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)
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
PrHel- Probability of helix
PrBet- Probability of beta bridge
ResN Nam Ab Fp SS PDBSS Env PrHel PrBet
A 1 VAL 79.1 0.35 C C P1 0.00 0.00
A 2 ALA 26.2 0.60 C C E 0.00 0.09
A 3 ILE 157.0 0.23 E C B1 0.13 0.88
A 4 LYS 105.5 0.72 E C P2 0.13 0.88
A 5 MET 172.0 0.30 E C B1 0.13 0.88
A 6 GLY 40.0 0.37 C C E 0.13 0.16
A 7 ALA 64.5 0.47 C C P1 0.13 0.00
A 8 ASP 54.5 0.77 T C P2 0.08 0.00
A 9 ASN 36.7 0.57 T C E 0.08 0.00
A 10 GLY 14.0 0.53 C C E 0.07 0.00
A 11 MET 33.1 0.80 C C E 0.13 0.00
A 12 LEU 97.5 0.49 C C P1 0.13 0.01
A 13 ALA 53.7 0.47 C C P1 0.13 0.07
A 14 PHE 188.1 0.34 C C B2 0.13 0.88
A 15 GLU 96.0 0.54 C C P1 0.13 0.88
A 16 PRO 66.5 0.56 C C P1 0.13 0.00
A 17 SER 34.9 0.81 C C E 0.13 0.00
A 18 THR 57.7 0.63 E E P2 0.13 0.86
A 19 ILE 139.9 0.29 E E B1 0.13 0.86
A 20 GLU 87.9 0.51 E E P1 0.13 0.88
A 21 ILE 157.0 0.35 E E B2 0.13 0.88
A 22 GLN 45.2 0.80 C E P2 0.16 0.00
A 23 ALA 47.2 0.56 T C P1 0.16 0.16
A 24 GLY 21.5 0.61 T C E 0.16 0.00
A 25 ASP 70.7 0.46 C C P1 0.16 0.30
A 26 THR 63.0 0.71 E E P2 0.13 0.88
A 27 VAL 129.9 0.24 E E B1 0.13 0.88
A 28 GLN 95.7 0.50 E E P1 0.13 0.88
A 29 TRP 234.0 0.16 E E B1 0.13 0.90
A 30 VAL 112.0 0.42 E E P1 0.13 0.90
A 31 ASN 122.7 0.41 E E B2 0.26 0.88
A 32 ASN 90.0 0.54 C C P1 0.26 0.00
A 33 LYS 91.2 0.71 C C P2 0.26 0.01
A 34 LEU 38.7 0.66 C C E 0.13 0.00
A 35 ALA 56.4 0.64 C C P2 0.13 0.01
A 36 PRO 70.4 0.47 C C P1 0.13 0.00
A 37 HIS 175.0 0.30 E C B1 0.13 0.90
A 38 ASN 117.8 0.37 E C B2 0.13 0.17
A 39 VAL 130.0 0.18 E C B1 0.13 0.88
A 40 VAL 111.6 0.48 E C P1 0.13 0.87
A 41 VAL 129.2 0.24 E C B1 0.13 0.87
A 42 GLU 51.1 0.68 T C P2 0.08 0.17
A 49 GLY 0.0 0.77 T C E 0.08 0.09
A 52 GLN 104.9 0.50 C C P1 0.22 0.30
A 53 PRO 0.0 0.86 G H E 0.96 0.00
A 54 GLU 50.1 0.69 G H P2 0.96 0.00
A 55 LEU 144.4 0.34 G H B2 0.96 0.00
A 56 SER 81.2 0.40 C C P1 0.07 0.00
A 57 HIS 111.3 0.53 E C P1 0.13 0.88
A 58 LYS 10.1 0.81 E C E 0.13 0.00
A 59 ASP 0.0 0.82 E C E 0.13 0.00
A 62 LEU 83.4 0.49 E C P1 0.13 0.17
A 63 ALA 70.5 0.46 E C P1 0.26 0.90
A 64 PHE 20.5 0.67 C C E 0.26 0.01
A 65 SER 22.2 0.74 C C E 0.26 0.00
A 66 PRO 10.6 0.83 T C E 0.34 0.17
A 67 GLY 21.1 0.56 T C E 0.34 0.00
A 68 GLU 102.2 0.56 C C P1 0.34 0.09
A 69 THR 73.7 0.54 E E P1 0.13 0.90
A 70 PHE 165.9 0.41 E E B2 0.13 0.90
A 71 GLU 83.4 0.56 E E P1 0.13 0.88
A 72 ALA 58.9 0.46 E E P1 0.13 0.88
A 73 THR 57.1 0.67 E E P2 0.13 0.88
A 74 PHE 188.9 0.22 C C B1 0.13 0.30
A 75 SER 27.9 0.59 C C E 0.13 0.00
A 76 GLU 0.0 0.86 C C E 0.13 0.00
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