
#######################################################
#                                                     #
#                        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  155 (  155),  selected  155 , name T0321TS168_5-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS168_5-D2.T0321_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      97      V      97           -
LGA    I      98      I      98           -
LGA    F      99      F      99           -
LGA    S     100      S     100           -
LGA    D     101      D     101           -
LGA    A     102      A     102           -
LGA    K     103      N     110           -
LGA    R     104      D     111           -
LGA    V     105      P     112           -
LGA    E     106      F     113           -
LGA    D     107      I     114           -
LGA    R     108      M     115           -
LGA    M     109      S     116           -
LGA    N     110      Q     117           -
LGA    D     111      N     118           -
LGA    P     112      E     119           -
LGA    F     113      V     120           -
LGA    I     114      K     121           -
LGA    M     115      G     122           -
LGA    S     116      K     123           -
LGA    Q     117      K     124           -
LGA    N     118      V     125           -
LGA    E     119      G     126           -
LGA    V     120      V     127           -
LGA    -       -      V     128           -
LGA    -       -      G     129           -
LGA    -       -      H     130           -
LGA    -       -      F     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    K     121      E     135           #
LGA    G     122      S     136          1.618
LGA    K     123      -       -           -
LGA    K     124      -       -           -
LGA    V     125      -       -           -
LGA    G     126      -       -           -
LGA    V     127      -       -           -
LGA    V     128      -       -           -
LGA    G     129      -       -           -
LGA    H     130      -       -           -
LGA    F     131      -       -           -
LGA    P     132      -       -           -
LGA    H     133      -       -           -
LGA    L     134      -       -           -
LGA    E     135      -       -           -
LGA    S     136      -       -           -
LGA    L     137      -       -           -
LGA    L     138      -       -           -
LGA    E     139      -       -           -
LGA    P     140      L     137           #
LGA    I     141      L     138          4.008
LGA    C     142      E     139          4.327
LGA    D     143      P     140           #
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      D     143           -
LGA    L     144      L     144          3.435
LGA    S     145      S     145          3.985
LGA    I     146      I     146          4.732
LGA    L     147      L     147          5.124
LGA    E     148      E     148          3.480
LGA    W     149      W     149          4.419
LGA    S     150      -       -           -
LGA    P     151      -       -           -
LGA    E     152      -       -           -
LGA    E     153      -       -           -
LGA    G     154      -       -           -
LGA    D     155      -       -           -
LGA    Y     156      -       -           -
LGA    P     157      S     150           #
LGA    -       -      P     151           -
LGA    L     158      E     152           #
LGA    P     159      E     153           -
LGA    A     160      G     154           -
LGA    S     161      D     155           #
LGA    E     162      Y     156           -
LGA    F     163      P     157           -
LGA    I     164      L     158           -
LGA    L     165      P     159           -
LGA    P     166      A     160           -
LGA    E     167      S     161           -
LGA    C     168      E     162           -
LGA    -       -      F     163           -
LGA    -       -      I     164           -
LGA    -       -      L     165           -
LGA    -       -      P     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      D     169           -
LGA    -       -      Y     170           -
LGA    D     169      V     171          3.085
LGA    Y     170      Y     172          2.440
LGA    V     171      I     173          2.258
LGA    Y     172      T     174          1.069
LGA    -       -      C     175           -
LGA    I     173      A     176          3.414
