
#######################################################
#                                                     #
#                        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   72 (   72),  selected   72 , name T0320TS464_5_1
# Molecule2: number of CA atoms  287 ( 2364),  selected  287 , name T0320.pdb
# PARAMETERS: T0320TS464_5_1.T0320.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      34      M       1           -
LGA    R      35      Q       2           -
LGA    L      36      L       3           -
LGA    T      37      S       4           -
LGA    R      38      K       5           -
LGA    F      58      A       6           -
LGA    S      59      A       7           -
LGA    Y      60      E       8           -
LGA    N      61      M       9           -
LGA    -       -      C      10           -
LGA    -       -      Y      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      T      14           -
LGA    -       -      N      15           -
LGA    -       -      S      16           -
LGA    -       -      Y      17           -
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      S      29           -
LGA    G      62      T      30           #
LGA    G      63      Q      31           -
LGA    -       -      E      32           -
LGA    K      64      A      33          4.481
LGA    D      65      I      34          2.784
LGA    -       -      R      35           -
LGA    C      66      L      36          4.478
LGA    Q      67      T      37          4.040
LGA    V      68      R      38          3.513
LGA    L      69      K      39          1.929
LGA    L      70      Y      40          3.746
LGA    L      71      L      41           #
LGA    L      72      L      42           #
LGA    Y      73      S      43          1.727
LGA    -       -      E      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    P     103      W      49           #
LGA    T     104      S      50          5.051
LGA    V     105      P      51          3.111
LGA    -       -      L      52           -
LGA    F     106      N      53          3.343
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    I     107      I      56          4.609
LGA    D     108      S      57          2.287
LGA    Q     109      F      58          2.242
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    -       -      N      61           -
LGA    -       -      G      62           -
LGA    S     138      G      63          1.503
LGA    G     139      K      64          2.126
LGA    A     140      D      65          1.815
LGA    S     141      C      66          0.935
LGA    V     142      Q      67          1.259
LGA    N     143      V      68          1.999
LGA    M     144      L      69          1.506
LGA    A     145      L      70          0.442
LGA    D     146      L      71          0.551
LGA    A     147      L      72          1.351
LGA    F     148      Y      73          1.621
LGA    R     149      L      74          0.906
LGA    D     150      S      75          0.852
LGA    F     151      C      76          1.333
LGA    I     152      L      77          1.920
LGA    K     153      W      78          2.707
LGA    I     154      E      79          2.659
LGA    Y     155      Y      80          2.337
LGA    -       -      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    P     156      K      84          4.212
LGA    E     157      A      85           -
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    T     158      F      97           #
LGA    E     159      P      98           #
LGA    A     160      M      99           -
LGA    I     161      Q     100          5.051
LGA    -       -      R     101           -
LGA    V     162      L     102          0.493
LGA    S     223      P     103           -
LGA    I     224      T     104           -
LGA    G     225      V     105           -
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    -       -      R     126           -
LGA    -       -      Y     127           -
LGA    -       -      C     128           -
LGA    -       -      L     129           -
LGA    -       -      S     130           -
LGA    -       -      L     131           -
LGA    -       -      Y     132           -
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    -       -      V     162           -
LGA    -       -      I     163           -
LGA    -       -      G     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      L     195           -
LGA    G     226      H     196          3.656
LGA    I     227      W     197           #
LGA    Y     292      D     198           -
LGA    L     293      L     199           -
LGA    V     294      T     200           -
LGA    D     295      N     201           -
LGA    D     296      I     202           -
LGA    T     297      W     203           -
LGA    L     298      S     204           -
LGA    E     299      F     205           -
LGA    R     300      L     206           -
LGA    A     301      L     207           -
LGA    G     302      Y     208           -
LGA    R     303      S     209           -
LGA    I     304      N     210           -
LGA    K     305      E     211           -
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   72  287    5.0     36    2.80     5.56      9.063     1.241

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.908408 * X  +  -0.401326 * Y  +   0.117183 * Z  +  46.427639
  Y_new =   0.395025 * X  +   0.732105 * Y  +  -0.554957 * Z  +  -2.424065
