SSEnvID

Protein secondary structure and environment assignment from atomic coordinates

SSEnvID is a program to recognize secondary structural elements in proteins from their atomic coordinates. It performs the same task as DSSP by Kabsch and Sander (1983) or STRIDE by Frishman & Argos (1995) with analyzing both hydrogen bond and mainchain dihedral angles, as well some probabilistic measures. SSEnvID also computes accessible surface area, polarity and environment classes as defined by Bowie, Luthy, Eisenberg (1991). SSEnvID's new feature is the probability (quality) of secondary structure assignment for each amino acids.

SSEnvID computes 3D protein characteristics which are used in structure prediction by measuring the compatibility between protein sequences and known protein structures.

SSEnvID output:


SSENVID - Protein secondary structure and environment assignment
             from atomic coordinates (Softberry Inc., 2001)

Name of PDB file: file.pdb

Ch   - Chain
ResN - PDB resnumber
Nam  - Amino acid sequence in three letter code
Ab   - Area Buried
Fp   - Fraction Polar
SS   - Secondary structure assignment (E-beta sheet, H,G,I-helices, T-turn)
PDBSS- Original PDB secondary structure assignment (if provided)
Env  - Side-Chain Environment Class
Phi  - Phi torsional angles
Psi  - Psi torsional angles
PrHel- Probability of helix
PrBet- Probability of beta bridge

