
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0291AL170_2_2
# Molecule2: number of CA atoms  281 ( 2231),  selected  281 , name T0291
# PARAMETERS: T0291AL170_2_2.T0291  -4  -ie  -d:5  -o1  -sia  
# 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    -       -      T       1           -
LGA    -       -      Y       2           -
LGA    -       -      V       3           -
LGA    -       -      D       4           -
LGA    -       -      P       5           -
LGA    -       -      H       6           -
LGA    -       -      V      15           -
LGA    -       -      H      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
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           -
LGA    -       -      G      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      C      42           -
LGA    -       -      S      43           -
LGA    -       -      G      44           -
LGA    -       -      R      45           -
LGA    -       -      L      46           -
LGA    -       -      K      47           -
LGA    -       -      L      48           -
LGA    -       -      P      49           -
LGA    -       -      S      50           -
LGA    -       -      K      51           -
LGA    -       -      K      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      S      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      I      58           -
LGA    -       -      K      59           -
LGA    -       -      T      60           -
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    -       -      V      63           -
LGA    -       -      G      64           -
LGA    -       -      Y      65           -
LGA    -       -      T      66           -
LGA    -       -      E      67           -
LGA    -       -      K      68           -
LGA    -       -      Q      69           -
LGA    -       -      R      70           -
LGA    -       -      R      71           -
LGA    -       -      D      72           -
LGA    -       -      F      73           -
LGA    -       -      L      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      A      77           -
LGA    -       -      S      78           -
LGA    -       -      I      79           -
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           -
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           -
LGA    -       -      E     109           -
LGA    -       -      N     110           -
LGA    -       -      G     111           -
LGA    -       -      S     112           -
LGA    -       -      L     113           -
LGA    -       -      D     114           -
LGA    -       -      S     115           -
LGA    -       -      F     116           -
LGA    -       -      L     117           -
LGA    -       -      R     118           -
LGA    -       -      K     119           -
LGA    -       -      H     120           -
LGA    -       -      D     121           -
LGA    -       -      A     122           -
LGA    -       -      Q     123           -
LGA    -       -      F     124           -
LGA    -       -      T     125           -
LGA    -       -      V     126           -
LGA    -       -      I     127           -
LGA    -       -      Q     128           -
LGA    -       -      L     129           -
LGA    -       -      V     130           -
LGA    -       -      G     131           -
LGA    G     172      M     132          2.925
LGA    L     173      L     133          1.226
LGA    G     174      R     134          1.794
LGA    -       -      G     135           -
LGA    -       -      I     136           -
LGA    R     175      A     137          1.426
LGA    V     176      S     138          2.765
LGA    -       -      G     139           -
LGA    -       -      M     140           -
LGA    L     177      K     141          2.339
LGA    -       -      Y     142           -
LGA    E     178      L     143          0.857
LGA    -       -      S     144           -
LGA    -       -      D     145           -
LGA    D     179      M     146          0.706
LGA    D     180      G     147          0.780
LGA    E     182      Y     148          4.097
LGA    -       -      V     149           -
LGA    -       -      H     150           -
LGA    -       -      R     151           -
LGA    -       -      D     152           -
LGA    -       -      L     153           -
LGA    -       -      A     154           -
LGA    -       -      A     155           -