  Z_new =   0.136929 * X  +   0.550418 * Y  +   0.823584 * Z  + -17.871954 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.589146   -2.552446  [ DEG:    33.7556   -146.2444 ]
  Theta =  -0.137360   -3.004232  [ DEG:    -7.8702   -172.1298 ]
  Phi   =   0.410187   -2.731405  [ DEG:    23.5020   -156.4980 ]
 
# 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: T0320TS464_5_1                                
REMARK     2: T0320.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_5_1.T0320.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   72  287   5.0   36   2.80    5.56   9.063
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_5_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  ILE    34      16.329  26.102  35.883  1.00  0.00
ATOM      2  CA  ARG    35      16.959  22.561  34.724  1.00  0.00
ATOM      3  CA  LEU    36      15.891  23.197  31.160  1.00  0.00
ATOM      4  CA  THR    37      17.878  26.434  31.058  1.00  0.00
ATOM      5  CA  ARG    38      20.983  24.563  32.375  1.00  0.00
ATOM      6  CA  PHE    58      15.379  15.725  33.008  1.00  0.00
ATOM      7  CA  SER    59      15.091  16.299  29.296  1.00  0.00
ATOM      8  CA  TYR    60      11.676  15.247  28.034  1.00  0.00
ATOM      9  CA  ASN    61      11.195  14.311  24.384  1.00  0.00
ATOM     10  CA  GLY    62       8.342  16.826  24.437  1.00  0.00
ATOM     11  CA  GLY    63       8.112  20.377  25.722  1.00  0.00
ATOM     12  CA  LYS    64       4.455  19.642  26.384  1.00  0.00
ATOM     13  CA  ASP    65       5.646  16.944  28.777  1.00  0.00
ATOM     14  CA  CYS    66       8.266  19.565  29.702  1.00  0.00
ATOM     15  CA  GLN    67       5.617  22.207  30.393  1.00  0.00
ATOM     16  CA  VAL    68       3.417  19.697  32.212  1.00  0.00
ATOM     17  CA  LEU    69       6.436  18.522  34.218  1.00  0.00
ATOM     18  CA  LEU    70       7.142  22.110  35.393  1.00  0.00
ATOM     19  CA  LEU    71       3.530  22.422  36.555  1.00  0.00
ATOM     20  CA  LEU    72       3.947  19.276  38.636  1.00  0.00
ATOM     21  CA  TYR    73       7.278  20.515  39.980  1.00  0.00
ATOM     22  CA  PRO   103      12.524  36.365  43.210  1.00  0.00
ATOM     23  CA  THR   104      14.187  37.207  39.904  1.00  0.00
ATOM     24  CA  VAL   105      14.946  34.459  37.383  1.00  0.00
ATOM     25  CA  PHE   106      17.367  35.257  34.566  1.00  0.00
ATOM     26  CA  ILE   107      16.859  32.988  31.607  1.00  0.00
ATOM     27  CA  ASP   108      19.860  32.582  29.310  1.00  0.00
ATOM     28  CA  GLN   109      18.838  30.670  26.158  1.00  0.00
ATOM     29  CA  SER   138      18.013  23.656  16.057  1.00  0.00
ATOM     30  CA  GLY   139      14.976  21.465  16.830  1.00  0.00
ATOM     31  CA  ALA   140      15.937  21.129  20.520  1.00  0.00
ATOM     32  CA  SER   141      16.331  24.877  21.196  1.00  0.00
ATOM     33  CA  VAL   142      12.919  25.307  19.561  1.00  0.00
ATOM     34  CA  ASN   143      11.399  22.793  21.994  1.00  0.00
ATOM     35  CA  MET   144      13.185  24.324  24.998  1.00  0.00
ATOM     36  CA  ALA   145      11.909  27.795  24.082  1.00  0.00
ATOM     37  CA  ASP   146       8.185  28.331  24.182  1.00  0.00
ATOM     38  CA  ALA   147       7.995  26.560  27.545  1.00  0.00
ATOM     39  CA  PHE   148      10.275  29.275  28.960  1.00  0.00
ATOM     40  CA  ARG   149       7.649  31.818  27.841  1.00  0.00
ATOM     41  CA  ASP   150       4.803  29.861  29.450  1.00  0.00
ATOM     42  CA  PHE   151       6.763  29.295  32.659  1.00  0.00
ATOM     43  CA  ILE   152       6.262  32.909  33.720  1.00  0.00
ATOM     44  CA  LYS   153       2.698  31.783  34.408  1.00  0.00
ATOM     45  CA  ILE   154       3.717  28.499  35.996  1.00  0.00
ATOM     46  CA  TYR   155       6.352  29.457  38.512  1.00  0.00
ATOM     47  CA  PRO   156       7.627  30.499  41.890  1.00  0.00
ATOM     48  CA  GLU   157       9.788  33.052  40.068  1.00  0.00
ATOM     49  CA  THR   158       8.260  36.519  40.630  1.00  0.00
ATOM     50  CA  GLU   159       9.866  37.823  37.409  1.00  0.00
ATOM     51  CA  ALA   160      11.626  36.142  34.518  1.00  0.00
ATOM     52  CA  ILE   161      13.924  38.173  32.257  1.00  0.00
ATOM     53  CA  VAL   162      15.098  36.297  29.192  1.00  0.00
ATOM     54  CA  SER   223       4.983   9.677  34.369  1.00  0.00
ATOM     55  CA  ILE   224       4.770  12.931  32.403  1.00  0.00
ATOM     56  CA  GLY   225       6.124  11.349  29.229  1.00  0.00
ATOM     57  CA  GLY   226       9.250  10.029  27.533  1.00  0.00
ATOM     58  CA  ILE   227      12.398  11.483  29.030  1.00  0.00
ATOM     59  CA  TYR   292      27.661  33.086  14.995  1.00  0.00
ATOM     60  CA  LEU   293      25.389  30.203  13.937  1.00  0.00
ATOM     61  CA  VAL   294      24.130  29.512  17.463  1.00  0.00
ATOM     62  CA  ASP   295      23.374  33.256  17.920  1.00  0.00
ATOM     63  CA  ASP   296      21.067  33.016  14.891  1.00  0.00
ATOM     64  CA  THR   297      19.254  29.969  16.250  1.00  0.00
ATOM     65  CA  LEU   298      18.704  31.641  19.626  1.00  0.00
ATOM     66  CA  GLU   299      17.240  34.690  17.839  1.00  0.00
ATOM     67  CA  ARG   300      15.060  32.481  15.631  1.00  0.00
ATOM     68  CA  ALA   301      13.450  30.992  18.746  1.00  0.00
ATOM     69  CA  GLY   302      13.073  34.192  20.741  1.00  0.00
ATOM     70  CA  ARG   303      15.783  33.317  23.276  1.00  0.00
ATOM     71  CA  ILE   304      18.551  35.830  22.376  1.00  0.00
ATOM     72  CA  LYS   305      18.987  36.973  26.014  1.00  0.00
TER
END
