
#######################################################
#                                                     #
#                        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  140 (  140),  selected  140 , name T0379TS168_4-D1
# Molecule2: number of CA atoms  140 ( 1126),  selected  140 , name T0379_D1.pdb
# PARAMETERS: T0379TS168_4-D1.T0379_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2          4.943
LGA    R       3      R       3          3.534
LGA    N       4      N       4          0.934
LGA    I       5      I       5          1.602
LGA    V       6      V       6          3.149
LGA    F       7      F       7          2.994
LGA    D       8      D       8          0.800
LGA    L       9      L       9          1.227
LGA    G      10      G      10          1.499
LGA    G      11      G      11          1.983
LGA    V      12      V      12          1.051
LGA    L      13      L      13          2.676
LGA    I      14      I      14          3.994
LGA    H      15      -       -           -
LGA    L      16      H      15           #
LGA    L      84      L      16           -
LGA    E      85      L      84          4.644
LGA    E      86      E      85          2.163
LGA    I      87      -       -           -
LGA    S      88      E      86          1.664
LGA    A      89      -       -           -
LGA    E      90      I      87           #
LGA    K      91      S      88          1.316
LGA    F      92      A      89          1.651
LGA    D      93      E      90          1.468
LGA    Y      94      K      91          1.207
LGA    I      95      F      92          1.151
LGA    D      96      D      93          1.042
LGA    S      97      Y      94          1.500
LGA    L      98      I      95          1.627
LGA    R      99      D      96          1.085
LGA    P     100      S      97          2.315
LGA    D     101      L      98          1.986
LGA    Y     102      R      99          4.360
LGA    -       -      P     100           -
LGA    -       -      D     101           -
LGA    -       -      Y     102           -
LGA    R     103      R     103          4.766
LGA    L     104      L     104          1.023
LGA    F     105      F     105          2.343
LGA    L     106      L     106          4.011
LGA    L     107      L     107          2.935
LGA    S     108      S     108          4.399
LGA    N     109      N     109           #
LGA    T     110      -       -           -
LGA    N     111      -       -           -
LGA    P     112      -       -           -
LGA    Y     113      -       -           -
LGA    V     114      T     110          4.975
LGA    L     115      N     111           -
LGA    -       -      P     112           -
LGA    -       -      Y     113           -
LGA    -       -      V     114           -
LGA    D     116      L     115           #
LGA    L     117      -       -           -
LGA    A     118      -       -           -
LGA    M     119      D     116           #
LGA    S     120      L     117          4.758
LGA    P     121      A     118          1.264
LGA    R     122      M     119          4.537
LGA    -       -      S     120           -
LGA    -       -      P     121           -
LGA    -       -      R     122           -
LGA    -       -      F     123           -
LGA    F     123      L     124          2.741
LGA    L     124      P     125          2.759
LGA    P     125      S     126           #
LGA    S     126      G     127          2.591
LGA    G     127      -       -           -
LGA    R     128      R     128          3.682
LGA    T     129      T     129          4.946
LGA    L     130      L     130          4.751
LGA    D     131      D     131           #
LGA    S     132      S     132          4.691
LGA    F     133      F     133          3.286
LGA    F     134      F     134          4.775
LGA    D     135      D     135          2.853
LGA    K     136      K     136          3.250
