
#######################################################
#                                                     #
#                        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   16 (  126),  selected   16 , name T0329TS677_1_1-D1
# Molecule2: number of CA atoms  141 ( 1070),  selected  141 , name T0329_D1.pdb
# PARAMETERS: T0329TS677_1_1-D1.T0329_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      Y       3           -
LGA    -       -      K       4           -
LGA    -       -      A       5           -
LGA    -       -      A       6           -
LGA    -       -      I       7           -
LGA    -       -      F       8           -
LGA    -       -      D       9           -
LGA    -       -      M      10           -
LGA    -       -      D      11           -
LGA    -       -      G      12           -
LGA    -       -      T      13           -
LGA    -       -      I      14           -
LGA    -       -      L      15           -
LGA    -       -      D      16           -
LGA    -       -      G     109           -
LGA    -       -      P     110           -
LGA    -       -      F     111           -
LGA    -       -      P     112           -
LGA    -       -      G     113           -
LGA    -       -      I     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      L     117           -
LGA    -       -      M     118           -
LGA    -       -      K     119           -
LGA    -       -      N     120           -
LGA    -       -      L     121           -
LGA    -       -      R     122           -
LGA    -       -      Q     123           -
LGA    -       -      K     124           -
LGA    -       -      G     125           -
LGA    -       -      V     126           -
LGA    -       -      K     127           -
LGA    -       -      L     128           -
LGA    -       -      A     129           -
LGA    -       -      V     130           -
LGA    -       -      V     131           -
LGA    -       -      S     132           -
LGA    -       -      N     133           -
LGA    -       -      K     134           -
LGA    -       -      P     135           -
LGA    -       -      N     136           -
LGA    -       -      E     137           -
LGA    -       -      A     138           -
LGA    -       -      V     139           -
LGA    -       -      Q     140           -
LGA    -       -      V     141           -
LGA    -       -      L     142           -
LGA    -       -      V     143           -
LGA    -       -      E     144           -
LGA    -       -      E     145           -
LGA    -       -      L     146           -
LGA    -       -      F     147           -
LGA    -       -      P     148           -
LGA    -       -      G     149           -
LGA    -       -      S     150           -
LGA    -       -      F     151           -
LGA    -       -      D     152           -
LGA    -       -      F     153           -
LGA    -       -      A     154           -
LGA    -       -      L     155           -
LGA    -       -      G     156           -
LGA    -       -      R     163           -
LGA    -       -      K     164           -
LGA    -       -      P     165           -
LGA    -       -      A     166           -
LGA    -       -      P     167           -
LGA    -       -      D     168           -
LGA    -       -      M     169           -
LGA    -       -      T     170           -
LGA    -       -      S     171           -
LGA    -       -      E     172           -
LGA    -       -      C     173           -
LGA    -       -      V     174           -
LGA    -       -      K     175           -
LGA    -       -      V     176           -
LGA    -       -      L     177           -
LGA    -       -      G     178           -
LGA    -       -      V     179           -
LGA    -       -      P     180           -
LGA    M       1      R     181          2.434
LGA    K       2      D     182          3.623
LGA    -       -      K     183           -