LGA    -       -      R     156           -
LGA    -       -      N     157           -
LGA    -       -      I     158           -
LGA    -       -      L     159           -
LGA    -       -      I     160           -
LGA    -       -      N     161           -
LGA    -       -      S     162           -
LGA    -       -      N     163           -
LGA    -       -      L     164           -
LGA    -       -      V     165           -
LGA    -       -      C     166           -
LGA    -       -      K     167           -
LGA    -       -      V     168           -
LGA    -       -      S     169           -
LGA    -       -      D     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      L     173           -
LGA    -       -      G     174           -
LGA    -       -      R     175           -
LGA    -       -      V     176           -
LGA    -       -      P     193           -
LGA    -       -      I     194           -
LGA    -       -      R     195           -
LGA    -       -      W     196           -
LGA    -       -      T     197           -
LGA    -       -      S     198           -
LGA    -       -      P     199           -
LGA    -       -      E     200           -
LGA    -       -      A     201           -
LGA    -       -      I     202           -
LGA    -       -      A     203           -
LGA    -       -      Y     204           -
LGA    -       -      R     205           -
LGA    -       -      K     206           -
LGA    -       -      F     207           -
LGA    -       -      T     208           -
LGA    A     183      S     209          3.469
LGA    A     184      A     210          3.913
LGA    Y     185      S     211           #
LGA    T     186      D     212          3.049
LGA    -       -      V     213           -
LGA    -       -      W     214           -
LGA    -       -      S     215           -
LGA    T     187      Y     216          1.711
LGA    -       -      G     217           -
LGA    R     188      I     218          2.515
LGA    G     189      V     219          3.001
LGA    -       -      L     220           -
LGA    G     190      W     221          0.570
LGA    -       -      E     222           -
LGA    -       -      V     223           -
LGA    K     191      M     224          2.967
LGA    -       -      S     225           -
LGA    -       -      Y     226           -
LGA    -       -      G     227           -
LGA    -       -      E     228           -
LGA    -       -      R     229           -
LGA    -       -      P     230           -
LGA    -       -      Y     231           -
LGA    -       -      W     232           -
LGA    -       -      E     233           -
LGA    -       -      M     234           -
LGA    -       -      S     235           -
LGA    -       -      N     236           -
LGA    -       -      Q     237           -
LGA    -       -      D     238           -
LGA    -       -      V     239           -
LGA    -       -      I     240           -
LGA    -       -      K     241           -
LGA    -       -      A     242           -
LGA    -       -      V     243           -
LGA    -       -      D     244           -
LGA    -       -      E     245           -
LGA    -       -      G     246           -
LGA    -       -      Y     247           -
LGA    -       -      R     248           -
LGA    -       -      L     249           -
LGA    -       -      P     250           -
LGA    -       -      P     251           -
LGA    -       -      P     252           -
LGA    -       -      M     253           -
LGA    -       -      D     254           -
LGA    -       -      C     255           -
LGA    -       -      P     256           -
LGA    -       -      A     257           -
LGA    -       -      A     258           -
LGA    I     192      L     259          2.946
LGA    -       -      Y     260           -
LGA    -       -      Q     261           -
LGA    -       -      L     262           -
LGA    -       -      M     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      C     266           -
LGA    -       -      W     267           -
LGA    -       -      Q     268           -
LGA    -       -      K     269           -
LGA    -       -      D     270           -
LGA    -       -      R     271           -
LGA    -       -      N     272           -
LGA    -       -      N     273           -
LGA    -       -      R     274           -
