!amino acid radius file by dfs  2/3/93 
!last modification 7/94 to change charged resnames to default
!pauling radii to match Wolfendon's transfer energies of side chains   
!use with parseres.crg
atom__res_radius_
N     ALA   1.5
CA    ALA   2.0
HN    ALA   1.0
HA    ALA   0.0
C     ALA   1.7
O     ALA   1.4 
CB    ALA   2.0
HB1   ALA   0.0
HB2   ALA   0.0
HB3   ALA   0.0
N     AR0   1.5         ! neutral arginine
CA    AR0   2.0
HN    AR0   1.0
HA    AR0   0.0
C     AR0   1.7
O     AR0   1.4
CB    AR0   2.0
HB1   AR0   0.0
HB2   AR0   0.0
HB3   AR0   0.0
CG    AR0   2.0
HG1   AR0   0.0
HG2   AR0   0.0
CD    AR0   2.0
HD1   AR0   0.0
HD2   AR0   0.0
NE    AR0   1.5
CZ    AR0   1.7
HE    AR0   0.0
NH1   AR0   1.5
HH1   AR0   1.0
HH2   AR0   1.0
HH11  AR0   1.0
HH12  AR0   1.0
NH2   AR0   1.5
HH21  AR0   1.0
HH22  AR0   1.0
N     ARG   1.5        ! charged arginine
CA    ARG   2.0
HN    ARG   1.0
HA    ARG   0.0
C     ARG   1.7
O     ARG   1.4
CB    ARG   2.0
HB1   ARG   0.0
HB2   ARG   0.0
HB3   ARG   0.0
CG    ARG   2.0
HG1   ARG   0.0
HG2   ARG   0.0
CD    ARG   2.0
HD1   ARG   0.0
HD2   ARG   0.0
NE    ARG   1.5
CZ    ARG   1.7
NH1   ARG   1.5
NH2   ARG   1.5
HE    ARG   1.0
HH1   ARG   1.0
HH2   ARG   1.0
HH11  ARG   1.0
HH12  ARG   1.0
HH21  ARG   1.0
HH22  ARG   1.0
N     ASN   1.5
CA    ASN   2.0
HN    ASN   1.0
HA    ASN   0.0
C     ASN   1.7
O     ASN   1.4
CB    ASN   2.0
HB1   ASN   0.0
HB2   ASN   0.0
HB3   ASN   0.0
CG    ASN   1.7
OD1   ASN   1.4
ND2   ASN   1.5
HD1   ASN   1.0
HD2   ASN   1.0
HD21  ASN   1.0
HD22  ASN   1.0
N     AS0   1.5    ! aspartate neutral
CA    AS0   2.0
HN    AS0   1.0
HA    AS0   0.0
C     AS0   1.7
O     AS0   1.4
CB    AS0   2.0
HB1   AS0   0.0
HB2   AS0   0.0
HB3   AS0   0.0
CG    AS0   1.7
OD1   AS0   1.4
OD2   AS0   1.4
HD2   AS0   1.0
N     ASP   1.5    ! aspartate charged
CA    ASP   2.0
HN    ASP   1.0
HA    ASP   0.0
C     ASP   1.7
O     ASP   1.4
CB    ASP   2.0
HB1   ASP   0.0
HB2   ASP   0.0
HB3   ASP   0.0
CG    ASP   1.7
OD1   ASP   1.4
OD2   ASP   1.4
N     CYS   1.5
CA    CYS   2.0
HN    CYS   1.0
HA    CYS   0.0
C     CYS   1.7
O     CYS   1.4
CB    CYS   2.0
HB1   CYS   0.0
HB2   CYS   0.0
HB3   CYS   0.0
SG    CYS   1.85
HG    CYS   1.0
N     CSS   1.5           !cystine in disulfide bridge
CA    CSS   2.0
HN    CSS   1.0
HA    CSS   0.0
C     CSS   1.7
O     CSS   1.4
CB    CSS   2.0
HB1   CSS   0.0
HB2   CSS   0.0
HB3   CSS   0.0
SG    CSS   1.85
N     CY-   1.5
CA    CY-   2.0
HN    CY-   1.0
HA    CY-   0.0
C     CY-   1.7
O     CY-   1.4
CB    CY-   2.0