Ch  ResN  Nam   Ab     Fp   SS  PDBSS  Env   Phi    Psi     PrHel  PrBet

 B   260  LEU   67.7   0.62  C    C   P2     ?     127.6    0.00    0.00
 B   261  PRO   16.6   0.88  C    C   E    -78.3   -23.5    0.00    0.00
 B   262  ASN   70.0   0.54  C    C   P1   -93.6     3.5    0.01    0.13
 B   263  GLN   89.0   0.58  C    C   P2   -42.8   121.5    0.13    0.00
 B   264  GLN  127.8   0.24  C    C   B1  -107.0   -31.4    0.33    0.00
 B   265  PHE  179.6   0.35  C    C   B2   -97.4   135.7    0.35    0.00
 B   266  GLY   25.7   0.60  C    C   E     82.8    13.8    0.35    0.00
 B   267  VAL  112.0   0.55  C    C   P1  -115.9   131.5    0.35    0.00
 B   268  SER   46.7   0.55  C    C   P1   -56.0   150.3    0.13    0.00
 B   269  LEU  146.0   0.27  H    H   B1   -59.6   -28.1    0.97    0.01
 B   270  GLN   43.7   0.81  H    H   P2   -69.5   -46.7    0.98    0.01
 B   271  HIS   60.6   0.76  H    H   P2   -70.5   -29.9    1.00    0.00
 B   272  LEU  145.2   0.38  H    H   B2   -64.2   -40.2    1.00    0.00
 B   273  GLN   76.3   0.68  H    H   P2   -76.3   -30.5    1.00    0.01
 B   274  GLU   49.2   0.70  H    H   P2   -63.8   -34.8    1.00    0.01
 B   275  LYS  116.1   0.59  T    C   B3   -95.9    15.3    0.25    0.00
 B   276  ASN   79.5   0.70  C    C   P2  -117.9   124.0    0.26    0.00
 B   277  PRO   37.7   0.90  C    C   E    -61.1   -27.5    0.26    0.00
 B   278  GLU   46.4   0.76  C    C   P2   -94.8   161.2    0.26    0.00
 B   279  GLN   15.3   0.75  C    C   E    -88.7    92.5    0.26    0.00
 B   280  GLU   95.6   0.65  C    C   P2  -119.1    90.1    0.26    0.00
 B   281  PRO   39.4   0.57  C    C   E    -66.9     1.4    0.13    0.00
 B   282  ILE  130.2   0.28  C    C   B1  -129.1   116.5    0.13    0.00
 B   283  PRO  114.3   0.26  C    C   B1   -57.8   153.7    0.13    0.00
 B   284  ILE  110.8   0.70  H    H   P2   -57.9   -40.5    0.99    0.09
 B   285  VAL  130.0   0.18  H    H   B1   -61.5   -39.2    0.99    0.09
 B   286  LEU  149.0   0.18  H    H   B1   -74.4   -42.5    0.99    0.09
 B   287  ARG  125.8   0.53  H    H   B3   -56.0   -50.5    0.99    0.07
 B   288  GLU   95.3   0.51  H    H   P1   -70.2   -47.9    0.99    0.09
 B   289  THR  113.0   0.19  H    H   P1   -62.3   -40.9    0.99    0.09
 B   290  VAL  126.6   0.20  H    H   B1   -64.9   -49.6    0.99    0.09
 B   291  ALA   11.9   0.70  H    H   E    -54.5   -44.4    0.99    0.07
 B   292  TYR  162.0   0.47  H    H   B3   -68.5   -45.3    0.99    0.17
 B   293  LEU  153.4   0.18  H    H   B1   -60.0   -46.4    0.99    0.16
 B   294  GLN   84.9   0.49  H    H   P1   -77.1    14.1    0.96    0.01
 B   295  ALA   26.5   0.76  H    H   E   -125.2   -13.3    0.96    0.17
 B   296  HIS   70.8   0.66  H    H   P2  -139.3   -13.4    0.96    0.12
 B   297  ALA   69.3   0.30  C    C   P1  -125.9    18.6    0.27    0.16
 B   298  LEU  106.2   0.58  T    C   P2   -62.5   -15.5    0.27    0.01
 B   299  THR   49.2   0.64  T    C   P2  -128.5    24.3    0.27    0.00
 B   300  THR   88.2   0.47  C    C   P1   -81.7   121.5    0.25    0.00
 B   301  GLU   56.9   0.75  T    C   P2   -53.2   116.2    0.25    0.16
 B   302  GLY   32.4   0.34  T    C   E     66.9    40.3    0.25    0.07
 B   303  ILE  156.9   0.31  T    C   B1   -68.4   126.8    0.23    0.00
 B   304  PHE  189.0   0.08  T    C   B1    88.0    -4.6    0.23    0.00
 B   305  ALA   38.6   0.43  T    C   E   -106.8   -22.1    0.23    0.00
 B   306  ARG   10.7   0.79  C    C   E    -97.2   148.1    0.23    0.00
 B   307  SER    3.1   0.82  C    C   E    -86.6   170.0    0.13    0.00