LGA    V     137      V     137          2.012
LGA    Y     138      Y     138          2.561
LGA    A     139      A     139          4.377
LGA    S     140      S     140          2.313
LGA    C     141      C     141          5.106
LGA    Q     142      Q     142          4.662
LGA    M     143      M     143          4.744
LGA    -       -      G     144           -
LGA    G     144      K     145          2.417
LGA    K     145      Y     146          4.468
LGA    Y     146      K     147          4.309
LGA    K     147      P     148          2.014
LGA    P     148      N     149          1.330
LGA    N     149      E     150          1.916
LGA    E     150      -       -           -
LGA    D     151      D     151          4.217
LGA    I     152      I     152          2.122
LGA    F     153      F     153          1.882
LGA    L     154      L     154          3.983
LGA    E     155      E     155          2.916
LGA    M     156      M     156          1.932
LGA    -       -      I     157           -
LGA    -       -      A     158           -
LGA    I     157      D     159           #
LGA    A     158      S     160          1.614
LGA    D     159      G     161           #
LGA    S     160      -       -           -
LGA    G     161      -       -           -
LGA    M     162      M     162          3.708
LGA    K     163      K     163          3.277
LGA    P     164      P     164          3.649
LGA    E     165      E     165          2.871
LGA    E     166      E     166          4.458
LGA    T     167      T     167          3.268
LGA    L     168      L     168          1.034
LGA    F     169      F     169          1.077
LGA    I     170      I     170          1.432
LGA    D     171      D     171          1.329
LGA    D     172      D     172          1.666
LGA    G     173      G     173          1.863
LGA    P     174      P     174          1.085
LGA    A     175      A     175          1.443
LGA    N     176      N     176          1.259
LGA    V     177      V     177          0.947
LGA    A     178      A     178          1.322
LGA    T     179      T     179          1.787
LGA    A     180      A     180          1.257
LGA    E     181      E     181          1.089
LGA    R     182      R     182          1.898
LGA    L     183      L     183          0.688
LGA    G     184      G     184          2.599
LGA    F     185      F     185          1.539
LGA    H     186      H     186          2.833
LGA    T     187      T     187          2.007
LGA    Y     188      Y     188          0.856
LGA    C     189      C     189          1.372
LGA    P     190      P     190          0.741
LGA    D     191      D     191          3.978
LGA    N     192      N     192           -
LGA    -       -      G     193           -
LGA    -       -      E     194           -
LGA    -       -      N     195           -
LGA    -       -      W     196           -
LGA    -       -      I     197           -
LGA    -       -      P     198           -
LGA    G     193      A     199           #
LGA    E     194      -       -           -
LGA    N     195      -       -           -
LGA    W     196      I     200           #
LGA    I     197      T     201          5.007
LGA    P     198      R     202          2.598
LGA    A     199      L     203          2.669
LGA    I     200      L     204          3.479
LGA    T     201      -       -           -
LGA    R     202      R     205          3.419
LGA    L     203      E     206           #
LGA    L     204      -       -           -
LGA    R     205      -       -           -
LGA    E     206      Q     207           #
LGA    Q     207      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  140  140    5.0    104    2.93    70.19     43.417     3.437

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.121460 * X  +   0.570331 * Y  +  -0.812385 * Z  +  57.528942
