
#######################################################
#                                                     #
#                        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   21 (  165),  selected   21 , name T0385TS009_1_4
# Molecule2: number of CA atoms  142 ( 1050),  selected  142 , name T0385.pdb
# PARAMETERS: T0385TS009_1_4.T0385.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    T     142      V      51           #
LGA    R     143      N      52          1.370
LGA    W     144      F      53          3.231
LGA    N     145      L      54          2.696
LGA    -       -      V      55           -
LGA    R     146      A      56          1.204
LGA    V     147      D      57          2.661
LGA    L     148      A      58          3.411
LGA    G     149      L      59          1.661
LGA    -       -      K      60           -
LGA    -       -      Q      61           -
LGA    A     150      H      62          2.170
LGA    W     151      R      63          1.608
LGA    -       -      H      64           -
LGA    P     152      R      65          3.563
LGA    I     153      R      66          1.803
LGA    -       -      D      67           -
LGA    -       -      D      68           -
LGA    -       -      V      69           -
LGA    -       -      I      70           -
LGA    -       -      V      71           -
LGA    -       -      M      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      A      75           -
LGA    -       -      R      76           -
LGA    -       -      G      77           -
LGA    -       -      V      78           -
LGA    -       -      T      79           -
LGA    -       -      A      80           -
LGA    -       -      P      81           -
LGA    T     154      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     155      A     103           #
LGA    A     156      V     104           -
LGA    -       -      R     105           -
LGA    -       -      M     106           -
LGA    F     157      E     107          5.854
LGA    -       -      N     108           -
LGA    -       -      D     109           -
LGA    P     158      G     110          2.123
LGA    -       -      A     111           -
LGA    -       -      T     112           -
LGA    G     159      A     113          1.552
LGA    G     160      W     114          0.469
LGA    D     161      R     115          0.840
LGA    E     162      A     116          2.318
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           -
LGA    -       -      P     152           -
LGA    -       -      I     153           -
LGA    -       -      T     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      F     157           -
LGA    -       -      P     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  142    5.0     17    2.58     0.00      8.325     0.634

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.738222 * X  +  -0.084372 * Y  +   0.669260 * Z  +  -8.571249
  Y_new =   0.376287 * X  +  -0.874946 * Y  +   0.304759 * Z  +   4.728359
  Z_new =   0.559853 * X  +   0.476814 * Y  +   0.677652 * Z  +  39.256378 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.613156   -2.528437  [ DEG:    35.1312   -144.8688 ]
  Theta =  -0.594208   -2.547384  [ DEG:   -34.0456   -145.9544 ]
  Phi   =   2.670198   -0.471394  [ DEG:   152.9911    -27.0089 ]
 
# 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                                
REMARK     2: T0385.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_1_4.T0385.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21  142   5.0   17   2.58    0.00   8.325
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_1_4
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM   1026  N   THR   142      36.671  16.873   6.467  1.00  0.00              
ATOM   1027  CA  THR   142      36.366  16.290   7.805  1.00  0.00              
ATOM   1028  C   THR   142      34.931  15.778   7.869  1.00  0.00              
ATOM   1029  O   THR   142      34.287  15.838   8.917  1.00  0.00              
ATOM   1030  CB  THR   142      37.328  15.140   8.152  1.00  0.00              
ATOM   1031  OG1 THR   142      38.283  14.976   7.096  1.00  0.00              
ATOM   1032  CG2 THR   142      38.064  15.434   9.451  1.00  0.00              