LGA    Y       3      C     184          2.899
LGA    -       -      V     185           -
LGA    -       -      Y     186           -
LGA    -       -      I     187           -
LGA    -       -      G     188           -
LGA    -       -      D     189           -
LGA    -       -      S     190           -
LGA    -       -      E     191           -
LGA    -       -      I     192           -
LGA    -       -      D     193           -
LGA    -       -      I     194           -
LGA    -       -      Q     195           -
LGA    -       -      T     196           -
LGA    -       -      A     197           -
LGA    -       -      R     198           -
LGA    -       -      N     199           -
LGA    -       -      S     200           -
LGA    -       -      E     201           -
LGA    K       4      M     202          2.486
LGA    A       5      D     203          0.905
LGA    A       6      E     204          0.506
LGA    I       7      I     205          0.490
LGA    F       8      A     206          0.989
LGA    D       9      V     207          0.563
LGA    M      10      N     208          1.092
LGA    D      11      W     209          3.182
LGA    G      12      G     210          2.033
LGA    T      13      F     211          3.466
LGA    I      14      R     212          1.992
LGA    L      15      S     213          3.698
LGA    D      16      V     214           -
LGA    -       -      P     215           -
LGA    -       -      F     216           -
LGA    -       -      L     217           -
LGA    -       -      Q     218           -
LGA    -       -      K     219           -
LGA    -       -      H     220           -
LGA    -       -      G     221           -
LGA    -       -      A     222           -
LGA    -       -      T     223           -
LGA    -       -      V     224           -
LGA    -       -      I     225           -
LGA    -       -      V     226           -
LGA    -       -      D     227           -
LGA    -       -      T     228           -
LGA    -       -      A     229           -
LGA    -       -      E     230           -
LGA    -       -      K     231           -
LGA    -       -      L     232           -
LGA    -       -      E     233           -
LGA    -       -      E     234           -
LGA    -       -      A     235           -
LGA    -       -      I     236           -
LGA    -       -      L     237           -
LGA    -       -      G     238           -
LGA    -       -      E     239           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16  141    5.0     15    2.33    13.33      8.523     0.618

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.602931 * X  +  -0.771179 * Y  +   0.204348 * Z  +  11.461202
  Y_new =   0.435140 * X  +   0.103199 * Y  +  -0.894429 * Z  +  -0.685035
  Z_new =   0.668676 * X  +   0.628198 * Y  +   0.397793 * Z  +  -3.455949 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.006302   -2.135291  [ DEG:    57.6569   -122.3431 ]
  Theta =  -0.732427   -2.409166  [ DEG:   -41.9650   -138.0350 ]
  Phi   =   0.625147   -2.516445  [ DEG:    35.8183   -144.1817 ]
 
# 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: T0329TS677_1_1-D1                             
REMARK     2: T0329_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS677_1_1-D1.T0329_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  141   5.0   15   2.33   13.33   8.523
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS677_1_1-D1
REMARK PARENT number 1
PFRMAT     TS
TARGET     T0329
PARENT     2ah5A
ATOM      1  N   MET     1      15.071   4.120  22.997  1.00  0.47
ATOM      2  CA  MET     1      16.054   4.759  23.901  1.00  0.47
ATOM      3  C   MET     1      15.817   4.330  25.307  1.00  0.47
ATOM      4  O   MET     1      15.389   3.202  25.547  1.00  0.47
ATOM      5  CB  MET     1      15.924   6.289  23.848  1.00  0.47
ATOM      6  CG  MET     1      14.602   6.800  24.422  1.00  0.47
ATOM      7  SD  MET     1      14.464   8.610  24.516  1.00  0.47