HB1   CY-   0.0
HB2   CY-   0.0
HB3   CY-   0.0
SG    CY-   1.85
N     GL0   1.5            ! neutral glutamic
CA    GL0   2.0
HN    GL0   1.0
HA    GL0   0.0
C     GL0   1.7
O     GL0   1.4
CB    GL0   2.0
HB1   GL0   0.0
HB2   GL0   0.0
HB3   GL0   0.0
CG    GL0   2.0
HG1   GL0   0.0
HG2   GL0   0.0
CD    GL0   1.7
OE1   GL0   1.4
OE2   GL0   1.4
HE2   GL0   1.0
N     GLU   1.5           ! charged glutamic
CA    GLU   2.0
HN    GLU   1.0
HA    GLU   0.0
C     GLU   1.7
O     GLU   1.4
CB    GLU   2.0
HB1   GLU   0.0
HB2   GLU   0.0
HB3   GLU   0.0
CG    GLU   2.0
HG1   GLU   0.0
HG2   GLU   0.0
CD    GLU   1.7
OE1   GLU   1.4
OE2   GLU   1.4
N     GLN   1.5
CA    GLN   2.0
HN    GLN   1.0
HA    GLN   0.0
C     GLN   1.7
O     GLN   1.4
CB    GLN   2.0
HB1   GLN   0.0
HB2   GLN   0.0
HB3   GLN   0.0
CG    GLN   2.0
HG1   GLN   0.0
HG2   GLN   0.0
CD    GLN   1.7
OE1   GLN   1.4
NE2   GLN   1.5
HE1   GLN   1.0
HE2   GLN   1.0
HE21  GLN   1.0
HE22  GLN   1.0
N     GLY   1.5
CA    GLY   2.0
HN    GLY   1.0
HA1   GLY   0.0
HA2   GLY   0.0
C     GLY   1.7
O     GLY   1.4
N     HIS   1.5
CA    HIS   2.0
HN    HIS   1.0
HA    HIS   0.0
C     HIS   1.7
O     HIS   1.4
CB    HIS   2.0
HB1   HIS   0.0
HB2   HIS   0.0
HB3   HIS   0.0
CG    HIS   1.7
ND1   HIS   1.5
CE1   HIS   1.7
NE2   HIS   1.5
CD2   HIS   1.7
HE1   HIS   1.0
HE2   HIS   1.0
HD2   HIS   1.0
N     HI+   1.5
CA    HI+   2.0
HN    HI+   1.0
HA    HI+   0.0
C     HI+   1.7
O     HI+   1.4
CB    HI+   2.0
CG    HI+   1.7
ND1   HI+   1.5
CE1   HI+   1.7
NE2   HI+   1.5
CD2   HI+   1.7
HB1   HI+   0.0
HB2   HI+   0.0
HB3   HI+   0.0
HD1   HI+   1.0
HE1   HI+   1.0
HE2   HI+   1.0
HD2   HI+   1.0
N     HID   1.5
CA    HID   2.0
HN    HID   1.0
HA    HID   0.0
C     HID   1.7
O     HID   1.4
CB    HID   2.0
HB1   HID   0.0
HB2   HID   0.0
HB3   HID   0.0
CG    HID   1.7
ND1   HID   1.5
CE1   HID   1.7
NE2   HID   1.5
CD2   HID   1.7
HD1   HID   1.0
HE1   HID   1.0
HD2   HID   1.0
N     ILE   1.5
CA    ILE   2.0
HN    ILE   1.0
HA    ILE   0.0
C     ILE   1.7
O     ILE   1.4
CB    ILE   2.0
HB    ILE   0.0
CG2   ILE   2.0
HG1   ILE   0.0
HG2   ILE   0.0
HG3   ILE   0.0
HG21  ILE   0.0
HG22  ILE   0.0
HG23  ILE   0.0
CG1   ILE   2.0
HG11  ILE   0.0
HG12  ILE   0.0
CD1   ILE   2.0
HD1   ILE   0.0
HD2   ILE   0.0
HD3   ILE   0.0
HD11  ILE   0.0
HD12  ILE   0.0
HD13  ILE   0.0
N     LEU   1.5
CA    LEU   2.0
HN    LEU   1.0
HA    LEU   0.0
C     LEU   1.7
O     LEU   1.4
CB    LEU   2.0
HB1   LEU   0.0
HB2   LEU   0.0
CG    LEU   2.0
HG    LEU   0.0
CD1   LEU   2.0
HD1   LEU   0.0