LGA    T     174      S     177          1.336
LGA    -       -      V     178           -
LGA    C     175      V     179          2.603
LGA    A     176      D     180           #
LGA    S     177      K     181          2.417
LGA    V     178      T     182          1.092
LGA    V     179      L     183          1.149
LGA    D     180      P     184          1.717
LGA    K     181      R     185          1.557
LGA    T     182      L     186          0.682
LGA    L     183      L     187          0.780
LGA    P     184      E     188          1.363
LGA    R     185      L     189          1.442
LGA    L     186      S     190          0.984
LGA    L     187      R     191          1.138
LGA    E     188      N     192           #
LGA    L     189      -       -           -
LGA    S     190      A     193          4.664
LGA    R     191      -       -           -
LGA    N     192      -       -           -
LGA    A     193      R     194          3.846
LGA    R     194      R     195           -
LGA    R     195      I     196           -
LGA    I     196      T     197           -
LGA    T     197      L     198           -
LGA    L     198      V     199           -
LGA    V     199      G     200           -
LGA    G     200      P     201           -
LGA    P     201      G     202          4.517
LGA    G     202      T     203          5.079
LGA    -       -      P     204           -
LGA    -       -      L     205           -
LGA    T     203      A     206           #
LGA    P     204      P     207           -
LGA    L     205      V     208           -
LGA    A     206      L     209           #
LGA    -       -      F     210           -
LGA    P     207      E     211           #
LGA    V     208      H     212          2.793
LGA    L     209      G     213          1.452
LGA    F     210      L     214          2.255
LGA    E     211      Q     215          2.534
LGA    H     212      -       -           -
LGA    G     213      -       -           -
LGA    L     214      -       -           -
LGA    Q     215      -       -           -
LGA    E     216      -       -           -
LGA    L     217      -       -           -
LGA    S     218      -       -           -
LGA    G     219      E     216          5.346
LGA    F     220      L     217          5.090
LGA    M     221      S     218           #
LGA    V     222      -       -           -
LGA    K     223      -       -           -
LGA    D     224      -       -           -
LGA    N     225      -       -           -
LGA    A     226      -       -           -
LGA    R     227      G     219          3.038
LGA    A     228      F     220          3.984
LGA    -       -      M     221           -
LGA    -       -      V     222           -
LGA    -       -      K     223           -
LGA    -       -      D     224           -
LGA    -       -      N     225           -
LGA    -       -      A     226           -
LGA    -       -      R     227           -
LGA    -       -      A     228           -
LGA    -       -      F     229           -
LGA    -       -      R     230           -
LGA    -       -      I     231           -
LGA    -       -      V     232           -
LGA    -       -      A     233           -
LGA    -       -      G     234           -
LGA    -       -      A     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      V     238           -
LGA    -       -      K     239           -
LGA    -       -      I     240           -
LGA    -       -      Y     241           -
LGA    -       -      S     242           -
LGA    -       -      A     243           -
LGA    -       -      G     244           -
LGA    F     229      Q     245          3.487
LGA    R     230      K     246          3.372
LGA    I     231      V     247          4.581
LGA    V     232      -       -           -
LGA    A     233      -       -           -
LGA    G     234      T     248          2.497
LGA    A     235      -       -           -
LGA    E     236      -       -           -
LGA    K     237      -       -           -
LGA    V     238      I     249           #
LGA    K     239      -       -           -
LGA    I     240      -       -           -
LGA    Y     241      -       -           -
LGA    S     242      -       -           -
LGA    A     243      K     250           #
LGA    G     244      K     251          4.065
LGA    Q     245      -       -           -
LGA    K     246      -       -           -
