
#######################################################
#                                                     #
#                        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   10 (   89),  selected   10 , name T0385TS009_1_4-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected  135 , name T0385_D1.pdb
# PARAMETERS: T0385TS009_1_4-D1.T0385_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    -       -      S      17           -
LGA    -       -      E      18           -
LGA    -       -      G      19           -
LGA    -       -      S      20           -
LGA    -       -      A      21           -
LGA    -       -      D      22           -
LGA    -       -      N      23           -
LGA    -       -      A      24           -
LGA    -       -      A      25           -
LGA    -       -      L      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      A      31           -
LGA    -       -      V      32           -
LGA    -       -      E      33           -
LGA    -       -      H      34           -
LGA    -       -      A      35           -
LGA    -       -      T      36           -
LGA    -       -      I      37           -
LGA    -       -      Y      38           -
LGA    -       -      G      39           -
LGA    -       -      Y      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      V      43           -
LGA    -       -      S      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      S      47           -
LGA    -       -      P      48           -
LGA    -       -      P      49           -
LGA    -       -      G      50           -
LGA    -       -      V      51           -
LGA    -       -      N      52           -
LGA    -       -      F      53           -
LGA    -       -      L      54           -
LGA    -       -      V      55           -
LGA    -       -      A      56           -
LGA    -       -      D      57           -
LGA    -       -      A      58           -
LGA    -       -      L      59           -
LGA    -       -      K      60           -
LGA    -       -      Q      61           -
LGA    -       -      H      62           -
LGA    T     142      R      63          2.435
LGA    R     143      H      64          4.742
LGA    W     144      R      65          1.178
LGA    N     145      R      66          4.655
LGA    R     146      D      67          1.388
LGA    -       -      D      68           -
LGA    V     147      V      69          2.115
LGA    L     148      I      70          4.029
LGA    G     149      V      71          3.061
LGA    A     150      M      72          1.929
LGA    -       -      L      73           -
LGA    W     151      S      74          0.745
LGA    -       -      A      75           -
LGA    -       -      R      76           -
LGA    -       -      G      77           -
LGA    -       -      V      78           -
LGA    -       -      T      79           -
LGA    -       -      A      80           -
LGA    -       -      P      81           -
LGA    -       -      I      82           -
LGA    -       -      A      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      G      86           -
LGA    -       -      Y      87           -
LGA    -       -      Q      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      M      91           -
LGA    -       -      Q      92           -
LGA    -       -      V      93           -
LGA    -       -      S      94           -
LGA    -       -      S      95           -
LGA    -       -      A      96           -
LGA    -       -      A      97           -
LGA    -       -      D      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      A     103           -
LGA    -       -      V     104           -
LGA    -       -      R     105           -
LGA    -       -      M     106           -
LGA    -       -      E     107           -
LGA    -       -      N     108           -
LGA    -       -      D     109           -
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    -       -      T     112           -
LGA    -       -      A     113           -
LGA    -       -      W     114           -
LGA    -       -      R     115           -
LGA    -       -      A     116           -
LGA    -       -      V     117           -
LGA    -       -      V     118           -
LGA    -       -      E     119           -
LGA    -       -      H     120           -
LGA    -       -      A     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      A     124           -
LGA    -       -      D     125           -
LGA    -       -      D     126           -
LGA    -       -      R     127           -