ATOM   1033  N   ARG   143      34.438  15.273   6.743  1.00  0.00              
ATOM   1034  CA  ARG   143      33.079  14.749   6.669  1.00  0.00              
ATOM   1035  C   ARG   143      32.199  15.341   7.765  1.00  0.00              
ATOM   1036  O   ARG   143      32.202  14.866   8.900  1.00  0.00              
ATOM   1037  CB  ARG   143      32.470  15.032   5.295  1.00  0.00              
ATOM   1038  CG  ARG   143      32.053  13.785   4.532  1.00  0.00              
ATOM   1039  CD  ARG   143      31.376  14.142   3.219  1.00  0.00              
ATOM   1040  NE  ARG   143      30.530  13.058   2.727  1.00  0.00              
ATOM   1041  CZ  ARG   143      29.211  13.011   2.883  1.00  0.00              
ATOM   1042  NH1 ARG   143      28.583  13.991   3.519  1.00  0.00              
ATOM   1043  NH2 ARG   143      28.522  11.984   2.402  1.00  0.00              
ATOM   1044  N   TRP   144      31.448  16.380   7.417  1.00  0.00              
ATOM   1045  CA  TRP   144      30.562  17.039   8.370  1.00  0.00              
ATOM   1046  C   TRP   144      31.355  17.717   9.482  1.00  0.00              
ATOM   1047  O   TRP   144      31.004  17.617  10.658  1.00  0.00              
ATOM   1048  CB  TRP   144      29.675  18.062   7.657  1.00  0.00              
ATOM   1049  CG  TRP   144      28.454  18.442   8.437  1.00  0.00              
ATOM   1050  CD1 TRP   144      27.415  19.216   8.007  1.00  0.00              
ATOM   1051  CD2 TRP   144      28.144  18.066   9.785  1.00  0.00              
ATOM   1052  NE1 TRP   144      26.476  19.345   9.001  1.00  0.00              
ATOM   1053  CE2 TRP   144      26.901  18.648  10.104  1.00  0.00              
ATOM   1054  CE3 TRP   144      28.798  17.295  10.750  1.00  0.00              
ATOM   1055  CZ2 TRP   144      26.297  18.482  11.350  1.00  0.00              
ATOM   1056  CZ3 TRP   144      28.196  17.131  11.984  1.00  0.00              
ATOM   1057  CH2 TRP   144      26.958  17.722  12.276  1.00  0.00              
ATOM   1058  N   ASN   145      32.426  18.405   9.103  1.00  0.00              
ATOM   1059  CA  ASN   145      33.271  19.101  10.068  1.00  0.00              
ATOM   1060  C   ASN   145      33.649  18.187  11.229  1.00  0.00              
ATOM   1061  O   ASN   145      33.921  18.654  12.335  1.00  0.00              
ATOM   1062  CB  ASN   145      34.533  19.636   9.387  1.00  0.00              
ATOM   1063  CG  ASN   145      34.764  21.108   9.664  1.00  0.00              
ATOM   1064  OD1 ASN   145      35.690  21.713   9.124  1.00  0.00              
ATOM   1065  ND2 ASN   145      33.919  21.690  10.508  1.00  0.00              
ATOM   1066  N   ARG   146      33.664  16.884  10.969  1.00  0.00              
ATOM   1067  CA  ARG   146      34.008  15.903  11.992  1.00  0.00              
ATOM   1068  C   ARG   146      33.193  16.122  13.263  1.00  0.00              
ATOM   1069  O   ARG   146      33.406  15.449  14.272  1.00  0.00              
ATOM   1070  CB  ARG   146      33.792  14.483  11.466  1.00  0.00              
ATOM   1071  CG  ARG   146      34.886  13.995  10.531  1.00  0.00              
ATOM   1072  CD  ARG   146      34.550  12.628   9.955  1.00  0.00              
ATOM   1073  NE  ARG   146      35.108  12.446   8.619  1.00  0.00              
ATOM   1074  CZ  ARG   146      36.409  12.384   8.353  1.00  0.00              
ATOM   1075  NH1 ARG   146      37.291  12.489   9.337  1.00  0.00              
ATOM   1076  NH2 ARG   146      36.824  12.217   7.105  1.00  0.00              
ATOM   1077  N   VAL   147      32.260  17.066  13.206  1.00  0.00              
ATOM   1078  CA  VAL   147      31.393  17.382  14.377  1.00  0.00              
ATOM   1079  C   VAL   147      32.154  17.217  15.688  1.00  0.00              
ATOM   1080  O   VAL   147      31.640  16.642  16.647  1.00  0.00              
ATOM   1081  CB  VAL   147      30.835  18.815  14.295  1.00  0.00              
ATOM   1082  CG1 VAL   147      29.319  18.790  14.176  1.00  0.00              
ATOM   1083  CG2 VAL   147      31.456  19.563  13.127  1.00  0.00              
ATOM   1084  N   LEU   148      33.382  17.726  15.721  1.00  0.00              
ATOM   1085  CA  LEU   148      34.216  17.636  16.914  1.00  0.00              