LGA    -       -      P     275           -
LGA    -       -      K     276           -
LGA    -       -      F     277           -
LGA    -       -      E     278           -
LGA    -       -      Q     279           -
LGA    -       -      I     280           -
LGA    -       -      V     281           -
LGA    -       -      S     282           -
LGA    -       -      I     283           -
LGA    -       -      L     284           -
LGA    -       -      D     285           -
LGA    -       -      K     286           -
LGA    -       -      L     287           -
LGA    -       -      I     288           -
LGA    -       -      R     289           -
LGA    -       -      N     290           -
LGA    -       -      P     291           -
LGA    -       -      G     292           -
LGA    -       -      S     293           -
LGA    -       -      L     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      I     297           -
LGA    -       -      T     298           -
LGA    -       -      S     299           -
LGA    -       -      S     305           -
LGA    -       -      N     306           -
LGA    -       -      L     307           -
LGA    -       -      L     308           -
LGA    -       -      L     309           -
LGA    -       -      D     310           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20  281    5.0     19    2.51    10.53      4.794     0.728

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.889565 * X  +   0.452816 * Y  +   0.060255 * Z  +  33.773766
  Y_new =   0.235917 * X  +   0.342446 * Y  +   0.909436 * Z  + -49.813416
  Z_new =   0.391173 * X  +   0.823218 * Y  +  -0.411455 * Z  +  48.406685 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.034295   -1.107298  [ DEG:   116.5565    -63.4435 ]
  Theta =  -0.401906   -2.739686  [ DEG:   -23.0275   -156.9725 ]
  Phi   =   2.882355   -0.259237  [ DEG:   165.1468    -14.8532 ]
 
# 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: T0291AL170_2_2                                
REMARK     2: T0291                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291AL170_2_2.T0291 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20  281   5.0   19   2.51   10.53   4.794
REMARK  ---------------------------------------------------------- 
MOLECULE T0291AL170_2_2
REMARK PARENT number 2
PARENT 1M14A
REMARK Aligment from pdb entry: 1M14A
ATOM   1077  N   GLY   172      10.428   8.540  45.065  1.00  0.00              
ATOM   1078  CA  GLY   172       9.769   7.685  46.036  1.00  0.00              
ATOM   1079  C   GLY   172       9.613   8.244  47.447  1.00  0.00              
ATOM   1080  O   GLY   172       9.034   7.591  48.306  1.00  0.00              
ATOM   1081  N   LEU   173      10.144   9.434  47.706  1.00  0.00              
ATOM   1082  CA  LEU   173      10.030  10.037  49.025  1.00  0.00              
ATOM   1083  C   LEU   173       9.639  11.492  48.886  1.00  0.00              
ATOM   1084  O   LEU   173       9.418  12.182  49.882  1.00  0.00              
ATOM   1085  N   GLY   174       9.523  11.951  47.644  1.00  0.00              
ATOM   1086  CA  GLY   174       9.175  13.344  47.369  1.00  0.00              
ATOM   1087  C   GLY   174       7.837  13.740  47.960  1.00  0.00              
ATOM   1088  O   GLY   174       6.884  12.956  47.955  1.00  0.00              
ATOM   1089  N   ARG   175       7.766  14.964  48.463  1.00  0.00              
ATOM   1090  CA  ARG   175       6.533  15.478  49.033  1.00  0.00              
ATOM   1091  C   ARG   175       6.215  16.871  48.516  1.00  0.00              
ATOM   1092  O   ARG   175       7.097  17.714  48.456  1.00  0.00              
ATOM   1093  N   VAL   176       4.978  17.084  48.064  1.00  0.00              
ATOM   1094  CA  VAL   176       4.537  18.406  47.591  1.00  0.00              
ATOM   1095  C   VAL   176       4.084  19.256  48.786  1.00  0.00              
ATOM   1096  O   VAL   176       3.309  18.795  49.624  1.00  0.00              
ATOM   1097  N   LEU   177       4.612  20.470  48.898  1.00  0.00              
ATOM   1098  CA  LEU   177       4.254  21.354  50.005  1.00  0.00              
ATOM   1099  C   LEU   177       3.070  22.253  49.667  1.00  0.00              
ATOM   1100  O   LEU   177       2.941  22.727  48.529  1.00  0.00              
ATOM   1101  N   GLU   178       2.239  22.526  50.674  1.00  0.00              