LGA    V     247      -       -           -
LGA    T     248      -       -           -
LGA    I     249      -       -           -
LGA    K     250      -       -           -
LGA    K     251      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  155  148    5.0     44    3.23    18.18     18.202     1.321

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.575063 * X  +   0.023063 * Y  +  -0.817784 * Z  +  15.307884
  Y_new =  -0.212813 * X  +   0.969407 * Y  +  -0.122310 * Z  +  42.166847
  Z_new =   0.789945 * X  +   0.244371 * Y  +   0.562378 * Z  +  61.849030 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.409916   -2.731677  [ DEG:    23.4865   -156.5135 ]
  Theta =  -0.910720   -2.230873  [ DEG:   -52.1804   -127.8196 ]
  Phi   =  -0.354441    2.787152  [ DEG:   -20.3079    159.6920 ]
 
# 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: T0321TS168_5-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS168_5-D2.T0321_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  155  148   5.0   44   3.23   18.18  18.202
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS168_5-D2
PFRMAT TS
TARGET T0321
MODEL 5
PARENT N/A
ATOM     97  CA  VAL    97      27.461  61.295  47.348  1.00 25.00           C
ATOM     98  CA  ILE    98      24.986  58.891  48.959  1.00 25.00           C
ATOM     99  CA  PHE    99      24.662  59.902  52.665  1.00 25.00           C
ATOM    100  CA  SER   100      28.437  60.497  52.414  1.00 25.00           C
ATOM    101  CA  ASP   101      28.859  59.527  56.095  1.00 25.00           C
ATOM    102  CA  ALA   102      26.829  56.333  55.511  1.00 25.00           C
ATOM    103  CA  LYS   103      29.004  55.476  52.478  1.00 25.00           C
ATOM    104  CA  ARG   104      32.170  56.032  54.560  1.00 25.00           C
ATOM    105  CA  VAL   105      30.788  53.760  57.315  1.00 25.00           C
ATOM    106  CA  GLU   106      29.993  51.056  54.720  1.00 25.00           C
ATOM    107  CA  ASP   107      33.544  51.332  53.310  1.00 25.00           C
ATOM    108  CA  ARG   108      34.996  51.003  56.839  1.00 25.00           C
ATOM    109  CA  MET   109      38.322  49.203  57.309  1.00 25.00           C
ATOM    110  CA  ASN   110      38.245  48.931  61.086  1.00 25.00           C
ATOM    111  CA  ASP   111      35.043  48.539  63.075  1.00 25.00           C
ATOM    112  CA  PRO   112      36.496  50.331  66.131  1.00 25.00           C
ATOM    113  CA  PHE   113      35.059  47.627  68.432  1.00 25.00           C
ATOM    114  CA  ILE   114      36.590  44.900  66.222  1.00 25.00           C
ATOM    115  CA  MET   115      39.502  45.074  68.644  1.00 25.00           C
ATOM    116  CA  SER   116      40.408  47.184  71.649  1.00 25.00           C
ATOM    117  CA  GLN   117      39.255  50.412  73.320  1.00 25.00           C
ATOM    118  CA  ASN   118      35.652  50.482  74.449  1.00 25.00           C
ATOM    119  CA  GLU   119      31.954  50.830  75.473  1.00 25.00           C
ATOM    120  CA  VAL   120      28.741  49.026  76.359  1.00 25.00           C
ATOM    121  CA  LYS   121      26.667  50.080  73.301  1.00 25.00           C
ATOM    122  CA  GLY   122      24.206  49.696  70.373  1.00 25.00           C
ATOM    123  CA  LYS   123      22.204  49.531  67.180  1.00 25.00           C
ATOM    124  CA  LYS   124      20.358  52.649  65.935  1.00 25.00           C
ATOM    125  CA  VAL   125      18.968  53.308  62.492  1.00 25.00           C
ATOM    126  CA  GLY   126      17.152  54.497  59.389  1.00 25.00           C
ATOM    127  CA  VAL   127      14.116  52.253  58.804  1.00 25.00           C
ATOM    128  CA  VAL   128      12.388  52.350  55.381  1.00 25.00           C
ATOM    129  CA  GLY   129      14.271  51.723  52.106  1.00 25.00           C
ATOM    130  CA  HIS   130      16.559  49.605  54.292  1.00 25.00           C
ATOM    131  CA  PHE   131      20.321  48.943  54.270  1.00 25.00           C
ATOM    132  CA  PRO   132      22.925  49.417  57.081  1.00 25.00           C
ATOM    133  CA  HIS   133      24.417  49.656  60.590  1.00 25.00           C
ATOM    134  CA  LEU   134      24.700  52.713  62.866  1.00 25.00           C
ATOM    135  CA  GLU   135      27.588  54.803  64.191  1.00 25.00           C
ATOM    136  CA  SER   136      29.221  51.600  65.430  1.00 25.00           C
ATOM    137  CA  LEU   137      27.065  48.631  66.313  1.00 25.00           C
ATOM    138  CA  LEU   138      28.032  46.350  69.142  1.00 25.00           C
