Contacts of the strand formed by residues 179 - 189 (chain C) in PDB entry 4IJ3


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LEU 179 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119C  ALA*     4.6     5.8    -      -       +      -
    122C  THR*     4.1    18.2    -      -       +      +
    149C  GLY*     3.2    35.7    -      -       -      +
    150C  TYR      3.8     3.8    -      -       -      +
    151C  PHE*     3.6    27.6    -      -       +      -
    175C  LEU*     3.6     3.1    -      -       -      -
    176C  GLU*     2.7    38.7    +      -       -      +
    177C  SER*     2.8    11.3    +      -       -      +
    178C  ASP*     1.3    83.3    -      -       +      +
    180C  TYR*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 180 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  THR*     3.4    27.8    -      -       +      +
    117C  SER*     5.8     0.5    -      -       -      -
    149C  GLY      3.0    16.8    +      -       -      -
    150C  TYR*     2.8    50.4    +      -       +      +
    151C  PHE*     3.8    26.6    -      +       -      -
    152C  PRO*     4.2     1.6    -      -       +      -
    153C  GLU*     3.8    51.3    +      -       +      -
    173C  ALA*     4.3     5.2    -      -       +      -
    174C  VAL*     3.5    10.8    -      -       -      -
    175C  LEU*     3.5    37.3    -      -       +      +
    179C  LEU*     1.3    71.3    -      -       -      +
    181C  THR*     1.3    67.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 181 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160B  LEU*     5.7     0.7    -      -       +      -
    178B  THR*     6.1     3.4    -      -       +      -
    146C  LEU*     4.1    16.2    -      -       +      -
    147C  VAL      3.3    16.8    -      -       -      +
    148C  LYS*     3.5    17.4    -      -       +      +
    149C  GLY*     3.3    11.8    +      -       -      -
    150C  TYR*     4.3     0.2    -      -       -      -
    172C  PRO      4.6     0.3    -      -       -      +
    173C  ALA*     3.6     1.3    -      -       -      -
    174C  VAL*     3.0    42.4    +      -       +      +
    176C  GLU*     3.1    29.4    +      -       -      +
    179C  LEU      4.4     0.5    +      -       -      -
    180C  TYR*     1.3    81.2    +      -       -      +
    182C  LEU*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 182 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146C  LEU*     3.5     6.3    -      -       -      +
    147C  VAL*     2.9    47.9    +      -       +      +
    150C  TYR*     3.4    21.5    -      -       -      +
    153C  GLU*     5.5     0.9    -      -       -      +
    155C  VAL*     3.5    18.8    -      -       +      +
    157C  VAL*     4.3     6.7    -      -       +      -
    170C  THR*     4.0    20.0    -      -       +      -
    171C  PHE      3.5    21.3    -      -       -      +
    172C  PRO      4.2     2.5    -      -       -      +
    173C  ALA*     3.7    13.9    -      -       +      +
    181C  THR*     1.3    76.5    -      -       -      +
    183C  SER*     1.3    92.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 183 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  VAL*     4.9     5.2    -      -       -      -
    135B  PHE*     4.0    14.4    -      -       -      -
    162B  SER*     6.0     0.2    -      -       -      -
    176B  SER*     3.0    27.5    +      -       -      -
    178B  THR*     4.7     3.2    +      -       -      -
    129C  LEU*     5.0     0.2    -      -       -      -
    145C  CYS      3.2    13.5    -      -       -      -
    146C  LEU*     4.0    13.5    -      -       -      -
    170C  THR*     3.7     0.2    -      -       -      -
    171C  PHE*     2.9    34.5    +      -       -      +
    182C  LEU*     1.3    84.5    -      -       -      +
    184C  SER*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 184 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  PHE*     3.6     5.5    -      -       -      -
    144C  GLY*     3.1     3.3    -      -       -      -
    145C  CYS*     2.9    34.6    +      -       -      +
    157C  VAL*     3.9    22.5    -      -       -      +
    159C  TRP*     3.0    25.6    +      -       -      -
    168C  VAL*     3.6     4.5    -      -       -      +
    169C  HIS      3.2     5.3    +      -       -      -
    170C  THR*     3.0    27.4    +      -       -      -
    182C  LEU*     4.3     0.4    -      -       -      +
    183C  SER*     1.3    75.4    -      -       -      +
    185C  SER*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 185 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  PHE*     3.3    39.5    -      -       -      -
    137B  ASN*     3.2    22.7    +      -       -      -
    142C  THR*     4.3     3.5    -      -       -      +
    143C  LEU      3.4     5.8    -      -       -      -
    159C  TRP*     4.4     0.2    -      -       -      -
    167C  GLY      5.1     0.3    +      -       -      -
    168C  VAL*     3.2     5.2    -      -       -      +
    169C  HIS*     2.7    50.1    +      -       -      +
    171C  PHE*     4.2     0.2    -      -       -      -
    184C  SER*     1.3    75.6    +      -       -      +
    186C  VAL*     1.3    60.8    +      -       -      +
    187C  THR*     5.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 186 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141C  VAL      4.1     0.2    -      -       -      +
    142C  THR*     3.5     1.4    -      -       -      +
    143C  LEU*     3.0    47.1    +      -       +      +
    159C  TRP*     3.7    39.9    -      -       +      +
    164C  LEU*     4.0    25.8    -      -       +      -
    166C  SER      4.6     1.8    -      -       -      +
    167C  GLY      3.3     6.1    -      -       -      +
    168C  VAL*     3.7    21.3    -      -       +      -
    185C  SER*     1.3    76.1    -      -       -      +
    187C  THR*     1.3    69.4    +      -       -      +
    188C  VAL*     4.3     8.2    -      -       +      +
    198C  VAL*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 187 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  ASN*     4.9     6.2    +      -       -      -
    140C  MET*     3.5    34.7    -      -       +      +
    141C  VAL      3.4    10.3    -      -       -      +
    142C  THR*     3.0    24.6    +      -       -      +
    166C  SER      4.5     9.0    -      -       -      +
    167C  GLY*     3.0    21.0    +      -       -      +
    185C  SER*     5.4     0.3    +      -       -      -
    186C  VAL*     1.3    77.4    -      -       -      +
    188C  VAL*     1.3    69.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 188 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140C  MET*     3.4     8.5    -      -       -      +
    141C  VAL*     2.7    54.6    +      -       +      +
    143C  LEU*     4.9     5.6    -      -       +      -
    164C  LEU*     4.0    36.8    -      -       +      -
    186C  VAL*     4.5     6.7    -      -       +      +
    187C  THR*     1.3    80.6    -      -       -      +
    189C  PRO*     1.3    71.0    -      -       +      +
    192C  THR*     3.5    14.1    -      -       -      +
    193C  TRP*     4.1    13.5    -      -       +      -
    198C  VAL*     4.8    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 189 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  SER      3.5     9.6    -      -       -      +
    140C  MET*     3.6    15.0    -      -       +      -
    141C  VAL*     4.2     0.2    -      -       -      -
    188C  VAL*     1.3    92.8    -      -       +      +
    190C  SER*     1.3    53.9    +      -       -      +
    191C  SER*     3.0    19.5    -      -       -      +
    192C  THR*     2.5    50.5    +      -       +      +
    193C  TRP      3.6     2.8    +      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il