
#######################################################
#                                                     #
#                        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   38 (  188),  selected   38 , name T0372TS261_1_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS261_1_4-D1.T0372_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    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    S      22      I       7          3.541
LGA    D      23      T       8          1.511
LGA    -       -      L       9           -
LGA    R      24      A      10          1.058
LGA    R      25      D      11           #
LGA    N      26      -       -           -
LGA    C      27      -       -           -
LGA    D      28      R      12           #
LGA    L      29      D      13          4.693
LGA    S      30      T      14          3.987
LGA    M      65      I      15           -
LGA    M      66      T      16           -
LGA    P      67      A      17           -
LGA    V      68      F      18           -
LGA    G      69      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    H      89      C      27          3.138
LGA    N      90      D      28           #
LGA    -       -      L      29           -
LGA    F      91      S      30          0.907
LGA    C      92      F      31          2.338
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    M      93      L      34          1.006
LGA    L      94      C      35          2.790
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    G      95      R      38          1.993
LGA    V      96      F      39          2.541
LGA    C      97      L      40          4.743
LGA    S      98      Y      41          4.404
LGA    N      99      D      42          1.648
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    M     100      A      63          2.622
LGA    R     101      Y      64          4.529
LGA    A     102      M      65           -
LGA    D     103      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    L     104      L      80          3.652
LGA    E     105      I      81          5.092
LGA    A     106      -       -           -
LGA    I     107      E      82          3.654
LGA    L     108      D      83          4.871
LGA    P     109      A      84           #
LGA    E     110      D      85          4.707
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    R     111      H     298           #
LGA    D     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   38  126    5.0     22    3.44     4.55     10.188     0.622

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.274595 * X  +   0.902024 * Y  +  -0.333092 * Z  +  47.678093
  Y_new =  -0.095485 * X  +   0.319117 * Y  +   0.942893 * Z  +  22.900349
  Z_new =   0.956807 * X  +   0.290719 * Y  +  -0.001498 * Z  + -26.798187 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.575949   -1.565644  [ DEG:    90.2952    -89.7048 ]
  Theta =  -1.275814   -1.865778  [ DEG:   -73.0988   -106.9012 ]
  Phi   =  -2.806941    0.334651  [ DEG:  -160.8259     19.1741 ]
 