 B   308  ALA   64.3   0.46  C    C   P1  -131.8   171.0    0.13    0.00
 B   309  ASN   16.5   0.72  C    C   E    -57.6   111.1    0.33    0.00
 B   310  THR   11.6   0.88  H    H   E    -52.3   -45.7    0.99    0.01
 B   311  GLN   38.0   0.81  H    H   E    -66.3   -30.7    0.99    0.01
 B   312  VAL   97.9   0.50  H    H   P1   -71.0   -32.7    0.99    0.01
 B   313  VAL  111.1   0.35  H    H   P1   -71.4   -34.5    1.00    0.01
 B   314  ARG   50.0   0.68  H    H   P2   -68.6   -28.3    1.00    0.01
 B   315  GLU   65.8   0.63  H    H   P2   -70.8   -41.3    1.00    0.01
 B   316  VAL  128.9   0.17  H    H   B1   -73.0   -32.4    1.00    0.01
 B   317  GLN  121.2   0.34  H    H   B2   -65.4   -42.1    1.00    0.01
 B   318  GLN   48.9   0.60  H    H   P2   -60.0   -44.6    1.00    0.09
 B   319  LYS  138.4   0.49  H    H   B3   -59.4   -43.0    1.00    0.15
 B   320  TYR  195.9   0.23  H    H   B1   -67.5   -38.0    0.98    0.14
 B   321  ASN  107.2   0.45  H    H   P1   -75.9   -15.6    0.97    0.01
 B   322  MET  111.1   0.57  T    C   P2   -94.3    -5.0    0.66    0.13
 B   323  GLY   17.3   0.78  T    C   E     74.8    14.9    0.13    0.15
 B   324  LEU   69.8   0.47  C    C   P1   -80.5   156.9    0.13    0.00
 B   325  PRO    0.0   0.82  C    C   E    -71.9   143.0    0.13    0.00
 B   326  VAL  129.2   0.37  C    C   B2  -125.9   124.6    0.01    0.00
 B   327  ASP   31.9   0.73  C    C   E   -122.6   113.4    0.10    0.00
 B   328  PHE  184.5   0.24  T    C   B1   -72.9     0.6    0.12    0.00
 B   329  ASP   38.0   0.78  T    C   E    -78.2   -39.7    0.12    0.00
 B   330  GLN   62.8   0.71  C    C   P2   -52.8   -37.5    0.13    0.00
 B   331  TYR  186.7   0.46  C    C   B3   -86.7   128.0    0.13    0.00
 B   332  ASN    0.0   0.97  C    C   E    -92.1    76.9    0.13    0.00
 B   333  GLU   98.2   0.58  C    C   P2  -170.8   122.4    0.33    0.00
 B   334  LEU   96.0   0.58  C    C   P2   -81.0   -15.2    0.75    0.00
 B   335  HIS  150.8   0.50  H    H   B3   -83.6   -14.9    0.85    0.01
 B   336  LEU  153.1   0.18  H    H   B1   -62.1   -54.3    0.99    0.09
 B   337  PRO  123.0   0.24  H    H   B1   -65.5   -26.7    0.99    0.09
 B   338  ALA   71.0   0.27  H    H   P1   -69.3   -43.2    0.99    0.01
 B   339  VAL  105.9   0.41  H    H   P1   -70.4   -33.5    0.99    0.01
 B   340  ILE  157.0   0.17  H    H   B1   -72.7   -35.3    0.99    0.09
 B   341  LEU  153.1   0.13  H    H   B1   -61.4   -52.7    0.99    0.09
 B   342  LYS  156.6   0.41  H    H   B2   -61.0   -40.4    1.00    0.01
 B   343  THR  100.7   0.58  H    H   P2   -61.2   -37.0    1.00    0.01
 B   344  PHE  186.9   0.18  H    H   B1   -61.6   -49.5    1.00    0.07
 B   345  LEU  152.5   0.12  H    H   B1   -62.9   -39.0    1.00    0.01
 B   346  ARG   70.2   0.68  H    H   P2   -67.6   -31.6    0.99    0.01
 B   347  GLU   68.7   0.67  T    C   P2   -87.2    -3.1    0.49    0.01
 B   348  LEU  149.8   0.41  C    C   B2   -62.7   133.5    0.13    0.00
 B   349  PRO   73.5   0.62  C    C   P2   -52.6   -20.9    0.13    0.00
 B   350  GLU   20.6   0.59  C    C   E   -146.5   134.1    0.13    0.00
 B   351  PRO  123.0   0.33  C    C   B2   -41.3   142.0    0.13    0.00
 B   352  LEU  154.0   0.15  T    C   B1   -57.8   -33.7    0.26    0.16
 B   353  LEU  150.8   0.13  T    C   B1   -83.1   -12.3    0.30    0.09
 B   354  THR   88.2   0.35  C    C   P1    71.2   148.5    0.53    0.00
 B   355  PHE  128.3   0.54  G    H   B3   -59.4   -18.6    0.97    0.00
 B   356  ASP    0.0   0.85  G    H   E    -73.3   -21.9    0.97    0.00
