
#######################################################
#                                                     #
#                        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   37 (  182),  selected   37 , name T0291TS261_1_2-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS261_1_2-D1.T0291_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       1           -
LGA    -       -      Y       2           -
LGA    T       1      V       3          5.214
LGA    Y       2      D       4          4.592
LGA    V       3      P       5          2.433
LGA    D       4      H       6           #
LGA    P       5      V      15           #
LGA    H       6      H      16          4.519
LGA    T       7      E      17          3.536
LGA    -       -      F      18           -
LGA    Y       8      A      19          3.293
LGA    E       9      K      20          3.538
LGA    D      10      E      21          4.797
LGA    K      20      L      22          4.194
LGA    -       -      D      23           -
LGA    -       -      A      24           -
LGA    -       -      T      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      S      28           -
LGA    -       -      I      29           -
LGA    -       -      D      30           -
LGA    -       -      K      31           -
LGA    -       -      V      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      A      35           -
LGA    -       -      G      36           -
LGA    -       -      E      37           -
LGA    F      38      F      38          3.751
LGA    G      39      G      39          2.285
LGA    E      40      E      40          2.403
LGA    -       -      V      41           -
LGA    -       -      C      42           -
LGA    -       -      S      43           -
LGA    -       -      G      44           -
LGA    -       -      R      45           -
LGA    -       -      L      46           -
LGA    -       -      K      47           -
LGA    S      50      L      48          3.261
LGA    -       -      P      49           -
LGA    -       -      S      50           -
LGA    -       -      K      51           -
LGA    -       -      K      52           -
LGA    K      51      E      53          2.937
LGA    K      52      I      54           -
LGA    E      53      S      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      I      58           -
LGA    -       -      K      59           -
LGA    -       -      T      60           -
LGA    -       -      L      61           -
LGA    K      62      K      62          1.068
LGA    V      63      V      63          1.482
LGA    G      64      G      64          3.014
LGA    Y      65      Y      65          1.724
LGA    T      66      T      66          0.460
LGA    E      67      E      67          0.704
LGA    K      68      K      68          0.665
LGA    Q      69      Q      69          0.939
LGA    R      70      R      70          0.602
LGA    R      71      R      71          0.816
LGA    D      72      D      72          1.138
LGA    F      73      F      73          1.414
LGA    L      74      L      74          1.251
LGA    G      75      G      75          1.048
LGA    E      76      E      76          0.915
LGA    A      77      A      77          1.271
LGA    S      78      S      78          1.618
LGA    I      79      I      79          1.670
LGA    -       -      M      80           -
LGA    -       -      G      81           -
LGA    -       -      Q      82           -
LGA    -       -      F      83           -
LGA    -       -      D      84           -