ATOM   1102  CA  GLU   178       1.088  23.391  50.482  1.00  0.00              
ATOM   1103  C   GLU   178       1.457  24.842  50.206  1.00  0.00              
ATOM   1104  O   GLU   178       2.581  25.152  49.791  1.00  0.00              
ATOM   1105  N   ASP   179       0.494  25.735  50.408  1.00  0.00              
ATOM   1106  CA  ASP   179       0.709  27.164  50.186  1.00  0.00              
ATOM   1107  C   ASP   179       1.099  27.853  51.490  1.00  0.00              
ATOM   1108  O   ASP   179       1.990  28.704  51.518  1.00  0.00              
ATOM   1109  N   ASP   180       0.412  27.465  52.564  1.00  0.00              
ATOM   1110  CA  ASP   180       0.634  28.008  53.903  1.00  0.00              
ATOM   1111  C   ASP   180       1.646  27.142  54.653  1.00  0.00              
ATOM   1112  O   ASP   180       1.816  27.269  55.870  1.00  0.00              
ATOM   1113  N   GLU   182       2.315  26.264  53.915  1.00  0.00              
ATOM   1114  CA  GLU   182       3.292  25.357  54.495  1.00  0.00              
ATOM   1115  C   GLU   182       4.702  25.750  54.073  1.00  0.00              
ATOM   1116  O   GLU   182       4.887  26.362  53.024  1.00  0.00              
ATOM   1117  N   ALA   183       5.686  25.421  54.907  1.00  0.00              
ATOM   1118  CA  ALA   183       7.083  25.741  54.614  1.00  0.00              
ATOM   1119  C   ALA   183       8.039  24.583  54.920  1.00  0.00              
ATOM   1120  O   ALA   183       9.227  24.663  54.610  1.00  0.00              
ATOM   1121  N   ALA   184       7.527  23.526  55.552  1.00  0.00              
ATOM   1122  CA  ALA   184       8.336  22.359  55.900  1.00  0.00              
ATOM   1123  C   ALA   184       7.511  21.090  56.096  1.00  0.00              
ATOM   1124  O   ALA   184       6.427  21.123  56.675  1.00  0.00              
ATOM   1125  N   TYR   185       8.032  19.975  55.600  1.00  0.00              
ATOM   1126  CA  TYR   185       7.368  18.689  55.711  1.00  0.00              
ATOM   1127  C   TYR   185       7.789  17.916  56.961  1.00  0.00              
ATOM   1128  O   TYR   185       8.977  17.661  57.187  1.00  0.00              
ATOM   1129  N   THR   186       6.792  17.497  57.739  1.00  0.00              
ATOM   1130  CA  THR   186       7.026  16.741  58.963  1.00  0.00              
ATOM   1131  C   THR   186       6.818  15.249  58.741  1.00  0.00              
ATOM   1132  O   THR   186       5.687  14.767  58.705  1.00  0.00              
ATOM   1133  N   THR   187       7.926  14.534  58.575  1.00  0.00              
ATOM   1134  CA  THR   187       7.915  13.092  58.352  1.00  0.00              
ATOM   1135  C   THR   187       7.461  12.338  59.596  1.00  0.00              
ATOM   1136  O   THR   187       7.364  12.915  60.676  1.00  0.00              
ATOM   1137  N   ARG   188       7.227  11.039  59.448  1.00  0.00              
ATOM   1138  CA  ARG   188       6.769  10.234  60.566  1.00  0.00              
ATOM   1139  C   ARG   188       7.362   8.825  60.543  1.00  0.00              
ATOM   1140  O   ARG   188       7.527   8.203  61.596  1.00  0.00              
ATOM   1141  N   GLY   189       7.702   8.338  59.351  1.00  0.00              
ATOM   1142  CA  GLY   189       8.263   7.001  59.216  1.00  0.00              
ATOM   1143  C   GLY   189       9.647   6.807  59.820  1.00  0.00              
ATOM   1144  O   GLY   189       9.807   6.791  61.047  1.00  0.00              
ATOM   1145  N   GLY   190      10.643   6.630  58.952  1.00  0.00              
ATOM   1146  CA  GLY   190      12.013   6.438  59.409  1.00  0.00              
ATOM   1147  C   GLY   190      12.781   5.439  58.562  1.00  0.00              
ATOM   1148  O   GLY   190      13.051   4.313  58.992  1.00  0.00              
ATOM   1149  N   LYS   191      13.158   5.866  57.363  1.00  0.00              
ATOM   1150  CA  LYS   191      13.889   5.018  56.430  1.00  0.00              
ATOM   1151  C   LYS   191      14.655   5.880  55.432  1.00  0.00              
ATOM   1152  O   LYS   191      14.914   5.466  54.299  1.00  0.00              
ATOM   1153  N   ILE   192      14.993   7.092  55.856  1.00  0.00              
ATOM   1154  CA  ILE   192      15.728   8.017  55.008  1.00  0.00              
ATOM   1155  C   ILE   192      17.227   7.788  55.216  1.00  0.00              
ATOM   1156  O   ILE   192      17.653   7.462  56.323  1.00  0.00              
TER
END