  Y_new =   0.746775 * X  +  -0.591672 * Y  +  -0.303730 * Z  +  16.176638
  Z_new =  -0.653892 * X  +  -0.569778 * Y  +  -0.497773 * Z  +  10.822592 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.288848    0.852745  [ DEG:  -131.1413     48.8587 ]
  Theta =   0.712717    2.428875  [ DEG:    40.8357    139.1643 ]
  Phi   =   1.409562   -1.732031  [ DEG:    80.7620    -99.2380 ]
 
# 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: T0379TS168_4-D1                               
REMARK     2: T0379_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS168_4-D1.T0379_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  140  140   5.0  104   2.93   70.19  43.417
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS168_4-D1
PFRMAT TS
TARGET T0379
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      47.630  23.824 -11.952  1.00 25.00           C
ATOM      2  CA  ILE     2      49.192  22.460  -8.793  1.00 25.00           C
ATOM      3  CA  ARG     3      51.003  24.491  -6.166  1.00 25.00           C
ATOM      4  CA  ASN     4      52.110  21.145  -4.716  1.00 25.00           C
ATOM      5  CA  ILE     5      55.354  19.910  -3.104  1.00 25.00           C
ATOM      6  CA  VAL     6      56.476  18.705   0.319  1.00 25.00           C
ATOM      7  CA  PHE     7      57.510  18.444   4.010  1.00 25.00           C
ATOM      8  CA  ASP     8      56.834  14.820   5.002  1.00 25.00           C
ATOM      9  CA  LEU     9      58.408  15.854   8.303  1.00 25.00           C
ATOM     10  CA  GLY    10      59.715  12.652   9.768  1.00 25.00           C
ATOM     11  CA  GLY    11      61.039  10.861   6.730  1.00 25.00           C
ATOM     12  CA  VAL    12      61.702  13.469   4.039  1.00 25.00           C
ATOM     13  CA  LEU    13      62.545  17.100   3.270  1.00 25.00           C
ATOM     14  CA  ILE    14      63.911  17.963   6.661  1.00 25.00           C
ATOM     15  CA  HIS    15      65.122  19.049  10.145  1.00 25.00           C
ATOM     16  CA  LEU    16      64.963  15.646  11.897  1.00 25.00           C
ATOM     84  CA  LEU    84      68.065  17.543  16.692  1.00 25.00           C
ATOM     85  CA  GLU    85      70.948  15.923  14.758  1.00 25.00           C
ATOM     86  CA  GLU    86      72.567  12.670  13.521  1.00 25.00           C
ATOM     87  CA  ILE    87      69.789  12.843  10.915  1.00 25.00           C
ATOM     88  CA  SER    88      71.943  15.745   9.610  1.00 25.00           C
ATOM     89  CA  ALA    89      73.344  18.871   7.956  1.00 25.00           C
ATOM     90  CA  GLU    90      72.081  16.737   5.036  1.00 25.00           C
ATOM     91  CA  LYS    91      68.461  17.350   6.123  1.00 25.00           C
ATOM     92  CA  PHE    92      69.127  21.116   6.309  1.00 25.00           C
ATOM     93  CA  ASP    93      70.663  21.043   2.801  1.00 25.00           C
ATOM     94  CA  TYR    94      67.610  19.148   1.477  1.00 25.00           C
ATOM     95  CA  ILE    95      65.280  21.726   3.089  1.00 25.00           C
ATOM     96  CA  ASP    96      67.289  24.572   1.497  1.00 25.00           C
ATOM     97  CA  SER    97      67.067  22.852  -1.917  1.00 25.00           C
ATOM     98  CA  LEU    98      63.282  22.450  -1.496  1.00 25.00           C
ATOM     99  CA  ARG    99      62.965  26.156  -0.585  1.00 25.00           C
ATOM    100  CA  PRO   100      61.815  28.903  -2.963  1.00 25.00           C
ATOM    101  CA  ASP   101      59.637  27.441  -5.678  1.00 25.00           C
ATOM    102  CA  TYR   102      58.504  24.073  -4.439  1.00 25.00           C
ATOM    103  CA  ARG   103      56.514  25.418  -1.507  1.00 25.00           C
ATOM    104  CA  LEU   104      53.567  23.811   0.212  1.00 25.00           C
ATOM    105  CA  PHE   105      51.620  20.509   0.499  1.00 25.00           C
ATOM    106  CA  LEU   106      51.681  17.260   2.541  1.00 25.00           C
ATOM    107  CA  LEU   107      51.767  13.823   4.169  1.00 25.00           C