LGA    -       -      H      85           -
LGA    -       -      P      86           -
LGA    -       -      N      87           -
LGA    -       -      I      88           -
LGA    -       -      I      89           -
LGA    -       -      R      90           -
LGA    -       -      L      91           -
LGA    -       -      E      92           -
LGA    -       -      G      93           -
LGA    -       -      V      94           -
LGA    -       -      V      95           -
LGA    T      96      T      96          0.793
LGA    -       -      K      97           -
LGA    -       -      S      98           -
LGA    -       -      K      99           -
LGA    -       -      P     100           -
LGA    -       -      V     101           -
LGA    -       -      M     102           -
LGA    -       -      I     103           -
LGA    -       -      V     104           -
LGA    -       -      T     105           -
LGA    -       -      E     106           -
LGA    -       -      Y     107           -
LGA    -       -      M     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37  100    5.0     33    2.63    69.70     25.040     1.209

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.539474 * X  +  -0.429662 * Y  +  -0.724126 * Z  +  16.784109
  Y_new =  -0.792569 * X  +   0.031211 * Y  +  -0.608983 * Z  +  55.455875
  Z_new =   0.284257 * X  +   0.902450 * Y  +  -0.323699 * Z  +  35.328808 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.915191   -1.226401  [ DEG:   109.7324    -70.2676 ]
  Theta =  -0.288232   -2.853361  [ DEG:   -16.5145   -163.4855 ]
  Phi   =  -0.973165    2.168428  [ DEG:   -55.7582    124.2418 ]
 
# 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: T0291TS261_1_2-D1                             
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS261_1_2-D1.T0291_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37  100   5.0   33   2.63   69.70  25.040
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS261_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0291
PARENT 1t46_A
ATOM   1146  N   THR     1      -7.805  28.350  56.273  1.00  4.55
ATOM   1147  CA  THR     1      -9.050  28.238  56.998  1.00  4.55
ATOM   1148  C   THR     1     -10.079  27.753  55.991  1.00  4.55
ATOM   1149  O   THR     1     -10.470  28.500  55.098  1.00  4.55
ATOM   1150  CB  THR     1      -9.438  29.603  57.573  1.00  4.55
ATOM   1151  N   TYR     2     -10.513  26.499  56.127  1.00  4.48
ATOM   1152  CA  TYR     2     -11.385  25.883  55.124  1.00  4.48
ATOM   1153  C   TYR     2     -12.785  26.500  55.064  1.00  4.48
ATOM   1154  O   TYR     2     -13.423  26.427  54.014  1.00  4.48
ATOM   1155  CB  TYR     2     -11.441  24.414  55.557  1.00  4.48
ATOM   1156  N   VAL     3     -13.244  27.113  56.155  1.00  4.13
ATOM   1157  CA  VAL     3     -14.524  27.827  56.143  1.00  4.13
ATOM   1158  C   VAL     3     -14.459  29.060  55.237  1.00  4.13
ATOM   1159  O   VAL     3     -15.491  29.613  54.857  1.00  4.13
ATOM   1160  CB  VAL     3     -14.980  28.233  57.567  1.00  4.13
ATOM   1161  N   ASP     4     -13.240  29.478  54.896  1.00  4.95
ATOM   1162  CA  ASP     4     -13.025  30.577  53.958  1.00  4.95
ATOM   1163  C   ASP     4     -12.882  30.064  52.524  1.00  4.95
ATOM   1164  O   ASP     4     -13.074  30.821  51.570  1.00  4.95
ATOM   1165  CB  ASP     4     -11.802  31.411  54.354  1.00  4.95
ATOM   1166  N   PRO     5     -12.533  28.784  52.378  1.00  4.99
ATOM   1167  CA  PRO     5     -12.557  28.127  51.073  1.00  4.99
