Contacts of the strand formed by residues 3 - 8 (chain A) in PDB entry 1S0O


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 VAL 3 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     3.2    39.7    -      -       +      -
      2A  ILE*     1.3    78.3    -      -       -      +
      4A  LEU*     1.3    64.0    +      -       -      +
      5A  PHE      4.1     0.2    -      -       -      -
    108A  TYR*     4.0    22.2    -      -       +      -
    109A  LEU      3.5     8.7    -      -       -      +
    110A  ASP*     5.1     0.7    -      -       -      -
    143A  GLY      3.7     0.5    -      -       -      +
    144A  ILE*     3.2    10.2    -      -       -      +
    145A  SER      2.9    36.0    +      -       -      +
    147A  ASN*     3.9    14.8    -      -       -      +
    148A  LYS*     4.2     6.7    -      -       +      -
    151A  ALA*     3.9    15.8    -      -       +      +
    237A  ILE*     3.8    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 4 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  VAL*     1.3    74.5    -      -       -      +
      5A  PHE*     1.3    57.2    +      -       -      +
      6A  VAL*     3.6    26.2    -      -       +      -
    108A  TYR      3.6     0.2    -      -       -      -
    109A  LEU*     2.7    48.6    +      -       +      +
    111A  ILE*     3.8    32.1    -      -       +      -
    121A  ALA      4.1     8.5    -      -       -      +
    124A  LEU*     4.5     4.5    -      -       +      -
    125A  GLY*     4.0    23.8    -      -       -      +
    128A  ILE*     4.1    21.1    -      -       +      -
    142A  VAL*     3.7    22.7    -      -       +      -
    143A  GLY      3.4     3.1    -      -       -      -
    144A  ILE*     3.9     6.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 5 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  VAL      4.1     0.2    -      -       -      -
      4A  LEU*     1.3    73.3    -      -       -      +
      6A  VAL*     1.3    61.7    +      -       -      +
      7A  ASP*     3.7    21.3    -      -       +      -
    106A  GLU*     3.6    49.4    -      -       +      -
    107A  ALA      3.4    14.4    -      -       -      -
    108A  TYR*     3.2    45.8    -      +       +      +
    141A  THR      3.7     0.7    -      -       -      +
    142A  VAL*     3.3     6.1    -      -       -      +
    143A  GLY      2.8    37.7    +      -       -      +
    151A  ALA*     3.8    11.9    -      -       +      +
    152A  LYS*     3.7    28.3    -      -       +      -
    155A  ALA*     3.6    26.9    -      -       +      -
    156A  ASP*     5.5     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 6 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     3.6    22.2    -      -       +      -
      5A  PHE*     1.3    80.4    -      -       -      +
      7A  ASP*     1.3    62.9    +      -       -      +
      8A  PHE*     3.9    16.7    -      -       +      -
     92A  LEU*     4.2    28.0    -      -       +      -
    106A  GLU*     2.9     7.5    -      -       -      +
    107A  ALA      2.8    37.6    +      -       -      +
    109A  LEU*     4.7     2.7    -      -       +      -
    128A  ILE*     4.5     3.6    -      -       +      -
    132A  ILE*     4.6     7.2    -      -       +      -
    140A  VAL*     3.8    31.4    -      -       +      -
    141A  THR      3.5     3.4    -      -       -      +
    142A  VAL*     4.3     7.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 7 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PHE*     3.7    21.0    -      -       +      -
      6A  VAL*     1.3    74.2    -      -       -      +
      8A  PHE*     1.3    63.7    +      -       -      +
      9A  ASP*     3.6     0.7    +      -       -      +
    105A  ASP*     2.9     9.0    -      -       -      +
    106A  GLU*     3.6     7.1    -      -       -      +
    140A  VAL*     4.2     0.2    -      -       -      -
    141A  THR*     2.9    34.3    +      -       -      +
    152A  LYS*     4.4     4.3    +      -       -      -
    155A  ALA*     4.9     4.3    -      -       +      -
    156A  ASP*     4.9     0.5    -      -       -      +
    159A  LYS*     3.1    26.7    +      -       -      +
    401A   CA      2.8    23.9    -      -       -      -
    402A   CA      2.3    29.3    -      -       -      -
    803A  TTP      4.4     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 8 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     3.9    19.5    -      -       +      -
      7A  ASP*     1.3    72.4    +      -       -      +
      9A  ASP*     1.3    60.5    +      -       -      +
     11A  PHE*     3.6    35.3    +      +       +      -
     85A  SER*     4.0     6.7    -      -       -      -
     88A  ILE*     3.4    41.1    -      -       +      -
     89A  MET*     3.7    24.0    -      -       +      -
     92A  LEU*     4.8     3.1    -      -       +      -
    104A  ILE      3.8     8.1    -      -       -      -
    105A  ASP*     2.8    41.9    +      -       +      +
    138A  ILE*     4.6     3.1    -      -       +      -
    139A  THR      4.5     1.1    -      -       -      +
    140A  VAL*     3.5    24.0    -      -       +      -
    402A   CA      2.3    31.7    -      -       -      -
    803A  TTP      3.5     1.1    +      -       -      -
----------------------------------------------------------
 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