Contacts of the strand formed by residues 238 - 243 (chain A) in PDB entry 5FFO


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 ASP 238 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  VAL*     3.5     9.2    -      -       -      +
    229A  GLY      2.9    32.0    +      -       -      +
    230A  ASP*     3.4     0.9    -      -       -      +
    231A  PHE*     3.0    26.0    +      -       +      +
    232A  ASN*     2.5    31.0    +      -       -      +
    234A  ASP*     4.6     0.3    -      -       -      +
    236A  ILE*     3.1    13.1    -      -       -      +
    237A  ASP*     1.3    73.3    -      -       -      +
    239A  PHE*     1.3    65.4    +      -       -      +
    240A  VAL*     3.8     2.3    +      -       -      +
    255A  ILE*     4.9     2.2    -      -       +      -
    256A  TYR      3.5    10.3    -      -       -      +
    257A  ASP*     3.2    10.0    -      -       -      +
    258A  GLY*     3.1    20.9    +      -       -      +
    264A  LEU*     4.1     8.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  THR*     4.1    22.4    -      -       +      -
    168A  ARG*     4.8     4.3    -      -       -      -
    170A  LEU*     3.7    35.9    -      -       +      -
    183A  LEU*     4.4    12.3    -      -       +      -
    185A  SER*     3.1    38.1    -      -       -      -
    208A  LEU*     4.5     3.6    -      -       +      -
    227A  ALA      4.2     2.2    -      -       -      -
    228A  VAL*     4.8     2.2    -      -       +      -
    237A  ASP      4.1     6.7    -      -       -      -
    238A  ASP*     1.3    74.8    -      -       -      +
    240A  VAL*     1.3    61.8    +      -       -      +
    254A  TYR      3.9     0.9    -      -       -      +
    255A  ILE*     3.5     4.0    -      -       -      +
    256A  TYR*     2.9    42.2    +      -       +      +
    257A  ASP      4.1     3.4    -      -       -      -
    258A  GLY*     3.7    30.1    -      -       -      -
    261A  MET*     3.9    29.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  LEU*     4.7     0.7    -      -       -      +
    226A  VAL*     3.2     6.4    -      -       -      +
    227A  ALA*     2.9    47.4    +      -       +      +
    228A  VAL*     5.2     0.2    -      -       -      -
    231A  PHE*     3.5    35.7    -      -       +      -
    238A  ASP      4.4     2.7    -      -       -      +
    239A  PHE*     1.3    76.4    -      -       -      +
    241A  SER*     1.3    66.1    +      -       -      +
    253A  VAL*     3.8    22.2    -      -       +      -
    254A  TYR      3.8     2.5    -      -       -      -
    255A  ILE*     4.1    16.6    -      -       +      -
    280A  VAL*     4.8    11.9    -      -       +      -
    281A  ALA      6.0     1.1    -      -       -      +
    282A  ALA*     5.2     3.1    -      -       +      -
    293A  VAL*     4.5    15.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  LEU*     3.8    27.2    -      -       -      +
    222A  LEU*     4.0     7.2    -      -       -      -
    223A  GLY*     3.2    28.4    +      -       -      -
    225A  SER      2.7    19.3    +      -       -      -
    226A  VAL*     4.2     1.6    -      -       -      -
    240A  VAL*     1.3    78.1    -      -       -      +
    242A  GLY*     1.3    61.0    +      -       -      +
    243A  VAL*     3.9     1.6    -      -       -      +
    253A  VAL*     3.4     6.4    -      -       -      +
    254A  TYR      3.0    35.4    +      -       -      -
    280A  VAL*     4.7     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  TYR      3.5     8.5    -      -       -      +
    223A  GLY      3.7     0.9    +      -       -      -
    224A  TYR*     3.6    12.6    +      -       -      +
    225A  SER*     3.2    14.4    +      -       -      -
    241A  SER*     1.3    75.7    +      -       -      +
    243A  VAL*     1.3    62.0    +      -       -      +
    244A  PRO*     3.5    12.2    -      -       -      +
    252A  MET      3.7     5.6    -      -       -      -
    253A  VAL*     3.9    10.5    -      -       -      -
    277A  GLY      3.5    19.7    -      -       -      -
    280A  VAL*     4.3     3.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  SER*     3.2    26.5    -      -       -      +
    221A  TYR      3.9     0.2    -      -       -      -
    222A  LEU*     3.7    26.9    -      -       +      +
    241A  SER      3.9     4.7    -      -       -      +
    242A  GLY*     1.3    78.1    -      -       -      +
    244A  PRO*     1.3    64.2    -      -       -      +
    245A  ARG      3.3     1.1    -      -       -      -
    246A  ALA*     3.1    26.2    +      -       +      -
    252A  MET      2.6    34.2    +      -       -      +
    254A  TYR*     3.4    41.7    -      -       +      +
----------------------------------------------------------
 Back to top of page


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