ATOM   1168  C   PRO     5     -14.004  28.060  50.578  1.00  4.99
ATOM   1169  O   PRO     5     -14.908  27.719  51.346  1.00  4.99
ATOM   1170  CB  PRO     5     -11.959  26.716  51.148  1.00  4.99
ATOM   1171  N   HIS     6     -14.234  28.416  49.315  1.00  5.72
ATOM   1172  CA  HIS     6     -15.567  28.282  48.716  1.00  5.72
ATOM   1173  C   HIS     6     -15.785  26.864  48.184  1.00  5.72
ATOM   1174  O   HIS     6     -14.831  26.242  47.702  1.00  5.72
ATOM   1175  CB  HIS     6     -15.544  29.295  47.559  1.00  5.72
ATOM   1176  N   THR     7     -17.012  26.354  48.295  1.00  3.81
ATOM   1177  CA  THR     7     -17.337  25.049  47.720  1.00  3.81
ATOM   1178  C   THR     7     -17.657  25.201  46.236  1.00  3.81
ATOM   1179  O   THR     7     -18.598  25.902  45.863  1.00  3.81
ATOM   1180  CB  THR     7     -18.495  24.359  48.461  1.00  3.81
ATOM   1181  N   TYR     8     -16.854  24.546  45.403  1.00  2.27
ATOM   1182  CA  TYR     8     -17.054  24.548  43.962  1.00  2.27
ATOM   1183  C   TYR     8     -18.206  23.616  43.589  1.00  2.27
ATOM   1184  O   TYR     8     -18.114  22.398  43.758  1.00  2.27
ATOM   1185  CB  TYR     8     -15.765  24.127  43.248  1.00  2.27
ATOM   1186  N   GLU     9     -19.285  24.202  43.076  1.00  4.34
ATOM   1187  CA  GLU     9     -20.485  23.453  42.702  1.00  4.34
ATOM   1188  C   GLU     9     -20.248  22.418  41.599  1.00  4.34
ATOM   1189  O   GLU     9     -21.076  21.527  41.398  1.00  4.34
ATOM   1190  CB  GLU     9     -21.611  24.414  42.300  1.00  4.34
ATOM   1191  N   ASP    10     -19.118  22.531  40.900  1.00  4.04
ATOM   1192  CA  ASP    10     -18.745  21.567  39.862  1.00  4.04
ATOM   1193  C   ASP    10     -18.624  20.137  40.403  1.00  4.04
ATOM   1194  O   ASP    10     -18.763  19.176  39.654  1.00  4.04
ATOM   1195  CB  ASP    10     -17.458  21.995  39.140  1.00  4.04
ATOM   1196  N   LYS    20     -18.389  20.010  41.708  1.00  5.01
ATOM   1197  CA  LYS    20     -18.259  18.702  42.340  1.00  5.01
ATOM   1198  C   LYS    20     -19.589  17.992  42.537  1.00  5.01
ATOM   1199  O   LYS    20     -19.622  16.774  42.717  1.00  5.01
ATOM   1200  CB  LYS    20     -17.563  18.832  43.698  1.00  5.01
ATOM   1201  N   PHE    38     -19.756  10.010  64.241  1.00  1.17
ATOM   1202  CA  PHE    38     -20.645  10.854  63.441  1.00  1.17
ATOM   1203  C   PHE    38     -20.525  10.631  61.943  1.00  1.17
ATOM   1204  O   PHE    38     -21.317  11.165  61.166  1.00  1.17
ATOM   1205  CB  PHE    38     -20.408  12.331  63.769  1.00  1.17
ATOM   1206  N   GLY    39     -19.537   9.840  61.539  1.00  2.86
ATOM   1207  CA  GLY    39     -19.293   9.609  60.128  1.00  2.86
ATOM   1208  C   GLY    39     -18.857   8.199  59.809  1.00  2.86
ATOM   1209  O   GLY    39     -18.422   7.452  60.689  1.00  2.86
ATOM   1210  N   GLU    40     -18.978   7.842  58.535  1.00  2.63
ATOM   1211  CA  GLU    40     -18.540   6.548  58.048  1.00  2.63
ATOM   1212  C   GLU    40     -18.104   6.642  56.593  1.00  2.63
ATOM   1213  O   GLU    40     -18.571   7.505  55.849  1.00  2.63
ATOM   1214  CB  GLU    40     -19.643   5.486  58.231  1.00  2.63
ATOM   1215  N   SER    50     -17.119   9.699  35.867  1.00  5.31
ATOM   1216  CA  SER    50     -16.052  10.112  34.953  1.00  5.31
ATOM   1217  C   SER    50     -16.428   9.831  33.496  1.00  5.31
ATOM   1218  O   SER    50     -16.117  10.625  32.607  1.00  5.31
ATOM   1219  CB  SER    50     -14.685   9.458  35.324  1.00  5.31
ATOM   1220  N   LYS    51     -17.108   8.706  33.275  1.00  4.03
ATOM   1221  CA  LYS    51     -17.537   8.267  31.949  1.00  4.03