ATOM    108  CA  SER   108      53.435  11.071   6.250  1.00 25.00           C
ATOM    109  CA  ASN   109      49.873  10.906   7.593  1.00 25.00           C
ATOM    110  CA  THR   110      48.331  14.344   7.845  1.00 25.00           C
ATOM    111  CA  ASN   111      47.150  17.643   9.449  1.00 25.00           C
ATOM    112  CA  PRO   112      48.385  20.331  11.830  1.00 25.00           C
ATOM    113  CA  TYR   113      50.103  19.258  15.081  1.00 25.00           C
ATOM    114  CA  VAL   114      52.974  17.703  13.080  1.00 25.00           C
ATOM    115  CA  LEU   115      53.343  20.932  11.053  1.00 25.00           C
ATOM    116  CA  ASP   116      53.427  22.982  14.287  1.00 25.00           C
ATOM    117  CA  LEU   117      56.112  20.657  15.719  1.00 25.00           C
ATOM    118  CA  ALA   118      58.178  21.031  12.516  1.00 25.00           C
ATOM    119  CA  MET   119      57.859  24.842  12.725  1.00 25.00           C
ATOM    120  CA  SER   120      58.987  24.761  16.384  1.00 25.00           C
ATOM    121  CA  PRO   121      61.998  22.595  15.433  1.00 25.00           C
ATOM    122  CA  ARG   122      63.044  25.613  13.363  1.00 25.00           C
ATOM    123  CA  PHE   123      65.498  25.207  10.418  1.00 25.00           C
ATOM    124  CA  LEU   124      68.613  27.392  10.611  1.00 25.00           C
ATOM    125  CA  PRO   125      68.237  28.619  14.174  1.00 25.00           C
ATOM    126  CA  SER   126      66.834  32.137  14.033  1.00 25.00           C
ATOM    127  CA  GLY   127      64.360  34.675  12.685  1.00 25.00           C
ATOM    128  CA  ARG   128      61.844  32.137  11.447  1.00 25.00           C
ATOM    129  CA  THR   129      63.846  30.553   8.614  1.00 25.00           C
ATOM    130  CA  LEU   130      61.930  27.634   7.174  1.00 25.00           C
ATOM    131  CA  ASP   131      59.114  29.520   5.391  1.00 25.00           C
ATOM    132  CA  SER   132      58.215  26.363   3.418  1.00 25.00           C
ATOM    133  CA  PHE   133      58.143  24.328   6.662  1.00 25.00           C
ATOM    134  CA  PHE   134      55.867  26.946   8.283  1.00 25.00           C
ATOM    135  CA  ASP   135      53.528  26.826   5.253  1.00 25.00           C
ATOM    136  CA  LYS   136      53.416  23.003   5.460  1.00 25.00           C
ATOM    137  CA  VAL   137      50.392  21.300   7.130  1.00 25.00           C
ATOM    138  CA  TYR   138      51.861  17.897   7.922  1.00 25.00           C
ATOM    139  CA  ALA   139      53.261  14.655   9.435  1.00 25.00           C
ATOM    140  CA  SER   140      51.068  13.096  12.181  1.00 25.00           C
ATOM    141  CA  CYS   141      47.917  11.686  13.701  1.00 25.00           C
ATOM    142  CA  GLN   142      46.059  15.037  13.720  1.00 25.00           C
ATOM    143  CA  MET   143      43.881  13.619  10.987  1.00 25.00           C
ATOM    144  CA  GLY   144      42.632  10.627  12.941  1.00 25.00           C
ATOM    145  CA  LYS   145      43.908   7.617  10.965  1.00 25.00           C
ATOM    146  CA  TYR   146      47.350   6.616  12.331  1.00 25.00           C
ATOM    147  CA  LYS   147      48.396   5.076   8.984  1.00 25.00           C
ATOM    148  CA  PRO   148      45.518   6.251   6.785  1.00 25.00           C
ATOM    149  CA  ASN   149      42.658   6.416   4.259  1.00 25.00           C
ATOM    150  CA  GLU   150      43.986   9.384   2.177  1.00 25.00           C
ATOM    151  CA  ASP   151      41.213  11.742   3.368  1.00 25.00           C
ATOM    152  CA  ILE   152      43.590  13.272   5.952  1.00 25.00           C
ATOM    153  CA  PHE   153      46.250  13.774   3.242  1.00 25.00           C
ATOM    154  CA  LEU   154      43.661  15.461   0.979  1.00 25.00           C
ATOM    155  CA  GLU   155      42.614  17.765   3.853  1.00 25.00           C
ATOM    156  CA  MET   156      46.279  18.669   4.497  1.00 25.00           C
ATOM    157  CA  ILE   157      46.766  19.443   0.778  1.00 25.00           C