# 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: T0372TS261_1_4-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS261_1_4-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38  126   5.0   22   3.44    4.55  10.188
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS261_1_4-D1
REMARK PARENT number 4
PFRMAT TS
TARGET T0372
PARENT 1hqv_A
ATOM   1094  N   SER    22      52.017  51.650   5.513  1.00  4.02
ATOM   1095  CA  SER    22      50.847  52.393   5.948  1.00  4.02
ATOM   1096  C   SER    22      50.794  52.397   7.471  1.00  4.02
ATOM   1097  O   SER    22      50.400  53.387   8.097  1.00  4.02
ATOM   1098  CB  SER    22      49.563  51.764   5.384  1.00  4.02
ATOM   1099  N   ASP    23      51.197  51.271   8.052  1.00  1.86
ATOM   1100  CA  ASP    23      51.223  51.071   9.497  1.00  1.86
ATOM   1101  C   ASP    23      52.482  51.727  10.046  1.00  1.86
ATOM   1102  O   ASP    23      53.426  51.045  10.445  1.00  1.86
ATOM   1103  CB  ASP    23      51.221  49.568   9.786  1.00  1.86
ATOM   1104  N   ARG    24      52.477  53.059  10.069  1.00  3.69
ATOM   1105  CA  ARG    24      53.617  53.850  10.521  1.00  3.69
ATOM   1106  C   ARG    24      54.054  53.641  11.965  1.00  3.69
ATOM   1107  O   ARG    24      55.250  53.536  12.242  1.00  3.69
ATOM   1108  CB  ARG    24      53.336  55.331  10.265  1.00  3.69
ATOM   1109  N   ARG    25      48.345  47.355  13.521  1.00  4.83
ATOM   1110  CA  ARG    25      47.000  47.656  13.043  1.00  4.83
ATOM   1111  C   ARG    25      46.962  49.006  12.329  1.00  4.83
ATOM   1112  O   ARG    25      47.505  49.997  12.822  1.00  4.83
ATOM   1113  CB  ARG    25      45.991  47.698  14.211  1.00  4.83
ATOM   1114  N   ASN    26      46.324  49.038  11.162  1.00  7.22
ATOM   1115  CA  ASN    26      46.185  50.270  10.396  1.00  7.22
ATOM   1116  C   ASN    26      44.919  50.972  10.864  1.00  7.22
ATOM   1117  O   ASN    26      43.836  50.390  10.858  1.00  7.22
ATOM   1118  CB  ASN    26      46.072  49.985   8.894  1.00  7.22
ATOM   1119  N   CYS    27      45.066  52.229  11.270  1.00  3.38
ATOM   1120  CA  CYS    27      43.943  53.012  11.767  1.00  3.38
ATOM   1121  C   CYS    27      43.389  53.932  10.705  1.00  3.38
ATOM   1122  O   CYS    27      44.011  54.148   9.673  1.00  3.38
ATOM   1123  CB  CYS    27      44.388  53.878  12.944  1.00  3.38
ATOM   1124  N   ASP    28      42.220  54.490  10.993  1.00  4.66
ATOM   1125  CA  ASP    28      41.555  55.422  10.092  1.00  4.66
ATOM   1126  C   ASP    28      42.545  56.478   9.626  1.00  4.66
ATOM   1127  O   ASP    28      42.576  56.859   8.455  1.00  4.66
ATOM   1128  CB  ASP    28      40.403  56.124  10.820  1.00  4.66
ATOM   1129  N   LEU    29      43.362  56.942  10.559  1.00  5.19
ATOM   1130  CA  LEU    29      44.326  57.980  10.263  1.00  5.19
ATOM   1131  C   LEU    29      45.472  57.548   9.363  1.00  5.19
ATOM   1132  O   LEU    29      45.899  58.305   8.496  1.00  5.19
ATOM   1133  CB  LEU    29      44.875  58.565  11.569  1.00  5.19
ATOM   1134  N   SER    30      45.984  56.343   9.561  1.00  4.58
ATOM   1135  CA  SER    30      47.099  55.884   8.741  1.00  4.58
ATOM   1136  C   SER    30      46.642  55.539   7.335  1.00  4.58
ATOM   1137  O   SER    30      47.368  55.758   6.371  1.00  4.58