ATOM   1222  C   LYS    51     -19.045   8.007  31.968  1.00  4.03
ATOM   1223  O   LYS    51     -19.543   7.316  32.857  1.00  4.03
ATOM   1224  CB  LYS    51     -16.778   7.001  31.550  1.00  4.03
ATOM   1225  N   LYS    52     -19.748   8.545  30.969  1.00  4.61
ATOM   1226  CA  LYS    52     -21.218   8.604  30.943  1.00  4.61
ATOM   1227  C   LYS    52     -21.971   7.292  31.215  1.00  4.61
ATOM   1228  O   LYS    52     -22.874   7.256  32.057  1.00  4.61
ATOM   1229  CB  LYS    52     -21.706   9.223  29.628  1.00  4.61
ATOM   1230  N   GLU    53     -21.614   6.230  30.500  1.00  5.96
ATOM   1231  CA  GLU    53     -22.274   4.937  30.677  1.00  5.96
ATOM   1232  C   GLU    53     -21.334   3.916  31.323  1.00  5.96
ATOM   1233  O   GLU    53     -21.199   2.782  30.849  1.00  5.96
ATOM   1234  CB  GLU    53     -22.825   4.417  29.341  1.00  5.96
ATOM   1235  N   LYS    62     -23.543  10.164  59.484  1.00  4.67
ATOM   1236  CA  LYS    62     -24.654   9.378  59.986  1.00  4.67
ATOM   1237  C   LYS    62     -25.791  10.349  60.317  1.00  4.67
ATOM   1238  O   LYS    62     -25.532  11.532  60.576  1.00  4.67
ATOM   1239  CB  LYS    62     -24.220   8.605  61.233  1.00  4.67
ATOM   1240  N   VAL    63     -27.040   9.876  60.284  1.00  4.63
ATOM   1241  CA  VAL    63     -28.197  10.678  60.719  1.00  4.63
ATOM   1242  C   VAL    63     -28.020  11.369  62.080  1.00  4.63
ATOM   1243  O   VAL    63     -28.640  12.415  62.308  1.00  4.63
ATOM   1244  CB  VAL    63     -29.316   9.641  60.810  1.00  4.63
ATOM   1245  N   GLY    64     -27.185  10.804  62.951  1.00  5.35
ATOM   1246  CA  GLY    64     -26.995  11.323  64.309  1.00  5.35
ATOM   1247  C   GLY    64     -25.939  12.432  64.421  1.00  5.35
ATOM   1248  O   GLY    64     -25.581  12.849  65.527  1.00  5.35
ATOM   1249  N   TYR    65     -25.439  12.905  63.285  1.00  4.73
ATOM   1250  CA  TYR    65     -24.431  13.958  63.302  1.00  4.73
ATOM   1251  C   TYR    65     -25.067  15.347  63.285  1.00  4.73
ATOM   1252  O   TYR    65     -26.168  15.539  62.756  1.00  4.73
ATOM   1253  CB  TYR    65     -23.473  13.791  62.164  1.00  4.73
ATOM   1254  N   THR    66     -24.350  16.306  63.862  1.00  4.69
ATOM   1255  CA  THR    66     -24.833  17.670  64.012  1.00  4.69
ATOM   1256  C   THR    66     -24.240  18.594  62.947  1.00  4.69
ATOM   1257  O   THR    66     -23.367  18.188  62.168  1.00  4.69
ATOM   1258  CB  THR    66     -24.489  18.190  65.414  1.00  4.69
ATOM   1259  N   GLU    67     -24.722  19.835  62.920  1.00  8.23
ATOM   1260  CA  GLU    67     -24.210  20.865  62.014  1.00  8.23
ATOM   1261  C   GLU    67     -22.687  20.990  62.085  1.00  8.23
ATOM   1262  O   GLU    67     -22.026  21.156  61.056  1.00  8.23
ATOM   1263  CB  GLU    67     -24.879  22.217  62.296  1.00  8.23
ATOM   1264  N   LYS    68     -22.134  20.892  63.296  1.00  6.80
ATOM   1265  CA  LYS    68     -20.690  20.963  63.491  1.00  6.80
ATOM   1266  C   LYS    68     -19.964  19.946  62.627  1.00  6.80
ATOM   1267  O   LYS    68     -18.920  20.252  62.036  1.00  6.80
ATOM   1268  CB  LYS    68     -20.335  20.748  64.981  1.00  6.80
ATOM   1269  N   GLN    69     -20.521  18.740  62.546  1.00  7.25
ATOM   1270  CA  GLN    69     -19.888  17.672  61.781  1.00  7.25
ATOM   1271  C   GLN    69     -20.102  17.869  60.289  1.00  7.25
ATOM   1272  O   GLN    69     -19.229  17.549  59.484  1.00  7.25
ATOM   1273  CB  GLN    69     -20.387  16.300  62.235  1.00  7.25
ATOM   1274  N   ARG    70     -21.256  18.410  59.917  1.00  5.76