 B   357  LEU  149.1   0.28  G    H   B1   -90.0    -1.4    0.97    0.00
 B   358  TYR  150.2   0.28  H    H   B1   -54.1   -49.8    0.99    0.09
 B   359  PRO   32.3   0.72  H    H   E    -59.6   -44.2    0.99    0.09
 B   360  HIS  123.2   0.34  H    H   B2   -57.6   -42.3    0.99    0.00
 B   361  VAL  130.0   0.14  H    H   B1   -66.8   -54.0    0.99    0.00
 B   362  VAL   72.6   0.49  H    H   P1   -63.0   -30.0    0.99    0.09
 B   363  GLY   19.7   0.82  T    C   E   -107.0    23.8    0.45    0.09
 B   364  PHE  184.6   0.24  G    H   B1   -57.2   -49.0    0.99    0.00
 B   365  LEU   69.8   0.64  G    H   P2   -67.7    -4.3    0.99    0.00
 B   366  ASN    0.0   0.85  G    H   E    -90.2    -7.1    0.99    0.00
 B   367  ILE  101.6   0.51  C    C   P1   -87.8   131.6    0.26    0.00
 B   368  ASP    0.0   0.84  C    C   E    -56.5   136.7    0.26    0.16
 B   369  GLU    0.0   0.88  G    H   E    -44.0   -42.9    0.97    0.22
 B   370  SER    0.3   0.83  G    H   E    -65.5   -22.1    0.97    0.00
 B   371  GLN   39.9   0.75  G    H   E   -103.9     6.3    0.97    0.16
 B   372  ARG  149.5   0.42  H    H   B2   -69.5   -42.3    0.97    0.22
 B   373  VAL   90.4   0.45  H    H   P1   -67.7   -56.0    0.99    0.01
 B   374  PRO   62.3   0.65  H    H   P2   -64.4   -30.0    0.99    0.01
 B   375  ALA   46.8   0.48  H    H   P1   -66.8   -42.5    0.99    0.01
 B   376  THR  113.0   0.15  H    H   P1   -70.0   -33.7    0.99    0.09
 B   377  LEU   69.5   0.59  H    H   P2   -59.9   -42.0    0.99    0.01
 B   378  GLN    0.0   0.78  H    H   E    -71.4   -28.2    0.96    0.01
 B   379  VAL  107.5   0.38  H    H   P1   -72.5   -44.8    0.96    0.01
 B   380  LEU  152.9   0.19  H    H   B1   -61.6   -25.5    0.97    0.01
 B   381  GLN   22.9   0.72  H    H   E    -68.9   -21.1    0.97    0.01
 B   382  THR   48.1   0.70  H    H   P2   -87.6    -9.3    0.97    0.00
 B   383  LEU  152.0   0.33  C    C   B2   -70.9   145.4    0.13    0.00
 B   384  PRO   54.6   0.69  C    C   P2   -63.1   142.8    0.13    0.00
 B   385  GLU   31.1   0.77  H    H   E    -48.1   -41.9    0.99    0.01
 B   386  GLU  105.5   0.47  H    H   P1   -68.5   -33.9    0.99    0.01
 B   387  ASN  113.8   0.24  H    H   P1   -69.6   -36.0    0.99    0.01
 B   388  TYR  173.7   0.43  H    H   B2   -68.2   -48.4    0.99    0.01
 B   389  GLN   98.2   0.52  H    H   P1   -63.3   -42.2    0.99    0.01
 B   390  VAL  129.9   0.17  H    H   B1   -63.2   -39.3    0.99    0.01
 B   391  LEU  154.0   0.11  H    H   B1   -69.1   -41.3    0.99    0.09
 B   392  ARG  121.8   0.52  H    H   B3   -62.4   -44.1    0.99    0.09
 B   393  PHE  100.0   0.47  H    H   P1   -62.9   -53.5    0.99    0.01
 B   394  LEU  149.3   0.10  H    H   B1   -57.5   -58.1    1.00    0.09
 B   395  THR  110.0   0.22  H    H   P1   -56.1   -35.9    1.00    0.09
 B   396  ALA   41.2   0.74  H    H   P2   -64.2   -36.5    1.00    0.09
 B   397  PHE  182.4   0.27  H    H   B1   -73.9   -40.1    1.00    0.14
 B   398  LEU  149.0   0.08  H    H   B1   -64.9   -36.6    0.99    0.01
 B   399  VAL   83.6   0.63  H    H   P2   -67.2   -18.3    0.99    0.01
 B   400  GLN   49.5   0.62  H    H   P2   -76.6   -40.3    0.99    0.14
 B   401  ILE  156.7   0.24  H    H   B1   -63.0   -43.7    0.99    0.01
 B   402  SER   70.2   0.55  H    H   P1   -68.9   -28.6    0.96    0.01
 B   403  ALA   13.4   0.85  H    H   E    -59.6   -24.2    0.96    0.01
 B   404  HIS   99.1   0.60  H    H   P2  -107.2    24.3    0.96    0.01
 B   405  SER   65.9   0.60  H    H   P2   -59.7   -20.1    0.99    0.15
 B   406  ASP    0.0   0.94  H    H   E    -70.0   -25.1    0.99    0.00