HD2   LEU   0.0
HD3   LEU   0.0
HD11  LEU   0.0
HD12  LEU   0.0
HD13  LEU   0.0
CD2   LEU   2.0
HD21  LEU   0.0
HD22  LEU   0.0
HD23  LEU   0.0
N     LY0   1.5            ! lysine neutral
CA    LY0   2.0
HN    LY0   1.0
HA    LY0   0.0
C     LY0   1.7
O     LY0   1.4
CB    LY0   2.0
HB1   LY0   0.0
HB2   LY0   0.0
HB3   LY0   0.0
CG    LY0   2.0
HG1   LY0   0.0
HG2   LY0   0.0
CD    LY0   2.0
HD1   LY0   0.0
HD2   LY0   0.0
CE    LY0   2.0
HE1   LY0   0.0
HE2   LY0   0.0
NZ    LY0   1.5
HZ1   LY0   1.0
HZ2   LY0   1.0
N     LYS   1.5           ! lysine charged
CA    LYS   2.0
HN    LYS   1.0
HA    LYS   0.0
C     LYS   1.7
O     LYS   1.4
CB    LYS   2.0
HB1   LYS   0.0
HB2   LYS   0.0
HB3   LYS   0.0
CG    LYS   2.0
HG1   LYS   0.0
HG2   LYS   0.0
CD    LYS   2.0
HD1   LYS   0.0
HD2   LYS   0.0
CE    LYS   2.0
HE1   LYS   0.0
HE2   LYS   0.0
NZ    LYS   2.0
HZ1   LYS   0.0
HZ2   LYS   0.0
HZ3   LYS   0.0
N     MET   1.5
CA    MET   2.0
HN    MET   1.0
HA    MET   0.0
C     MET   1.7
O     MET   1.4
CB    MET   2.0
HB1   MET   0.0
HB2   MET   0.0
HB3   MET   0.0
CG    MET   2.0
HG1   MET   0.0
HG2   MET   0.0
SD    MET   1.85
CE    MET   2.0
HE1   MET   0.0
HE2   MET   0.0
HE3   MET   0.0
N     PHE   1.5
CA    PHE   2.0
HN    PHE   1.0
HA    PHE   0.0
C     PHE   1.7
O     PHE   1.4
CB    PHE   2.0
HB1   PHE   0.0
HB2   PHE   0.0
HB3   PHE   0.0
CG    PHE   1.7
CD1   PHE   1.7
HD1   PHE   1.0
CE1   PHE   1.7
HE1   PHE   1.0
CZ    PHE   1.7
HZ    PHE   1.0
CE2   PHE   1.7
HE2   PHE   1.0
CD2   PHE   1.7
HD2   PHE   1.0
N     PRO   1.5
CA    PRO   2.0
HA    PRO   0.0
CD    PRO   2.0
HD1   PRO   0.0
HD2   PRO   0.0
C     PRO   1.7
O     PRO   1.4
CB    PRO   2.0
HB1   PRO   0.0
HB2   PRO   0.0
CG    PRO   2.0
HG1   PRO   0.0
HG2   PRO   0.0
N     SER   1.5
CA    SER   2.0
HN    SER   1.0
HA    SER   0.0
C     SER   1.7
O     SER   1.4
CB    SER   2.0
HB1   SER   0.0
HB2   SER   0.0
HB3   SER   0.0
OG    SER   1.4
HG    SER   1.0
N     THR   1.5
CA    THR   2.0
HN    THR   1.0
HA    THR   0.0
C     THR   1.7
O     THR   1.4
CB    THR   2.0
HB    THR   0.0
OG1   THR   1.4
HG1   THR   1.0
CG2   THR   2.0
HG2   THR   0.0
HG21  THR   0.0
HG22  THR   0.0
HG23  THR   0.0
N     TRP   1.5
CA    TRP   2.0
HN    TRP   1.0
HA    TRP   0.0
C     TRP   1.7
O     TRP   1.4
CB    TRP   2.0
HB1   TRP   0.0
HB2   TRP   0.0
HB3   TRP   0.0
CG    TRP   1.7
CD1   TRP   1.7
NE1   TRP   1.5
CE2   TRP   1.7
CD2   TRP   1.7
HD1   TRP   1.0
HE1   TRP   1.0
CE3   TRP   1.7
HE3   TRP   1.0
CZ3   TRP   1.7
HZ3   TRP   1.0
CH2   TRP   1.7
HH2   TRP   1.0