ATOM    139  CA  GLU   139      29.081  45.398  72.723  1.00 25.00           C
ATOM    140  CA  PRO   140      26.413  43.370  74.433  1.00 25.00           C
ATOM    141  CA  ILE   141      23.484  45.615  75.336  1.00 25.00           C
ATOM    142  CA  CYS   142      21.386  43.884  72.655  1.00 25.00           C
ATOM    143  CA  ASP   143      22.030  41.885  69.564  1.00 25.00           C
ATOM    144  CA  LEU   144      19.014  40.464  67.784  1.00 25.00           C
ATOM    145  CA  SER   145      17.101  40.871  64.547  1.00 25.00           C
ATOM    146  CA  ILE   146      14.799  43.903  65.000  1.00 25.00           C
ATOM    147  CA  LEU   147      13.129  46.441  62.731  1.00 25.00           C
ATOM    148  CA  GLU   148      11.588  47.875  59.563  1.00 25.00           C
ATOM    149  CA  TRP   149       9.195  49.295  57.049  1.00 25.00           C
ATOM    150  CA  SER   150       5.863  50.889  57.731  1.00 25.00           C
ATOM    151  CA  PRO   151       3.006  52.665  55.961  1.00 25.00           C
ATOM    152  CA  GLU   152       3.495  55.979  57.754  1.00 25.00           C
ATOM    153  CA  GLU   153       2.169  53.984  60.722  1.00 25.00           C
ATOM    154  CA  GLY   154       4.902  52.359  62.705  1.00 25.00           C
ATOM    155  CA  ASP   155       7.174  54.918  61.064  1.00 25.00           C
ATOM    156  CA  TYR   156       9.819  52.169  61.505  1.00 25.00           C
ATOM    157  CA  PRO   157      11.888  55.099  62.895  1.00 25.00           C
ATOM    158  CA  LEU   158      14.502  53.161  64.863  1.00 25.00           C
ATOM    159  CA  PRO   159      12.833  52.119  68.147  1.00 25.00           C
ATOM    160  CA  ALA   160      13.029  48.438  67.108  1.00 25.00           C
ATOM    161  CA  SER   161      16.741  48.851  66.258  1.00 25.00           C
ATOM    162  CA  GLU   162      17.365  50.480  69.668  1.00 25.00           C
ATOM    163  CA  PHE   163      15.548  47.593  71.408  1.00 25.00           C
ATOM    164  CA  ILE   164      17.665  45.059  69.469  1.00 25.00           C
ATOM    165  CA  LEU   165      16.125  42.715  72.033  1.00 25.00           C
ATOM    166  CA  PRO   166      18.390  39.907  73.142  1.00 25.00           C
ATOM    167  CA  GLU   167      15.276  37.879  73.911  1.00 25.00           C
ATOM    168  CA  CYS   168      15.746  36.249  70.508  1.00 25.00           C
ATOM    169  CA  ASP   169      13.855  39.199  69.065  1.00 25.00           C
ATOM    170  CA  TYR   170      11.671  42.286  69.369  1.00 25.00           C
ATOM    171  CA  VAL   171       9.834  43.908  66.403  1.00 25.00           C
ATOM    172  CA  TYR   172       8.495  47.045  64.720  1.00 25.00           C
ATOM    173  CA  ILE   173       7.243  47.297  61.126  1.00 25.00           C
ATOM    174  CA  THR   174       3.782  46.746  59.699  1.00 25.00           C
ATOM    175  CA  CYS   175       1.490  46.904  56.633  1.00 25.00           C
ATOM    176  CA  ALA   176      -0.496  44.293  58.608  1.00 25.00           C
ATOM    177  CA  SER   177      -0.214  41.832  55.687  1.00 25.00           C
ATOM    178  CA  VAL   178       3.565  42.434  55.514  1.00 25.00           C
ATOM    179  CA  VAL   179       3.859  41.821  59.283  1.00 25.00           C
ATOM    180  CA  ASP   180       1.868  38.569  58.935  1.00 25.00           C
ATOM    181  CA  LYS   181       4.155  37.447  56.075  1.00 25.00           C
ATOM    182  CA  THR   182       7.242  38.225  58.205  1.00 25.00           C
ATOM    183  CA  LEU   183       5.773  36.212  61.113  1.00 25.00           C
ATOM    184  CA  PRO   184       5.087  33.268  58.762  1.00 25.00           C
ATOM    185  CA  ARG   185       8.683  33.439  57.458  1.00 25.00           C
ATOM    186  CA  LEU   186      10.011  33.459  61.050  1.00 25.00           C
ATOM    187  CA  LEU   187       7.842  30.417  61.894  1.00 25.00           C
ATOM    188  CA  GLU   188       9.158  28.589  58.797  1.00 25.00           C
ATOM    189  CA  LEU   189      12.759  29.402  59.817  1.00 25.00           C
ATOM    190  CA  SER   190      12.082  28.083  63.349  1.00 25.00           C
ATOM    191  CA  ARG   191      15.373  26.209  62.990  1.00 25.00           C
ATOM    192  CA  ASN   192      15.750  26.250  66.765  1.00 25.00           C
ATOM    193  CA  ALA   193      14.273  29.562  67.686  1.00 25.00           C
ATOM    194  CA  ARG   194      15.984  31.128  64.688  1.00 25.00           C
ATOM    195  CA  ARG   195      16.177  34.739  65.744  1.00 25.00           C