ATOM      8  CE  MET     1      14.382   8.861  22.718  1.00  0.47
ATOM      9  N   LYS     2      16.153   5.234  26.255  1.00  0.58
ATOM     10  CA  LYS     2      15.986   5.071  27.672  1.00  0.58
ATOM     11  C   LYS     2      14.735   4.303  27.951  1.00  0.58
ATOM     12  O   LYS     2      14.742   3.075  28.000  1.00  0.58
ATOM     13  CB  LYS     2      15.897   6.410  28.422  1.00  0.58
ATOM     14  CG  LYS     2      17.196   7.216  28.373  1.00  0.58
ATOM     15  CD  LYS     2      17.548   7.723  26.973  1.00  0.58
ATOM     16  CE  LYS     2      18.847   8.528  26.923  1.00  0.58
ATOM     17  NZ  LYS     2      19.112   8.977  25.538  1.00  0.58
ATOM     18  N   TYR     3      13.616   5.029  28.127  1.00  0.74
ATOM     19  CA  TYR     3      12.350   4.418  28.401  1.00  0.74
ATOM     20  C   TYR     3      12.009   3.502  27.274  1.00  0.74
ATOM     21  O   TYR     3      11.763   3.944  26.153  1.00  0.74
ATOM     22  CB  TYR     3      11.227   5.463  28.521  1.00  0.74
ATOM     23  CG  TYR     3       9.911   4.786  28.367  1.00  0.74
ATOM     24  CD1 TYR     3       9.266   4.204  29.433  1.00  0.74
ATOM     25  CD2 TYR     3       9.322   4.743  27.124  1.00  0.74
ATOM     26  CE1 TYR     3       8.049   3.588  29.253  1.00  0.74
ATOM     27  CE2 TYR     3       8.108   4.130  26.939  1.00  0.74
ATOM     28  CZ  TYR     3       7.470   3.551  28.007  1.00  0.74
ATOM     29  OH  TYR     3       6.222   2.920  27.817  1.00  0.74
ATOM     30  N   LYS     4      12.013   2.181  27.545  1.00  0.58
ATOM     31  CA  LYS     4      11.660   1.245  26.524  1.00  0.58
ATOM     32  C   LYS     4      10.326   0.655  26.861  1.00  0.58
ATOM     33  O   LYS     4       9.465   0.528  25.994  1.00  0.58
ATOM     34  CB  LYS     4      12.666   0.088  26.401  1.00  0.58
ATOM     35  CG  LYS     4      12.786  -0.765  27.665  1.00  0.58
ATOM     36  CD  LYS     4      13.560  -2.068  27.447  1.00  0.58
ATOM     37  CE  LYS     4      13.683  -2.928  28.706  1.00  0.58
ATOM     38  NZ  LYS     4      12.391  -3.584  28.999  1.00  0.58
ATOM     39  N   ALA     5      10.105   0.296  28.143  1.00  0.23
ATOM     40  CA  ALA     5       8.870  -0.346  28.497  1.00  0.23
ATOM     41  C   ALA     5       8.179   0.429  29.576  1.00  0.23
ATOM     42  O   ALA     5       8.804   1.178  30.324  1.00  0.23
ATOM     43  CB  ALA     5       9.059  -1.780  29.023  1.00  0.23
ATOM     44  N   ALA     6       6.840   0.264  29.669  1.00  0.21
ATOM     45  CA  ALA     6       6.077   0.961  30.667  1.00  0.21
ATOM     46  C   ALA     6       5.370  -0.047  31.520  1.00  0.21
ATOM     47  O   ALA     6       4.788  -1.005  31.013  1.00  0.21
ATOM     48  CB  ALA     6       4.989   1.880  30.085  1.00  0.21
ATOM     49  N   ILE     7       5.404   0.152  32.855  1.00  0.31
ATOM     50  CA  ILE     7       4.739  -0.761  33.742  1.00  0.31
ATOM     51  C   ILE     7       3.653  -0.019  34.459  1.00  0.31
ATOM     52  O   ILE     7       3.811   1.146  34.821  1.00  0.31
ATOM     53  CB  ILE     7       5.650  -1.414  34.743  1.00  0.31
ATOM     54  CG1 ILE     7       6.307  -0.380  35.669  1.00  0.31
ATOM     55  CG2 ILE     7       6.657  -2.277  33.965  1.00  0.31
ATOM     56  CD1 ILE     7       7.103  -1.025  36.804  1.00  0.31
ATOM     57  N   PHE     8       2.498  -0.688  34.665  1.00  0.22
ATOM     58  CA  PHE     8       1.383  -0.031  35.282  1.00  0.22
ATOM     59  C   PHE     8       0.955  -0.790  36.497  1.00  0.22
ATOM     60  O   PHE     8       1.076  -2.012  36.569  1.00  0.22
ATOM     61  CB  PHE     8       0.122   0.014  34.397  1.00  0.22
ATOM     62  CG  PHE     8       0.366   0.870  33.205  1.00  0.22
ATOM     63  CD1 PHE     8       1.040   0.372  32.115  1.00  0.22
ATOM     64  CD2 PHE     8      -0.100   2.164  33.170  1.00  0.22
ATOM     65  CE1 PHE     8       1.258   1.158  31.008  1.00  0.22
ATOM     66  CE2 PHE     8       0.116   2.954  32.066  1.00  0.22