LGA    -       -      V     128           -
LGA    -       -      F     129           -
LGA    -       -      A     130           -
LGA    -       -      S     131           -
LGA    -       -      T     132           -
LGA    -       -      A     133           -
LGA    -       -      L     134           -
LGA    -       -      T     135           -
LGA    -       -      E     136           -
LGA    -       -      S     137           -
LGA    -       -      A     138           -
LGA    -       -      V     139           -
LGA    -       -      M     140           -
LGA    -       -      A     141           -
LGA    -       -      T     142           -
LGA    -       -      R     143           -
LGA    -       -      W     144           -
LGA    -       -      N     145           -
LGA    -       -      R     146           -
LGA    -       -      V     147           -
LGA    -       -      L     148           -
LGA    -       -      G     149           -
LGA    -       -      A     150           -
LGA    -       -      W     151           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  135    5.0     10    2.96    10.00      4.949     0.327

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.109710 * X  +  -0.496625 * Y  +   0.861004 * Z  +   6.234462
  Y_new =   0.715758 * X  +  -0.640522 * Y  +  -0.278248 * Z  +  29.221041
  Z_new =   0.689677 * X  +   0.585744 * Y  +   0.425735 * Z  +  67.614250 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.942291   -2.199302  [ DEG:    53.9893   -126.0107 ]
  Theta =  -0.761042   -2.380550  [ DEG:   -43.6045   -136.3955 ]
  Phi   =   1.722891   -1.418701  [ DEG:    98.7144    -81.2856 ]
 
# 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: T0385TS009_1_4-D1                             
REMARK     2: T0385_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_1_4-D1.T0385_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  135   5.0   10   2.96   10.00   4.949
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_1_4-D1
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM   1026  N   THR   142      36.474  11.441  22.460  1.00  0.00              
ATOM   1027  CA  THR   142      36.260  11.083  23.892  1.00  0.00              
ATOM   1028  C   THR   142      34.940  11.643  24.408  1.00  0.00              
ATOM   1029  O   THR   142      34.827  12.016  25.577  1.00  0.00              
ATOM   1030  CB  THR   142      36.278   9.558  24.101  1.00  0.00              
ATOM   1031  OG1 THR   142      36.537   8.904  22.852  1.00  0.00              
ATOM   1032  CG2 THR   142      37.356   9.170  25.103  1.00  0.00              
ATOM   1033  N   ARG   143      33.943  11.698  23.531  1.00  0.00              
ATOM   1034  CA  ARG   143      32.628  12.212  23.897  1.00  0.00              
ATOM   1035  C   ARG   143      32.714  13.132  25.110  1.00  0.00              
ATOM   1036  O   ARG   143      32.727  12.670  26.251  1.00  0.00              
ATOM   1037  CB  ARG   143      31.995  12.953  22.718  1.00  0.00              
ATOM   1038  CG  ARG   143      30.669  12.371  22.258  1.00  0.00              
ATOM   1039  CD  ARG   143      30.055  13.206  21.147  1.00  0.00              
ATOM   1040  NE  ARG   143      28.613  13.004  21.043  1.00  0.00              
ATOM   1041  CZ  ARG   143      27.704  13.825  21.558  1.00  0.00              
ATOM   1042  NH1 ARG   143      28.089  14.910  22.216  1.00  0.00              
ATOM   1043  NH2 ARG   143      26.412  13.560  21.414  1.00  0.00              
ATOM   1044  N   TRP   144      32.770  14.435  24.856  1.00  0.00              
ATOM   1045  CA  TRP   144      32.855  15.421  25.926  1.00  0.00              
ATOM   1046  C   TRP   144      34.171  15.300  26.687  1.00  0.00              
ATOM   1047  O   TRP   144      34.195  15.347  27.917  1.00  0.00              
ATOM   1048  CB  TRP   144      32.702  16.836  25.363  1.00  0.00              
ATOM   1049  CG  TRP   144      32.320  17.853  26.394  1.00  0.00              
ATOM   1050  CD1 TRP   144      31.978  19.156  26.173  1.00  0.00              
ATOM   1051  CD2 TRP   144      32.241  17.652  27.811  1.00  0.00              
ATOM   1052  NE1 TRP   144      31.690  19.780  27.363  1.00  0.00              
ATOM   1053  CE2 TRP   144      31.845  18.877  28.384  1.00  0.00              
ATOM   1054  CE3 TRP   144      32.468  16.556  28.648  1.00  0.00              
ATOM   1055  CZ2 TRP   144      31.670  19.036  29.758  1.00  0.00              
ATOM   1056  CZ3 TRP   144      32.292  16.716  30.010  1.00  0.00              
ATOM   1057  CH2 TRP   144      31.897  17.947  30.555  1.00  0.00              