ATOM   1086  C   LEU   148      34.026  16.297  17.620  1.00  0.00              
ATOM   1087  O   LEU   148      33.909  16.242  18.844  1.00  0.00              
ATOM   1088  CB  LEU   148      35.689  17.835  16.553  1.00  0.00              
ATOM   1089  CG  LEU   148      36.258  16.899  15.484  1.00  0.00              
ATOM   1090  CD1 LEU   148      35.374  15.673  15.318  1.00  0.00              
ATOM   1091  CD2 LEU   148      37.684  16.496  15.827  1.00  0.00              
ATOM   1092  N   GLY   149      33.995  15.222  16.841  1.00  0.00              
ATOM   1093  CA  GLY   149      33.818  13.899  17.413  1.00  0.00              
ATOM   1094  C   GLY   149      32.963  13.919  18.664  1.00  0.00              
ATOM   1095  O   GLY   149      33.126  13.083  19.552  1.00  0.00              
ATOM   1096  N   ALA   150      32.046  14.878  18.739  1.00  0.00              
ATOM   1097  CA  ALA   150      31.160  15.004  19.890  1.00  0.00              
ATOM   1098  C   ALA   150      31.815  14.452  21.152  1.00  0.00              
ATOM   1099  O   ALA   150      31.315  14.648  22.260  1.00  0.00              
ATOM   1100  CB  ALA   150      30.765  16.458  20.099  1.00  0.00              
ATOM   1101  N   TRP   151      32.936  13.758  20.977  1.00  0.00              
ATOM   1102  CA  TRP   151      33.660  13.176  22.099  1.00  0.00              
ATOM   1103  C   TRP   151      33.019  13.560  23.428  1.00  0.00              
ATOM   1104  O   TRP   151      33.609  13.383  24.495  1.00  0.00              
ATOM   1105  CB  TRP   151      33.724  11.654  21.964  1.00  0.00              
ATOM   1106  CG  TRP   151      35.119  11.118  21.856  1.00  0.00              
ATOM   1107  CD1 TRP   151      35.483   9.824  21.621  1.00  0.00              
ATOM   1108  CD2 TRP   151      36.336  11.863  21.980  1.00  0.00              
ATOM   1109  NE1 TRP   151      36.852   9.716  21.589  1.00  0.00              
ATOM   1110  CE2 TRP   151      37.399  10.956  21.808  1.00  0.00              
ATOM   1111  CE3 TRP   151      36.629  13.209  22.219  1.00  0.00              
ATOM   1112  CZ2 TRP   151      38.735  11.349  21.867  1.00  0.00              
ATOM   1113  CZ3 TRP   151      37.954  13.598  22.278  1.00  0.00              
ATOM   1114  CH2 TRP   151      38.994  12.672  22.102  1.00  0.00              
ATOM   1115  N   PRO   152      31.790  14.092  23.377  1.00  0.00              
ATOM   1116  CA  PRO   152      31.057  14.506  24.578  1.00  0.00              
ATOM   1117  C   PRO   152      30.988  13.387  25.612  1.00  0.00              
ATOM   1118  O   PRO   152      30.272  13.492  26.607  1.00  0.00              
ATOM   1119  CB  PRO   152      31.898  15.666  25.113  1.00  0.00              
ATOM   1120  CG  PRO   152      33.299  15.317  24.735  1.00  0.00              
ATOM   1121  CD  PRO   152      31.024  14.332  22.141  1.00  0.00              
ATOM   1122  N   ILE   153      31.737  12.317  25.369  1.00  0.00              
ATOM   1123  CA  ILE   153      31.764  11.151  26.299  1.00  0.00              
ATOM   1124  C   ILE   153      30.414  10.443  26.334  1.00  0.00              
ATOM   1125  O   ILE   153      29.712  10.473  27.344  1.00  0.00              
ATOM   1126  CB  ILE   153      32.854  10.139  25.904  1.00  0.00              
ATOM   1127  CG2 ILE   153      34.238  10.740  26.102  1.00  0.00              
ATOM   1128  CG1 ILE   153      32.664   9.688  24.454  1.00  0.00              
ATOM   1129  CD1 ILE   153      33.516   8.499  24.066  1.00  0.00              
ATOM   1130  N   THR   154      30.057   9.806  25.223  1.00  0.00              
ATOM   1131  CA  THR   154      28.763   9.072  25.122  1.00  0.00              
ATOM   1132  C   THR   154      27.620  10.018  24.770  1.00  0.00              
ATOM   1133  O   THR   154      26.550   9.968  25.376  1.00  0.00              
ATOM   1134  CB  THR   154      28.831   7.949  24.071  1.00  0.00              
ATOM   1135  OG1 THR   154      29.976   8.145  23.233  1.00  0.00              
ATOM   1136  CG2 THR   154      28.931   6.591  24.750  1.00  0.00              
ATOM   1137  N   ALA   155      27.853  10.878  23.783  1.00  0.00              