ATOM    158  CA  ALA   158      43.645  21.661   0.805  1.00 25.00           C
ATOM    159  CA  ASP   159      44.954  23.509   3.893  1.00 25.00           C
ATOM    160  CA  SER   160      48.334  24.041   2.173  1.00 25.00           C
ATOM    161  CA  GLY   161      47.013  25.738  -0.984  1.00 25.00           C
ATOM    162  CA  MET   162      44.388  24.027  -3.173  1.00 25.00           C
ATOM    163  CA  LYS   163      42.918  20.902  -4.768  1.00 25.00           C
ATOM    164  CA  PRO   164      42.801  17.178  -5.532  1.00 25.00           C
ATOM    165  CA  GLU   165      46.121  16.248  -7.199  1.00 25.00           C
ATOM    166  CA  GLU   166      47.998  18.603  -4.833  1.00 25.00           C
ATOM    167  CA  THR   167      50.533  16.666  -2.816  1.00 25.00           C
ATOM    168  CA  LEU   168      53.301  14.766  -4.507  1.00 25.00           C
ATOM    169  CA  PHE   169      54.116  12.740  -1.333  1.00 25.00           C
ATOM    170  CA  ILE   170      57.337  12.232   0.544  1.00 25.00           C
ATOM    171  CA  ASP   171      57.846   8.799   2.094  1.00 25.00           C
ATOM    172  CA  ASP   172      59.610   6.424   4.508  1.00 25.00           C
ATOM    173  CA  GLY   173      57.120   4.190   6.172  1.00 25.00           C
ATOM    174  CA  PRO   174      55.652   2.062   3.416  1.00 25.00           C
ATOM    175  CA  ALA   175      52.464   3.019   5.308  1.00 25.00           C
ATOM    176  CA  ASN   176      52.870   6.663   4.200  1.00 25.00           C
ATOM    177  CA  VAL   177      53.330   5.532   0.570  1.00 25.00           C
ATOM    178  CA  ALA   178      50.175   3.374   0.817  1.00 25.00           C
ATOM    179  CA  THR   179      48.224   6.347   2.239  1.00 25.00           C
ATOM    180  CA  ALA   180      49.468   8.565  -0.625  1.00 25.00           C
ATOM    181  CA  GLU   181      48.399   5.915  -3.175  1.00 25.00           C
ATOM    182  CA  ARG   182      44.938   5.710  -1.549  1.00 25.00           C
ATOM    183  CA  LEU   183      43.989   9.014  -3.124  1.00 25.00           C
ATOM    184  CA  GLY   184      46.036  11.522  -5.180  1.00 25.00           C
ATOM    185  CA  PHE   185      49.703  11.073  -6.036  1.00 25.00           C
ATOM    186  CA  HIS   186      52.081   8.326  -7.160  1.00 25.00           C
ATOM    187  CA  THR   187      54.092   7.753  -4.048  1.00 25.00           C
ATOM    188  CA  TYR   188      57.682   8.810  -3.724  1.00 25.00           C
ATOM    189  CA  CYS   189      60.091   6.134  -2.505  1.00 25.00           C
ATOM    190  CA  PRO   190      62.637   7.700  -0.157  1.00 25.00           C
ATOM    191  CA  ASP   191      65.581   6.612  -2.325  1.00 25.00           C
ATOM    192  CA  ASN   192      64.294   5.164  -5.532  1.00 25.00           C
ATOM    193  CA  GLY   193      62.639   8.486  -6.320  1.00 25.00           C
ATOM    194  CA  GLU   194      64.193  10.335  -9.292  1.00 25.00           C
ATOM    195  CA  ASN   195      61.064   9.646 -11.389  1.00 25.00           C
ATOM    196  CA  TRP   196      58.847  10.966  -8.559  1.00 25.00           C
ATOM    197  CA  ILE   197      60.998  14.125  -8.315  1.00 25.00           C
ATOM    198  CA  PRO   198      60.718  14.638 -12.100  1.00 25.00           C
ATOM    199  CA  ALA   199      56.916  14.229 -11.899  1.00 25.00           C
ATOM    200  CA  ILE   200      56.766  16.788  -9.054  1.00 25.00           C
ATOM    201  CA  THR   201      58.871  19.237 -11.113  1.00 25.00           C
ATOM    202  CA  ARG   202      56.540  18.757 -14.113  1.00 25.00           C
ATOM    203  CA  LEU   203      53.496  19.404 -11.882  1.00 25.00           C
ATOM    204  CA  LEU   204      55.134  22.589 -10.527  1.00 25.00           C
ATOM    205  CA  ARG   205      55.861  23.765 -14.098  1.00 25.00           C
ATOM    206  CA  GLU   206      52.220  23.101 -15.084  1.00 25.00           C
ATOM    207  CA  GLN   207      51.057  26.758 -15.250  1.00 25.00           C
TER
END