ATOM   1138  CB  SER    30      47.749  54.657   9.364  1.00  4.58
ATOM   1139  N   MET    65      45.755  56.702   1.138  1.00  2.83
ATOM   1140  CA  MET    65      44.811  56.856   0.051  1.00  2.83
ATOM   1141  C   MET    65      44.975  58.181  -0.667  1.00  2.83
ATOM   1142  O   MET    65      45.566  59.120  -0.138  1.00  2.83
ATOM   1143  CB  MET    65      43.386  56.700   0.577  1.00  2.83
ATOM   1144  N   MET    66      44.451  58.257  -1.882  1.00  4.39
ATOM   1145  CA  MET    66      44.574  59.468  -2.663  1.00  4.39
ATOM   1146  C   MET    66      43.308  59.740  -3.427  1.00  4.39
ATOM   1147  O   MET    66      42.865  58.885  -4.189  1.00  4.39
ATOM   1148  CB  MET    66      45.724  59.324  -3.655  1.00  4.39
ATOM   1149  N   PRO    67      42.727  60.922  -3.225  1.00  5.96
ATOM   1150  CA  PRO    67      41.516  61.307  -3.948  1.00  5.96
ATOM   1151  C   PRO    67      41.945  62.086  -5.184  1.00  5.96
ATOM   1152  O   PRO    67      41.122  62.556  -5.960  1.00  5.96
ATOM   1153  CB  PRO    67      40.582  62.166  -3.074  1.00  5.96
ATOM   1154  N   VAL    68      43.255  62.217  -5.362  1.00  3.76
ATOM   1155  CA  VAL    68      43.782  62.924  -6.517  1.00  3.76
ATOM   1156  C   VAL    68      43.554  64.428  -6.600  1.00  3.76
ATOM   1157  O   VAL    68      43.959  65.049  -7.584  1.00  3.76
ATOM   1158  CB  VAL    68      43.200  62.244  -7.768  1.00  3.76
ATOM   1159  N   GLY    69      42.920  65.022  -5.589  1.00  2.82
ATOM   1160  CA  GLY    69      42.657  66.459  -5.604  1.00  2.82
ATOM   1161  C   GLY    69      43.559  67.234  -4.660  1.00  2.82
ATOM   1162  O   GLY    69      43.333  68.410  -4.411  1.00  2.82
ATOM   1163  N   HIS    89      35.877  44.855  16.139  1.00  4.09
ATOM   1164  CA  HIS    89      35.756  46.284  16.443  1.00  4.09
ATOM   1165  C   HIS    89      36.993  46.830  17.160  1.00  4.09
ATOM   1166  O   HIS    89      37.011  46.961  18.380  1.00  4.09
ATOM   1167  CB  HIS    89      34.513  46.533  17.304  1.00  4.09
ATOM   1168  N   ASN    90      38.023  47.149  16.383  1.00  4.46
ATOM   1169  CA  ASN    90      39.286  47.655  16.911  1.00  4.46
ATOM   1170  C   ASN    90      39.676  48.962  16.232  1.00  4.46
ATOM   1171  O   ASN    90      40.847  49.338  16.234  1.00  4.46
ATOM   1172  CB  ASN    90      40.386  46.623  16.666  1.00  4.46
ATOM   1173  N   PHE    91      38.699  49.646  15.647  1.00  2.88
ATOM   1174  CA  PHE    91      38.957  50.907  14.960  1.00  2.88
ATOM   1175  C   PHE    91      40.204  50.797  14.079  1.00  2.88
ATOM   1176  O   PHE    91      41.112  51.626  14.158  1.00  2.88
ATOM   1177  CB  PHE    91      39.128  52.029  15.978  1.00  2.88
ATOM   1178  N   CYS    92      40.240  49.766  13.242  1.00  3.64
ATOM   1179  CA  CYS    92      41.375  49.561  12.361  1.00  3.64
ATOM   1180  C   CYS    92      41.314  48.195  11.717  1.00  3.64
ATOM   1181  O   CYS    92      40.353  47.457  11.924  1.00  3.64
ATOM   1182  CB  CYS    92      42.678  49.744  13.157  1.00  3.64
ATOM   1183  N   MET    93      42.329  47.854  10.930  1.00  4.59
ATOM   1184  CA  MET    93      42.377  46.552  10.267  1.00  4.59
ATOM   1185  C   MET    93      43.763  45.976  10.392  1.00  4.59