ATOM   1275  CA  ARG    70     -21.490  18.731  58.509  1.00  5.76
ATOM   1276  C   ARG    70     -20.512  19.801  58.030  1.00  5.76
ATOM   1277  O   ARG    70     -19.954  19.697  56.938  1.00  5.76
ATOM   1278  CB  ARG    70     -22.936  19.168  58.275  1.00  5.76
ATOM   1279  N   ARG    71     -20.297  20.818  58.858  1.00  7.32
ATOM   1280  CA  ARG    71     -19.302  21.851  58.576  1.00  7.32
ATOM   1281  C   ARG    71     -17.907  21.259  58.400  1.00  7.32
ATOM   1282  O   ARG    71     -17.181  21.656  57.494  1.00  7.32
ATOM   1283  CB  ARG    71     -19.274  22.895  59.693  1.00  7.32
ATOM   1284  N   ASP    72     -17.552  20.310  59.265  1.00  5.50
ATOM   1285  CA  ASP    72     -16.246  19.660  59.218  1.00  5.50
ATOM   1286  C   ASP    72     -16.098  18.867  57.929  1.00  5.50
ATOM   1287  O   ASP    72     -15.034  18.890  57.296  1.00  5.50
ATOM   1288  CB  ASP    72     -16.061  18.751  60.425  1.00  5.50
ATOM   1289  N   PHE    73     -17.164  18.168  57.541  1.00  3.30
ATOM   1290  CA  PHE    73     -17.129  17.363  56.318  1.00  3.30
ATOM   1291  C   PHE    73     -17.037  18.263  55.089  1.00  3.30
ATOM   1292  O   PHE    73     -16.280  17.974  54.152  1.00  3.30
ATOM   1293  CB  PHE    73     -18.341  16.429  56.249  1.00  3.30
ATOM   1294  N   LEU    74     -17.788  19.360  55.101  1.00  7.91
ATOM   1295  CA  LEU    74     -17.702  20.355  54.036  1.00  7.91
ATOM   1296  C   LEU    74     -16.314  20.981  53.979  1.00  7.91
ATOM   1297  O   LEU    74     -15.772  21.210  52.893  1.00  7.91
ATOM   1298  CB  LEU    74     -18.771  21.441  54.206  1.00  7.91
ATOM   1299  N   GLY    75     -15.737  21.258  55.148  1.00  1.58
ATOM   1300  CA  GLY    75     -14.376  21.784  55.204  1.00  1.58
ATOM   1301  C   GLY    75     -13.365  20.814  54.598  1.00  1.58
ATOM   1302  O   GLY    75     -12.512  21.226  53.816  1.00  1.58
ATOM   1303  N   GLU    76     -13.481  19.534  54.959  1.00  4.44
ATOM   1304  CA  GLU    76     -12.626  18.477  54.401  1.00  4.44
ATOM   1305  C   GLU    76     -12.772  18.388  52.882  1.00  4.44
ATOM   1306  O   GLU    76     -11.781  18.221  52.156  1.00  4.44
ATOM   1307  CB  GLU    76     -12.953  17.127  55.045  1.00  4.44
ATOM   1308  N   ALA    77     -14.007  18.501  52.412  1.00  8.98
ATOM   1309  CA  ALA    77     -14.300  18.513  50.986  1.00  8.98
ATOM   1310  C   ALA    77     -13.579  19.684  50.304  1.00  8.98
ATOM   1311  O   ALA    77     -12.947  19.504  49.268  1.00  8.98
ATOM   1312  CB  ALA    77     -15.823  18.578  50.758  1.00  8.98
ATOM   1313  N   SER    78     -13.654  20.874  50.907  1.00  3.30
ATOM   1314  CA  SER    78     -13.025  22.060  50.328  1.00  3.30
ATOM   1315  C   SER    78     -11.499  21.965  50.348  1.00  3.30
ATOM   1316  O   SER    78     -10.830  22.437  49.422  1.00  3.30
ATOM   1317  CB  SER    78     -13.482  23.323  51.065  1.00  3.30
ATOM   1318  N   ILE    79     -10.957  21.358  51.404  1.00  2.42
ATOM   1319  CA  ILE    79      -9.514  21.136  51.519  1.00  2.42
ATOM   1320  C   ILE    79      -9.035  20.202  50.412  1.00  2.42
ATOM   1321  O   ILE    79      -8.048  20.497  49.734  1.00  2.42
ATOM   1322  CB  ILE    79      -9.136  20.600  52.921  1.00  2.42
ATOM   1323  N   THR    96     -24.126  17.284  48.393  1.00  4.58
ATOM   1324  CA  THR    96     -24.221  18.149  49.566  1.00  4.58
ATOM   1325  C   THR    96     -25.630  18.616  49.830  1.00  4.58
ATOM   1326  O   THR    96     -25.903  19.209  50.877  1.00  4.58
ATOM   1327  CB  THR    96     -23.320  19.388  49.429  1.00  4.58
TER
END