 B   407  GLN   31.8   0.73  H    H   E   -101.9   -45.0    0.99    0.00
 B   408  ASN  123.0   0.43  H    H   B2   -84.5   -18.0    0.99    0.07
 B   409  LYS   22.7   0.87  C    C   E     76.9     2.0    0.10    0.16
 B   410  MET  162.3   0.42  C    C   B2   -96.8    88.9    0.01    0.01
 B   411  THR   45.3   0.80  C    C   P2   -76.2   175.6    0.08    0.01
 B   412  ASN   81.7   0.57  H    H   P2   -61.1   -34.7    0.99    0.09
 B   413  THR   48.7   0.64  H    H   P2   -64.4   -46.6    0.99    0.01
 B   414  ASN   57.6   0.55  H    H   P1   -68.5   -32.7    0.99    0.01
 B   415  LEU  153.5   0.25  H    H   B1   -73.4   -39.4    0.99    0.09
 B   416  ALA   69.8   0.31  H    H   P1   -60.5   -37.3    0.99    0.09
 B   417  VAL   43.9   0.69  H    H   P2   -60.1   -52.2    0.99    0.01
 B   418  VAL   93.2   0.47  H    H   P1   -78.8   -21.7    0.99    0.01
 B   419  PHE  184.7   0.11  H    H   B1   -93.8   -34.4    0.99    0.09
 B   420  GLY   40.0   0.41  H    H   E    -36.9   -60.7    0.99    0.14
 B   421  PRO   81.4   0.60  H    H   P2   -64.4   -11.0    0.99    0.01
 B   422  ASN  120.4   0.32  H    H   B1   -91.3   -13.9    0.99    0.00
 B   423  LEU  146.2   0.23  H    H   B1   -99.7   -18.3    0.90    0.16
 B   424  LEU  154.0   0.22  C    C   B1  -165.8   143.5    0.12    0.00
 B   425  TRP  198.2   0.51  C    C   B3  -156.5   172.3    0.04    0.00
 B   426  ALA   62.5   0.41  C    C   P1  -105.4   170.4    0.13    0.00
 B   427  LYS    0.0   0.65  C    C   E    -65.2   -19.4    0.13    0.00
 B   428  ASP   55.7   0.50  C    C   P1  -129.9   144.6    0.13    0.00
 B   429  ALA    0.0   0.85  H    H   E    -57.1   -43.6    0.99    0.01
 B   430  ALA   12.9   0.67  H    H   E    -58.7   -45.1    0.99    0.01
 B   431  ILE   58.3   0.58  H    H   P2   -63.7   -39.7    0.99    0.01
 B   432  THR   92.8   0.42  H    H   P1   -63.4   -45.3    0.99    0.09
 B   433  LEU   29.0   0.70  H    H   E    -56.0   -38.1    0.98    0.11
 B   434  LYS   12.2   0.80  H    H   E    -68.0   -30.6    0.97    0.01
 B   435  ALA   66.7   0.33  H    H   P1  -101.2     5.5    0.89    0.09
 B   436  ILE  120.2   0.45  H    H   B2   -60.9   -35.7    0.99    0.11
 B   437  ASN    0.0   0.80  H    H   E    -70.4   -45.5    0.99    0.01
 B   438  PRO   96.5   0.50  H    H   P1   -63.1   -33.0    0.99    0.01
 B   439  ILE  154.6   0.35  H    H   B2   -65.8   -45.6    0.99    0.01
 B   440  ASN   97.0   0.47  H    H   P1   -71.1   -27.9    1.00    0.01
 B   441  THR   47.6   0.47  H    H   P1   -70.5   -39.0    1.00    0.01
 B   442  PHE  188.2   0.18  H    H   B1   -71.2   -33.4    1.00    0.01
 B   443  THR  111.1   0.26  H    H   P1   -67.0   -45.2    1.00    0.11
 B   444  LYS   80.1   0.70  H    H   P2   -62.9   -33.7    1.00    0.01
 B   445  PHE  143.5   0.36  H    H   B2   -69.0   -30.1    1.00    0.01
 B   446  LEU  152.6   0.13  H    H   B1   -70.6   -36.8    1.00    0.11
 B   447  LEU  152.8   0.27  H    H   B1   -77.8   -43.6    1.00    0.01
 B   448  ASP   60.8   0.61  H    H   P2   -63.0   -31.3    0.98    0.01
 B   449  HIS  107.1   0.55  T    C   P1  -119.6    27.1    0.38    0.01
 B   450  GLN  115.1   0.43  H    H   B2   -47.8   -46.4    1.00    0.09
 B   451  GLY    4.8   0.84  H    H   E    -67.1   -25.4    1.00    0.00
 B   452  GLU   21.9   0.62  H    H   E    -88.3   -21.2    1.00    0.00
 B   453  LEU  152.7   0.24  H    H   B1   -96.8   -34.3    1.00    0.09
 B   454  PHE  189.0   0.33  C    C   B1  -120.0   134.1    0.00    0.00
 B   455  PRO   11.4   0.83  C    C   E    -70.1     ?      0.00    0.00