ATOM   1138  CA  ALA   155      26.844  11.836  23.347  1.00  0.00              
ATOM   1139  C   ALA   155      25.983  12.302  24.517  1.00  0.00              
ATOM   1140  O   ALA   155      25.027  13.055  24.335  1.00  0.00              
ATOM   1141  CB  ALA   155      27.503  13.030  22.673  1.00  0.00              
ATOM   1142  N   ALA   156      26.330  11.848  25.717  1.00  0.00              
ATOM   1143  CA  ALA   156      25.591  12.217  26.918  1.00  0.00              
ATOM   1144  C   ALA   156      24.520  13.259  26.609  1.00  0.00              
ATOM   1145  O   ALA   156      23.962  13.877  27.516  1.00  0.00              
ATOM   1146  CB  ALA   156      24.958  10.986  27.550  1.00  0.00              
ATOM   1147  N   PHE   157      24.240  13.448  25.324  1.00  0.00              
ATOM   1148  CA  PHE   157      23.238  14.415  24.892  1.00  0.00              
ATOM   1149  C   PHE   157      23.393  15.738  25.635  1.00  0.00              
ATOM   1150  O   PHE   157      22.742  15.977  26.652  1.00  0.00              
ATOM   1151  CB  PHE   157      23.328  14.644  23.382  1.00  0.00              
ATOM   1152  CG  PHE   157      22.175  15.423  22.817  1.00  0.00              
ATOM   1153  CD1 PHE   157      21.996  16.757  23.144  1.00  0.00              
ATOM   1154  CD2 PHE   157      21.271  14.824  21.959  1.00  0.00              
ATOM   1155  CE1 PHE   157      20.936  17.474  22.623  1.00  0.00              
ATOM   1156  CE2 PHE   157      20.210  15.542  21.439  1.00  0.00              
ATOM   1157  CZ  PHE   157      20.041  16.861  21.768  1.00  0.00              
ATOM   1158  N   PRO   158      24.266  16.620  25.126  1.00  0.00              
ATOM   1159  CA  PRO   158      24.513  17.929  25.738  1.00  0.00              
ATOM   1160  C   PRO   158      23.809  18.067  27.083  1.00  0.00              
ATOM   1161  O   PRO   158      23.881  19.114  27.728  1.00  0.00              
ATOM   1162  CB  PRO   158      26.030  17.937  25.934  1.00  0.00              
ATOM   1163  CG  PRO   158      26.574  17.379  24.661  1.00  0.00              
ATOM   1164  CD  PRO   158      25.077  16.404  23.916  1.00  0.00              
ATOM   1165  N   GLY   159      23.129  17.005  27.502  1.00  0.00              
ATOM   1166  CA  GLY   159      22.424  17.032  28.770  1.00  0.00              
ATOM   1167  C   GLY   159      22.939  18.115  29.697  1.00  0.00              
ATOM   1168  O   GLY   159      22.346  18.385  30.741  1.00  0.00              
ATOM   1169  N   GLY   160      24.047  18.741  29.316  1.00  0.00              
ATOM   1170  CA  GLY   160      24.620  19.793  30.136  1.00  0.00              
ATOM   1171  C   GLY   160      23.611  20.396  31.094  1.00  0.00              
ATOM   1172  O   GLY   160      22.998  19.688  31.891  1.00  0.00              
ATOM   1173  N   ASP   161      23.437  21.712  31.017  1.00  0.00              
ATOM   1174  CA  ASP   161      22.496  22.411  31.884  1.00  0.00              
ATOM   1175  C   ASP   161      21.474  21.449  32.478  1.00  0.00              
ATOM   1176  O   ASP   161      21.726  20.249  32.587  1.00  0.00              
ATOM   1177  CB  ASP   161      23.240  23.145  33.001  1.00  0.00              
ATOM   1178  CG  ASP   161      24.059  22.209  33.868  1.00  0.00              
ATOM   1179  OD1 ASP   161      23.523  21.158  34.278  1.00  0.00              
ATOM   1180  OD2 ASP   161      25.237  22.526  34.136  1.00  0.00              
ATOM   1181  N   GLU   162      20.318  21.984  32.862  1.00  0.00              
ATOM   1182  CA  GLU   162      19.256  21.173  33.446  1.00  0.00              
ATOM   1183  C   GLU   162      18.006  22.008  33.707  1.00  0.00              
ATOM   1184  O   GLU   162      16.988  21.397  34.092  1.00  0.00              
ATOM   1185  CB  GLU   162      18.919  19.993  32.534  1.00  0.00              
ATOM   1186  CG  GLU   162      19.387  18.647  33.063  1.00  0.00              
ATOM   1187  CD  GLU   162      18.646  17.484  32.433  1.00  0.00              
ATOM   1188  OE1 GLU   162      18.856  17.228  31.229  1.00  0.00              
ATOM   1189  OE2 GLU   162      17.857  16.827  33.145  1.00  0.00              
ATOM   1190  OXT GLU   162      18.097  23.239  33.514  1.00  0.00              
TER
END