CZ2   TRP   1.7
HZ2   TRP   1.0
N     TYR   1.5
CA    TYR   2.0
HN    TYR   1.0
HA    TYR   0.0
C     TYR   1.7
O     TYR   1.4
CB    TYR   2.0
HB1   TYR   0.0
HB2   TYR   0.0
HB3   TYR   0.0
CG    TYR   1.7
CD1   TYR   1.7
HD1   TYR   1.0
CE1   TYR   1.7
HE1   TYR   1.0
CZ    TYR   1.7
OH    TYR   1.4
HH    TYR   1.0
CE2   TYR   1.7
HE2   TYR   1.0
CD2   TYR   1.7
HD2   TYR   1.0
N     TY-   1.5
CA    TY-   2.0
HN    TY-   1.0
HA    TY-   0.0
C     TY-   1.7
O     TY-   1.4
CB    TY-   2.0
HB1   TY-   0.0
HB2   TY-   0.0
HB3   TY-   0.0
CG    TY-   1.7
CD1   TY-   1.7
HD1   TY-   1.0
CE1   TY-   1.7
HE1   TY-   1.0
CZ    TY-   1.7
OH    TY-   1.4
CE2   TY-   1.7
HE2   TY-   1.0
CD2   TY-   1.7
HD2   TY-   1.0
N     VAL   1.5
CA    VAL   2.0
HN    VAL   1.0
HA    VAL   0.0
C     VAL   1.7
O     VAL   1.4
CB    VAL   2.0
HB    VAL   0.0
CG1   VAL   2.0
HG1   VAL   0.0
HG2   VAL   0.0
HG3   VAL   0.0
HG11  VAL   0.0
HG12  VAL   0.0
HG13  VAL   0.0
CG2   VAL   2.0
HG21  VAL   0.0
HG22  VAL   0.0
HG23  VAL   0.0
CA    ACE   2.0      !neutral N-cap
HA1   ACE   0.0
HA2   ACE   0.0
HA3   ACE   0.0
C     ACE   1.7
O     ACE   1.4
N     N-M   1.5      !neutral C-cap
CA    N-M   2.0
HN1   N-M   1.0
H1    N-M   1.0
HA1   N-M   0.0
HA2   N-M   0.0
HA3   N-M   0.0
N     BKN   1.5      !neutral N-terminus
CA    BKN   2.0
HN1   BKN   1.0
HN2   BKN   1.0
H1    BKN   1.0
H2    BKN   1.0
HA    BKN   0.0
C     BKN   1.7
O     BKN   1.4
N     BK+   2.0      !charged N-terminus
CA    BK+   2.0
HN1   BK+   0.0
HN2   BK+   0.0
HN3   BK+   0.0
H1    BK+   0.0
H2    BK+   0.0
H3    BK+   0.0
HA    BK+   0.0
C     BK+   1.7
O     BK+   1.4
N     BKC   1.5      !neutral C-terminus
HN    BKC   1.0
CA    BKC   2.0
HA    BKC   0.0
C     BKC   1.7
O1    BKC   1.4
O2    BKC   1.4
H2    BKC   1.0
N     BK-   1.5      !charged C-terminus
HN    BK-   1.0
CA    BK-   2.0
HA    BK-   0.0
C     BK-   1.7
O1    BK-   1.4
O2    BK-   1.4
N     PRN   1.5      !N-terminal proline, neutral
HN    PRN   1.0
CA    PRN   2.0
HA    PRN   0.0
CD    PRN   2.0
HD1   PRN   0.0
HD2   PRN   0.0
C     PRN   1.7
O     PRN   1.4
CB    PRN   2.0
HB1   PRN   0.0
HB2   PRN   0.0
CG    PRN   2.0
HG1   PRN   0.0
HG2   PRN   0.0
N     PR+   2.0      !N-terminal proline, charged
HN1   PR+   0.0
HN2   PR+   0.0
H1    PR+   0.0
H2    PR+   0.0
CA    PR+   2.0
HA    PR+   0.0
CD    PR+   2.0
HD1   PR+   0.0
HD2   PR+   0.0
C     PR+   1.7
O     PR+   1.4
CB    PR+   2.0
HB1   PR+   0.0
HB2   PR+   0.0
CG    PR+   2.0
HG1   PR+   0.0
HG2   PR+   0.0
OH    H2O   1.4
HH1   H2O   1.0
HH2   H2O   1.0