ATOM   1186  O   MET    93      44.728  46.721  10.528  1.00  4.59
ATOM   1187  CB  MET    93      42.048  46.646   8.759  1.00  4.59
ATOM   1188  N   LEU    94      43.851  44.647  10.362  1.00  4.97
ATOM   1189  CA  LEU    94      45.134  43.954  10.443  1.00  4.97
ATOM   1190  C   LEU    94      45.563  43.616   9.024  1.00  4.97
ATOM   1191  O   LEU    94      44.870  43.959   8.066  1.00  4.97
ATOM   1192  CB  LEU    94      45.004  42.668  11.260  1.00  4.97
ATOM   1193  N   GLY    95      46.689  42.930   8.885  1.00  2.00
ATOM   1194  CA  GLY    95      47.180  42.590   7.561  1.00  2.00
ATOM   1195  C   GLY    95      46.135  41.896   6.700  1.00  2.00
ATOM   1196  O   GLY    95      45.761  42.390   5.628  1.00  2.00
ATOM   1197  N   VAL    96      45.666  40.747   7.171  1.00  2.92
ATOM   1198  CA  VAL    96      44.667  39.981   6.448  1.00  2.92
ATOM   1199  C   VAL    96      43.494  40.816   5.950  1.00  2.92
ATOM   1200  O   VAL    96      43.144  40.756   4.770  1.00  2.92
ATOM   1201  CB  VAL    96      44.130  38.858   7.321  1.00  2.92
ATOM   1202  N   CYS    97      42.880  41.578   6.848  1.00  2.64
ATOM   1203  CA  CYS    97      41.741  42.405   6.478  1.00  2.64
ATOM   1204  C   CYS    97      42.186  43.514   5.520  1.00  2.64
ATOM   1205  O   CYS    97      41.420  43.965   4.672  1.00  2.64
ATOM   1206  CB  CYS    97      41.112  43.041   7.725  1.00  2.64
ATOM   1207  N   SER    98      43.431  43.952   5.663  1.00  3.86
ATOM   1208  CA  SER    98      43.932  45.007   4.811  1.00  3.86
ATOM   1209  C   SER    98      43.939  44.582   3.356  1.00  3.86
ATOM   1210  O   SER    98      43.600  45.375   2.480  1.00  3.86
ATOM   1211  CB  SER    98      45.340  45.425   5.214  1.00  3.86
ATOM   1212  N   ASN    99      44.338  43.342   3.085  1.00  3.61
ATOM   1213  CA  ASN    99      44.348  42.889   1.705  1.00  3.61
ATOM   1214  C   ASN    99      42.932  43.029   1.164  1.00  3.61
ATOM   1215  O   ASN    99      42.732  43.199  -0.034  1.00  3.61
ATOM   1216  CB  ASN    99      44.871  41.432   1.574  1.00  3.61
ATOM   1217  N   MET   100      39.371  46.229  -2.233  1.00  5.28
ATOM   1218  CA  MET   100      38.197  47.102  -2.266  1.00  5.28
ATOM   1219  C   MET   100      38.510  48.483  -2.890  1.00  5.28
ATOM   1220  O   MET   100      37.720  49.019  -3.678  1.00  5.28
ATOM   1221  CB  MET   100      37.646  47.274  -0.845  1.00  5.28
ATOM   1222  N   ARG   101      39.661  49.052  -2.540  1.00  7.15
ATOM   1223  CA  ARG   101      40.056  50.351  -3.073  1.00  7.15
ATOM   1224  C   ARG   101      40.414  50.210  -4.548  1.00  7.15
ATOM   1225  O   ARG   101      40.093  51.068  -5.369  1.00  7.15
ATOM   1226  CB  ARG   101      41.269  50.940  -2.302  1.00  7.15
ATOM   1227  N   ALA   102      41.074  49.108  -4.867  1.00  7.71
ATOM   1228  CA  ALA   102      41.473  48.823  -6.220  1.00  7.71
ATOM   1229  C   ALA   102      40.259  48.657  -7.135  1.00  7.71
ATOM   1230  O   ALA   102      40.220  49.243  -8.212  1.00  7.71
ATOM   1231  CB  ALA   102      42.331  47.568  -6.251  1.00  7.71
ATOM   1232  N   ASP   103      39.267  47.871  -6.720  1.00  4.78
ATOM   1233  CA  ASP   103      38.082  47.705  -7.556  1.00  4.78
