Contacts of the strand formed by residues 181 - 188 (chain F) in PDB entry 1I3R


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 PHE 181 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27E  ASP      5.6     0.7    -      -       -      -
     29E  ASP*     4.8     1.1    -      -       -      -
    147F  ASP*     2.9    24.8    +      -       -      -
    148F  PHE*     3.1    42.6    +      -       +      -
    149F  TYR*     4.0    20.0    -      +       -      -
    150F  PRO      3.9     2.0    -      -       -      -
    151F  GLY*     3.4    33.2    -      -       -      -
    173F  LEU*     3.6    30.5    -      -       +      -
    174F  VAL      3.2    15.0    -      -       -      -
    175F  ARG*     3.7    49.6    -      -       +      -
    176F  ASN*     3.5     5.2    +      -       -      -
    179F  TRP      5.6     0.4    -      -       -      -
    180F  THR*     1.3    76.1    -      -       -      +
    182F  GLN*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 182 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  LEU*     3.7    16.6    -      -       -      +
     93E  SER*     2.9    29.6    +      -       -      +
     94E  ARG*     3.0    14.4    +      -       -      +
     95E  SER*     4.7     4.2    +      -       -      -
     96E  PRO*     5.5     1.2    -      -       -      +
    145F  VAL      3.4     7.6    -      -       -      -
    146F  SER*     4.1    15.9    -      -       -      -
    147F  ASP      4.7     0.2    -      -       -      +
    148F  PHE*     4.0     1.3    -      -       -      -
    173F  LEU*     4.2     0.3    -      -       -      -
    174F  VAL*     2.9    47.4    +      -       +      +
    176F  ASN*     2.8    29.7    +      -       -      +
    181F  PHE*     1.3    77.3    -      -       -      +
    183F  THR*     1.3    65.6    +      -       -      +
    184F  LEU*     5.7     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 183 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144F  SER*     4.4     0.3    +      -       -      -
    145F  VAL*     3.0    57.0    +      -       +      +
    148F  PHE*     3.8    14.4    -      -       +      -
    153F  ILE*     4.8     9.9    -      -       +      -
    155F  VAL*     5.2     0.2    -      -       +      -
    170F  SER*     3.7     9.7    +      -       -      -
    171F  THR*     3.8     6.7    -      -       -      -
    172F  GLY      3.1    21.9    +      -       -      -
    173F  LEU*     4.6     3.6    -      -       +      -
    174F  VAL*     5.1     0.2    -      -       -      -
    182F  GLN*     1.3    82.1    +      -       -      +
    184F  LEU*     1.3    80.5    +      -       -      +
    185F  VAL*     4.4    10.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 184 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96E  PRO*     6.0     0.4    -      -       +      -
    128F  TYR*     4.1    10.8    -      -       -      +
    142F  VAL*     3.8    11.4    -      -       +      -
    143F  CYS      3.8     1.8    -      -       -      -
    144F  SER*     3.6    29.2    -      -       -      +
    170F  SER*     3.1     7.1    +      -       -      -
    171F  THR*     3.0    51.0    +      -       +      +
    182F  GLN*     5.7     4.0    -      -       -      +
    183F  THR*     1.3    87.5    +      -       -      +
    185F  VAL*     1.3    62.5    +      -       -      +
    186F  MET*     3.8    25.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 185 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143F  CYS*     3.1    24.6    +      -       -      +
    155F  VAL*     3.7    48.7    -      -       +      +
    157F  TRP*     2.9    28.3    +      -       +      +
    168F  ILE*     4.0    24.0    -      -       +      -
    169F  VAL      3.5     4.3    -      -       -      +
    170F  SER*     4.2    12.8    -      -       -      +
    183F  THR*     4.4    10.5    -      -       +      +
    184F  LEU*     1.3    73.5    -      -       -      +
    186F  MET*     1.3    59.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 186 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128F  TYR*     5.6     0.2    -      -       -      +
    130F  THR*     5.2     1.8    -      -       +      +
    140F  LEU*     3.7    34.8    -      -       +      -
    141F  LEU      3.3     4.9    -      -       -      +
    142F  VAL*     3.4    34.1    -      -       +      -
    157F  TRP*     3.9     1.8    -      -       -      -
    167F  GLY      3.5     0.7    -      -       -      +
    168F  ILE*     3.4     6.6    -      -       -      +
    169F  VAL*     2.6    47.9    +      -       +      +
    171F  THR*     5.2     2.7    -      -       +      -
    184F  LEU*     4.1    32.8    -      -       +      +
    185F  VAL*     1.3    76.7    -      -       -      +
    187F  LEU*     1.3    60.2    +      -       -      +
    188F  GLU      4.1     0.2    -      -       -      -
    313G  NAG      5.9     2.5    -      -       -      -
     20H  VAL*     4.9    16.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 187 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140F  LEU*     3.0     4.2    -      -       -      +
    141F  LEU*     2.8    37.1    +      -       +      +
    157F  TRP*     3.7    40.1    -      -       +      +
    158F  PHE      5.4     0.4    -      -       -      +
    164F  GLU*     4.2    17.9    -      -       +      -
    166F  THR      3.9    11.4    -      -       -      +
    167F  GLY      3.4     3.6    -      -       -      +
    168F  ILE*     3.4    21.8    -      -       +      -
    186F  MET*     1.3    74.1    -      -       -      +
    188F  GLU*     1.3    64.0    +      -       -      +
    189F  THR*     3.5    26.2    +      -       +      +
    197F  TYR*     4.0    27.8    -      -       +      -
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Residues in contact with GLU 188 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138F  HIS*     5.9     5.4    -      -       +      -
    139F  ASN      4.3     3.4    -      -       -      +
    140F  LEU*     3.4    22.2    -      -       +      +
    166F  THR      5.2     0.2    -      -       -      +
    167F  GLY*     2.7    41.0    +      -       -      +
    169F  VAL*     3.3    28.4    -      -       +      +
    187F  LEU*     1.3    70.7    -      -       -      +
    189F  THR*     1.3    70.1    +      -       -      +
    313G  NAG      4.6     8.8    -      -       -      +
----------------------------------------------------------
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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