ATOM   1058  N   ASN   145      35.263  15.140  25.948  1.00  0.00              
ATOM   1059  CA  ASN   145      36.585  15.010  26.551  1.00  0.00              
ATOM   1060  C   ASN   145      36.581  13.971  27.667  1.00  0.00              
ATOM   1061  O   ASN   145      37.393  14.037  28.591  1.00  0.00              
ATOM   1062  CB  ASN   145      37.623  14.639  25.490  1.00  0.00              
ATOM   1063  CG  ASN   145      38.830  15.557  25.509  1.00  0.00              
ATOM   1064  OD1 ASN   145      39.719  15.447  24.666  1.00  0.00              
ATOM   1065  ND2 ASN   145      38.861  16.469  26.474  1.00  0.00              
ATOM   1066  N   ARG   146      35.663  13.016  27.576  1.00  0.00              
ATOM   1067  CA  ARG   146      35.553  11.962  28.579  1.00  0.00              
ATOM   1068  C   ARG   146      35.489  12.544  29.986  1.00  0.00              
ATOM   1069  O   ARG   146      35.484  11.809  30.974  1.00  0.00              
ATOM   1070  CB  ARG   146      34.321  11.096  28.311  1.00  0.00              
ATOM   1071  CG  ARG   146      34.498  10.097  27.180  1.00  0.00              
ATOM   1072  CD  ARG   146      33.203   9.353  26.891  1.00  0.00              
ATOM   1073  NE  ARG   146      33.092   8.974  25.486  1.00  0.00              
ATOM   1074  CZ  ARG   146      33.886   8.093  24.884  1.00  0.00              
ATOM   1075  NH1 ARG   146      34.852   7.497  25.568  1.00  0.00              
ATOM   1076  NH2 ARG   146      33.710   7.811  23.601  1.00  0.00              
ATOM   1077  N   VAL   147      35.439  13.870  30.072  1.00  0.00              
ATOM   1078  CA  VAL   147      35.374  14.568  31.387  1.00  0.00              
ATOM   1079  C   VAL   147      36.172  13.820  32.449  1.00  0.00              
ATOM   1080  O   VAL   147      35.709  13.642  33.576  1.00  0.00              
ATOM   1081  CB  VAL   147      35.900  16.013  31.285  1.00  0.00              
ATOM   1082  CG1 VAL   147      34.790  17.006  31.589  1.00  0.00              
ATOM   1083  CG2 VAL   147      36.492  16.268  29.908  1.00  0.00              
ATOM   1084  N   LEU   148      37.374  13.386  32.083  1.00  0.00              
ATOM   1085  CA  LEU   148      38.238  12.656  33.003  1.00  0.00              
ATOM   1086  C   LEU   148      37.429  11.719  33.893  1.00  0.00              
ATOM   1087  O   LEU   148      37.660  11.641  35.100  1.00  0.00              
ATOM   1088  CB  LEU   148      39.295  11.865  32.231  1.00  0.00              
ATOM   1089  CG  LEU   148      38.774  10.892  31.171  1.00  0.00              
ATOM   1090  CD1 LEU   148      37.305  10.578  31.406  1.00  0.00              
ATOM   1091  CD2 LEU   148      39.605   9.617  31.158  1.00  0.00              
ATOM   1092  N   GLY   149      36.480  11.011  33.291  1.00  0.00              
ATOM   1093  CA  GLY   149      35.652  10.089  34.048  1.00  0.00              
ATOM   1094  C   GLY   149      35.424  10.551  35.474  1.00  0.00              
ATOM   1095  O   GLY   149      35.243   9.738  36.379  1.00  0.00              
ATOM   1096  N   ALA   150      35.433  11.865  35.678  1.00  0.00              
ATOM   1097  CA  ALA   150      35.225  12.437  37.003  1.00  0.00              
ATOM   1098  C   ALA   150      35.681  11.475  38.096  1.00  0.00              
ATOM   1099  O   ALA   150      35.776  11.847  39.265  1.00  0.00              
ATOM   1100  CB  ALA   150      35.961  13.761  37.131  1.00  0.00              
ATOM   1101  N   TRP   151      35.960  10.234  37.707  1.00  0.00              
ATOM   1102  CA  TRP   151      36.404   9.217  38.651  1.00  0.00              
ATOM   1103  C   TRP   151      36.586   9.803  40.047  1.00  0.00              
ATOM   1104  O   TRP   151      37.188   9.182  40.925  1.00  0.00              
ATOM   1105  CB  TRP   151      35.412   8.054  38.693  1.00  0.00              
ATOM   1106  CG  TRP   151      36.005   6.743  38.274  1.00  0.00              
ATOM   1107  CD1 TRP   151      35.344   5.560  38.109  1.00  0.00              
ATOM   1108  CD2 TRP   151      37.380   6.483  37.967  1.00  0.00              
ATOM   1109  NE1 TRP   151      36.222   4.578  37.718  1.00  0.00              
ATOM   1110  CE2 TRP   151      37.480   5.120  37.624  1.00  0.00              
ATOM   1111  CE3 TRP   151      38.536   7.269  37.949  1.00  0.00              
ATOM   1112  CZ2 TRP   151      38.688   4.526  37.266  1.00  0.00              
ATOM   1113  CZ3 TRP   151      39.734   6.678  37.595  1.00  0.00              
ATOM   1114  CH2 TRP   151      39.804   5.319  37.257  1.00  0.00              
TER
END