ATOM   1234  C   ASP   103      37.393  49.049  -7.778  1.00  4.78
ATOM   1235  O   ASP   103      36.871  49.307  -8.862  1.00  4.78
ATOM   1236  CB  ASP   103      37.077  46.721  -6.935  1.00  4.78
ATOM   1237  N   LEU   104      37.386  49.914  -6.768  1.00  7.83
ATOM   1238  CA  LEU   104      36.745  51.220  -6.918  1.00  7.83
ATOM   1239  C   LEU   104      37.470  52.139  -7.889  1.00  7.83
ATOM   1240  O   LEU   104      36.830  52.916  -8.592  1.00  7.83
ATOM   1241  CB  LEU   104      36.623  51.925  -5.572  1.00  7.83
ATOM   1242  N   GLU   105      38.798  52.066  -7.920  1.00  5.59
ATOM   1243  CA  GLU   105      39.594  52.891  -8.823  1.00  5.59
ATOM   1244  C   GLU   105      39.256  52.507 -10.254  1.00  5.59
ATOM   1245  O   GLU   105      39.118  53.373 -11.129  1.00  5.59
ATOM   1246  CB  GLU   105      41.098  52.675  -8.582  1.00  5.59
ATOM   1247  N   ALA   106      39.118  51.204 -10.493  1.00  4.88
ATOM   1248  CA  ALA   106      38.800  50.716 -11.824  1.00  4.88
ATOM   1249  C   ALA   106      37.439  51.234 -12.226  1.00  4.88
ATOM   1250  O   ALA   106      37.255  51.724 -13.350  1.00  4.88
ATOM   1251  CB  ALA   106      38.850  49.181 -11.869  1.00  4.88
ATOM   1252  N   ILE   107      36.476  51.142 -11.317  1.00  5.75
ATOM   1253  CA  ILE   107      35.147  51.663 -11.615  1.00  5.75
ATOM   1254  C   ILE   107      35.241  53.156 -11.963  1.00  5.75
ATOM   1255  O   ILE   107      34.678  53.626 -12.955  1.00  5.75
ATOM   1256  CB  ILE   107      34.207  51.492 -10.414  1.00  5.75
ATOM   1257  N   LEU   108      35.962  53.899 -11.134  1.00  8.32
ATOM   1258  CA  LEU   108      36.125  55.330 -11.333  1.00  8.32
ATOM   1259  C   LEU   108      36.694  55.646 -12.723  1.00  8.32
ATOM   1260  O   LEU   108      36.145  56.463 -13.460  1.00  8.32
ATOM   1261  CB  LEU   108      37.057  55.880 -10.262  1.00  8.32
ATOM   1262  N   PRO   109      37.788  54.992 -13.085  1.00  1.00
ATOM   1263  CA  PRO   109      38.401  55.246 -14.383  1.00  1.00
ATOM   1264  C   PRO   109      37.502  54.828 -15.539  1.00  1.00
ATOM   1265  O   PRO   109      37.560  55.416 -16.618  1.00  1.00
ATOM   1266  CB  PRO   109      39.727  54.513 -14.510  1.00  1.00
ATOM   1267  N   GLU   110      36.693  53.798 -15.333  1.00  6.96
ATOM   1268  CA  GLU   110      35.802  53.368 -16.391  1.00  6.96
ATOM   1269  C   GLU   110      34.820  54.484 -16.720  1.00  6.96
ATOM   1270  O   GLU   110      34.603  54.813 -17.886  1.00  6.96
ATOM   1271  CB  GLU   110      35.001  52.112 -16.002  1.00  6.96
ATOM   1272  N   ARG   111      34.231  55.086 -15.695  1.00  6.61
ATOM   1273  CA  ARG   111      33.270  56.139 -15.958  1.00  6.61
ATOM   1274  C   ARG   111      33.848  57.542 -16.093  1.00  6.61
ATOM   1275  O   ARG   111      33.160  58.437 -16.552  1.00  6.61
ATOM   1276  CB  ARG   111      32.151  56.089 -14.922  1.00  6.61
ATOM   1277  N   ASP   117      35.102  57.749 -15.698  1.00  2.79
ATOM   1278  CA  ASP   117      35.707  59.064 -15.881  1.00  2.79
ATOM   1279  C   ASP   117      36.101  59.077 -17.346  1.00  2.79
ATOM   1280  O   ASP   117      37.286  58.961 -17.665  1.00  2.79
ATOM   1281  CB  ASP   117      36.949  59.212 -15.013  1.00  2.79
TER
END