ATOM     67  CZ  PHE     8       0.797   2.453  30.984  1.00  0.22
ATOM     68  N   ASP     9       0.451  -0.047  37.501  1.00  0.26
ATOM     69  CA  ASP     9      -0.147  -0.640  38.660  1.00  0.26
ATOM     70  C   ASP     9      -1.521  -0.970  38.172  1.00  0.26
ATOM     71  O   ASP     9      -1.920  -0.468  37.125  1.00  0.26
ATOM     72  CB  ASP     9      -0.279   0.343  39.839  1.00  0.26
ATOM     73  CG  ASP     9      -0.536  -0.439  41.121  1.00  0.26
ATOM     74  OD1 ASP     9      -0.762  -1.675  41.033  1.00  0.26
ATOM     75  OD2 ASP     9      -0.502   0.196  42.208  1.00  0.26
ATOM     76  N   MET    10      -2.288  -1.805  38.895  1.00  0.48
ATOM     77  CA  MET    10      -3.578  -2.214  38.409  1.00  0.48
ATOM     78  C   MET    10      -4.633  -1.436  39.117  1.00  0.48
ATOM     79  O   MET    10      -5.116  -0.423  38.612  1.00  0.48
ATOM     80  CB  MET    10      -3.870  -3.702  38.663  1.00  0.48
ATOM     81  CG  MET    10      -5.252  -4.138  38.175  1.00  0.48
ATOM     82  SD  MET    10      -5.457  -4.159  36.371  1.00  0.48
ATOM     83  CE  MET    10      -7.244  -4.466  36.471  1.00  0.48
ATOM     84  N   ASP    11      -5.053  -1.921  40.298  1.00  0.45
ATOM     85  CA  ASP    11      -6.081  -1.221  41.002  1.00  0.45
ATOM     86  C   ASP    11      -5.585   0.126  41.426  1.00  0.45
ATOM     87  O   ASP    11      -4.446   0.283  41.864  1.00  0.45
ATOM     88  CB  ASP    11      -6.671  -2.011  42.192  1.00  0.45
ATOM     89  CG  ASP    11      -5.579  -2.447  43.163  1.00  0.45
ATOM     90  OD1 ASP    11      -4.456  -2.783  42.702  1.00  0.45
ATOM     91  OD2 ASP    11      -5.873  -2.486  44.386  1.00  0.45
ATOM     92  N   GLY    12      -6.442   1.155  41.244  1.00  0.22
ATOM     93  CA  GLY    12      -6.118   2.500  41.642  1.00  0.22
ATOM     94  C   GLY    12      -5.455   3.225  40.501  1.00  0.22
ATOM     95  O   GLY    12      -5.298   4.445  40.551  1.00  0.22
ATOM     96  N   THR    13      -5.030   2.490  39.449  1.00  0.24
ATOM     97  CA  THR    13      -4.365   3.064  38.299  1.00  0.24
ATOM     98  C   THR    13      -5.231   2.845  37.080  1.00  0.24
ATOM     99  O   THR    13      -5.830   3.786  36.559  1.00  0.24
ATOM    100  CB  THR    13      -3.027   2.442  38.035  1.00  0.24
ATOM    101  OG1 THR    13      -2.177   2.621  39.159  1.00  0.24
ATOM    102  CG2 THR    13      -2.415   3.112  36.791  1.00  0.24
ATOM    103  N   ILE    14      -5.231   1.598  36.535  1.00  0.59
ATOM    104  CA  ILE    14      -6.141   1.258  35.463  1.00  0.59
ATOM    105  C   ILE    14      -7.469   1.413  36.084  1.00  0.59
ATOM    106  O   ILE    14      -8.427   1.839  35.435  1.00  0.59
ATOM    107  CB  ILE    14      -6.093  -0.165  34.989  1.00  0.59
ATOM    108  CG1 ILE    14      -4.836  -0.426  34.150  1.00  0.59
ATOM    109  CG2 ILE    14      -7.404  -0.439  34.228  1.00  0.59
ATOM    110  CD1 ILE    14      -3.531  -0.317  34.925  1.00  0.59
ATOM    111  N   LEU    15      -7.527   0.923  37.340  1.00  0.89
ATOM    112  CA  LEU    15      -8.484   1.407  38.270  1.00  0.89
ATOM    113  C   LEU    15      -9.388   0.595  39.023  1.00  0.89
ATOM    114  O   LEU    15      -9.015  -0.327  39.741  1.00  0.89
ATOM    115  CB  LEU    15      -9.246   2.679  37.896  1.00  0.89
ATOM    116  CG  LEU    15      -8.918   3.890  38.798  1.00  0.89
ATOM    117  CD1 LEU    15      -9.329   3.606  40.256  1.00  0.89
ATOM    118  CD2 LEU    15      -7.465   4.361  38.670  1.00  0.89
ATOM    119  N   ASP    16     -10.588   1.190  38.963  1.00  0.88
ATOM    120  CA  ASP    16     -11.902   0.864  39.371  1.00  0.88
ATOM    121  C   ASP    16     -12.128   0.416  40.751  1.00  0.88
ATOM    122  O   ASP    16     -13.093   0.858  41.361  1.00  0.88
ATOM    123  CB  ASP    16     -12.408  -0.431  38.814  1.00  0.88
ATOM    124  CG  ASP    16     -11.503  -0.959  37.754  1.00  0.88
ATOM    125  OD1 ASP    16     -11.193  -0.280  36.741  1.00  0.88
ATOM    126  OD2 ASP    16     -11.070  -2.107  38.011  1.00  0.88
TER
END