ATOM    196  CA  ILE   196      13.470  36.451  63.580  1.00 25.00           C
ATOM    197  CA  THR   197      12.177  39.754  64.866  1.00 25.00           C
ATOM    198  CA  LEU   198       8.903  39.978  63.056  1.00 25.00           C
ATOM    199  CA  VAL   199       6.605  43.027  62.566  1.00 25.00           C
ATOM    200  CA  GLY   200       3.070  43.558  63.905  1.00 25.00           C
ATOM    201  CA  PRO   201       2.396  47.255  64.724  1.00 25.00           C
ATOM    202  CA  GLY   202      -1.144  46.337  63.843  1.00 25.00           C
ATOM    203  CA  THR   203      -3.438  43.388  64.241  1.00 25.00           C
ATOM    204  CA  PRO   204      -3.414  39.823  62.802  1.00 25.00           C
ATOM    205  CA  LEU   205      -0.952  36.912  62.854  1.00 25.00           C
ATOM    206  CA  ALA   206       2.387  38.201  64.220  1.00 25.00           C
ATOM    207  CA  PRO   207       1.065  37.902  67.802  1.00 25.00           C
ATOM    208  CA  VAL   208      -0.087  34.318  67.104  1.00 25.00           C
ATOM    209  CA  LEU   209       3.362  33.462  65.676  1.00 25.00           C
ATOM    210  CA  PHE   210       5.043  34.944  68.781  1.00 25.00           C
ATOM    211  CA  GLU   211       2.739  32.885  71.042  1.00 25.00           C
ATOM    212  CA  HIS   212       3.585  29.718  69.062  1.00 25.00           C
ATOM    213  CA  GLY   213       5.695  28.441  66.167  1.00 25.00           C
ATOM    214  CA  LEU   214       8.803  30.543  66.689  1.00 25.00           C
ATOM    215  CA  GLN   215       9.577  32.392  69.929  1.00 25.00           C
ATOM    216  CA  GLU   216      11.499  34.689  67.653  1.00 25.00           C
ATOM    217  CA  LEU   217       8.505  35.709  65.642  1.00 25.00           C
ATOM    218  CA  SER   218       8.275  38.763  67.886  1.00 25.00           C
ATOM    219  CA  GLY   219       5.098  40.919  68.129  1.00 25.00           C
ATOM    220  CA  PHE   220       5.532  44.602  68.904  1.00 25.00           C
ATOM    221  CA  MET   221       7.988  47.397  69.736  1.00 25.00           C
ATOM    222  CA  VAL   222       5.548  49.708  67.962  1.00 25.00           C
ATOM    223  CA  LYS   223       3.676  53.009  67.686  1.00 25.00           C
ATOM    224  CA  ASP   224       4.976  55.312  70.344  1.00 25.00           C
ATOM    225  CA  ASN   225       2.267  56.077  72.912  1.00 25.00           C
ATOM    226  CA  ALA   226      -0.096  53.532  74.526  1.00 25.00           C
ATOM    227  CA  ARG   227       1.362  50.750  72.334  1.00 25.00           C
ATOM    228  CA  ALA   228       4.910  51.790  73.332  1.00 25.00           C
ATOM    229  CA  PHE   229       3.911  51.738  77.030  1.00 25.00           C
ATOM    230  CA  ARG   230       2.400  48.245  76.598  1.00 25.00           C
ATOM    231  CA  ILE   231       5.615  47.037  74.903  1.00 25.00           C
ATOM    232  CA  VAL   232       7.700  48.479  77.775  1.00 25.00           C
ATOM    233  CA  ALA   233       5.452  46.713  80.324  1.00 25.00           C
ATOM    234  CA  GLY   234       5.839  43.414  78.418  1.00 25.00           C
ATOM    235  CA  ALA   235       9.643  43.853  78.382  1.00 25.00           C
ATOM    236  CA  GLU   236       9.626  44.529  82.152  1.00 25.00           C
ATOM    237  CA  LYS   237       7.519  41.383  82.731  1.00 25.00           C
ATOM    238  CA  VAL   238       9.959  39.328  80.611  1.00 25.00           C
ATOM    239  CA  LYS   239      12.910  40.716  82.620  1.00 25.00           C
ATOM    240  CA  ILE   240      11.135  39.816  85.893  1.00 25.00           C
ATOM    241  CA  TYR   241      10.492  36.270  84.599  1.00 25.00           C
ATOM    242  CA  SER   242       8.221  35.080  81.728  1.00 25.00           C
ATOM    243  CA  ALA   243       7.612  35.265  78.021  1.00 25.00           C
ATOM    244  CA  GLY   244       4.098  36.480  77.314  1.00 25.00           C
ATOM    245  CA  GLN   245       2.513  39.876  76.678  1.00 25.00           C
ATOM    246  CA  LYS   246      -0.056  42.030  74.932  1.00 25.00           C
ATOM    247  CA  VAL   247      -3.077  43.293  73.138  1.00 25.00           C
ATOM    248  CA  THR   248      -6.284  44.304  74.851  1.00 25.00           C
ATOM    249  CA  ILE   249      -8.689  46.356  76.969  1.00 25.00           C
ATOM    250  CA  LYS   250     -11.842  48.391  76.227  1.00 25.00           C
ATOM    251  CA  LYS   251     -14.391  49.630  78.755  1.00 25.00           C
TER
END
