   232      19.346  59.757  95.722  1.00  0.00                              
ATOM   4127  H   MET   233      16.192  61.772  95.797  1.00  0.00                              
ATOM   4129  N   MET   233      15.996  61.266  95.022  1.00  0.00                              
ATOM   4131  CA  MET   233      15.293  61.901  93.905  1.00  0.00                              
ATOM   4133  CB  MET   233      14.027  62.613  94.380  1.00  0.00                              
ATOM   4135  C   MET   233      16.183  62.924  93.211  1.00  0.00                              
ATOM   4137  O   MET   233      16.800  63.759  93.875  1.00  0.00                              
ATOM   4139  CG  MET   233      14.321  63.778  95.306  1.00  0.00                              
ATOM   4141  SD  MET   233      14.477  63.263  97.029  1.00  0.00                              
ATOM   4143  CE  MET   233      12.965  63.938  97.692  1.00  0.00                              
ATOM   4145  H   LYS   234      15.750  62.228  91.407  1.00  0.00                              
ATOM   4147  N   LYS   234      16.222  62.901  91.882  1.00  0.00                              
ATOM   4149  CA  LYS   234      17.004  63.888  91.147  1.00  0.00                              
ATOM   4151  CB  LYS   234      17.283  65.071  92.078  1.00  0.00                              
ATOM   4153  C   LYS   234      18.322  63.286  90.660  1.00  0.00                              
ATOM   4155  O   LYS   234      19.311  64.002  90.497  1.00  0.00                              
ATOM   4157  CG  LYS   234      18.131  66.172  91.461  1.00  0.00                              
ATOM   4159  CD  LYS   234      17.275  67.314  90.932  1.00  0.00                              
ATOM   4161  CE  LYS   234      17.918  67.958  89.712  1.00  0.00                              
ATOM   4163  NZ  LYS   234      16.958  68.836  88.979  1.00  0.00                              
ATOM   4165  H   ASN   235      17.511  61.510  90.411  1.00  0.00                              
ATOM   4167  N   ASN   235      18.324  61.982  90.380  1.00  0.00                              
ATOM   4169  CA  ASN   235      19.538  61.259  90.000  1.00  0.00                              
ATOM   4171  CB  ASN   235      19.909  60.262  91.105  1.00  0.00                              
ATOM   4173  C   ASN   235      19.360  60.519  88.677  1.00  0.00                              
ATOM   4175  O   ASN   235      18.714  59.466  88.632  1.00  0.00                              
ATOM   4177  CG  ASN   235      21.233  59.557  90.874  1.00  0.00                              
ATOM   4179  ND2 ASN   235      22.024  59.427  91.933  1.00  0.00                              
ATOM   4181 HD21 ASN   235      21.724  59.758  92.763  1.00  0.00                              
ATOM   4183 HD22 ASN   235      22.856  58.994  91.840  1.00  0.00                              
ATOM   4185  OD1 ASN   235      21.529  59.096  89.767  1.00  0.00                              
ATOM   4187  H   THR   236      20.522  61.803  87.734  1.00  0.00                              
ATOM   4189  N   THR   236      19.978  61.048  87.621  1.00  0.00                              
ATOM   4191  CA  THR   236      19.836  60.494  86.274  1.00  0.00                              
ATOM   4193  CB  THR   236      20.551  61.387  85.233  1.00  0.00                              
ATOM   4195  C   THR   236      20.395  59.077  86.202  1.00  0.00                              
ATOM   4197  O   THR   236      21.612  58.887  86.128  1.00  0.00                              
ATOM   4199  CG2 THR   236      20.648  60.720  83.863  1.00  0.00                              
ATOM   4201  OG1 THR   236      19.832  62.620  85.106  1.00  0.00                              
TER 
END
