Contacts of the strand formed by residues 85 - 89 (chain F) in PDB entry 1S89


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 85 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125C  PHE*     6.3     0.2    -      -       +      -
     12F  LYS*     4.2    23.6    -      -       +      -
     13F  HIS      3.3     2.8    +      -       -      -
     14F  ILE*     4.1    17.3    -      -       +      -
     15F  ALA      3.0    24.3    +      -       -      -
     83F  ILE*     3.3     9.6    -      -       -      +
     84F  ASP*     1.3    85.2    -      -       +      +
     86F  LEU*     1.3    65.2    +      -       -      +
     87F  ILE*     4.0    24.5    -      -       +      -
    114F  ILE*     4.4     1.3    -      -       -      -
    115F  PRO*     3.6    25.1    -      -       +      +
    126F  ILE*     4.8     3.6    -      -       +      -
    132F  PHE*     4.2    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 86 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15F  ALA*     3.7    24.5    -      -       +      +
     17F  VAL*     4.4     9.6    -      -       +      -
     74F  VAL*     4.3    12.1    -      -       +      -
     78F  ILE*     4.3     6.5    -      -       +      -
     85F  VAL*     1.3    75.5    -      -       -      +
     87F  ILE*     1.3    65.8    +      -       -      +
     88F  PHE*     4.1    20.9    -      -       +      -
    105F  LEU*     4.2    20.9    -      -       +      -
    106F  LEU*     4.5     5.4    -      -       +      -
    109F  ALA*     3.9    22.7    -      -       +      -
    114F  ILE*     4.3    12.3    -      -       +      +
    115F  PRO      3.0    10.1    +      -       -      +
    116F  VAL*     3.3    16.3    -      -       +      -
    117F  ALA      2.8    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 87 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14F  ILE*     4.0     9.9    -      -       +      -
     15F  ALA      3.0     8.8    +      -       -      +
     16F  LEU*     3.6    24.9    -      -       +      -
     17F  VAL*     2.9    26.2    +      -       -      +
     26F  LEU*     4.2    15.8    -      -       +      +
     29F  TRP*     4.3    22.7    -      -       +      -
     85F  VAL*     4.0    15.3    -      -       +      -
     86F  LEU*     1.3    78.9    -      -       -      +
     88F  PHE*     1.3    59.1    +      -       -      +
     89F  PHE*     3.5    33.0    -      -       +      -
    117F  ALA*     3.6    17.3    -      -       +      +
    123F  ALA*     4.6     6.7    -      -       +      +
    126F  ILE*     5.4     6.1    -      -       +      -
    132F  PHE*     6.3     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 88 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17F  VAL*     3.1    31.2    -      -       +      -
     18F  ALA      4.6     0.2    -      -       -      -
     19F  HIS*     3.9    25.6    -      +       -      -
     71F  ASP*     4.4     1.8    -      -       -      -
     86F  LEU*     3.8    18.5    -      -       +      -
     87F  ILE*     1.3    75.3    -      -       -      +
     89F  PHE*     1.3    61.5    +      -       -      +
     90F  TRP*     3.1    34.0    +      -       +      -
    102F  VAL*     3.9    28.9    -      -       +      -
    105F  LEU*     3.5    30.1    -      -       +      -
    106F  LEU*     4.3    20.4    -      -       +      -
    116F  VAL*     5.6     0.2    -      -       +      -
    117F  ALA      2.8    11.3    +      -       -      +
    118F  THR*     3.3    18.5    -      -       -      -
    206F  PGA      4.0     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 89 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17F  VAL      2.9     8.6    +      -       -      -
     18F  ALA*     3.5     5.8    -      -       +      -
     19F  HIS      3.1    22.3    +      -       -      -
     22F  CYS*     3.3    20.7    -      -       +      +
     25F  MET*     4.1    13.2    -      -       +      -
     26F  LEU*     3.8    38.8    -      -       +      -
     29F  TRP*     4.5     7.6    -      +       +      -
     87F  ILE*     3.5    24.7    -      -       +      -
     88F  PHE*     1.3    75.5    -      -       -      +
     90F  TRP*     1.3    59.7    +      -       -      +
    117F  ALA      4.3     2.2    -      -       -      -
    118F  THR      4.1     5.8    -      -       -      +
    119F  ASN*     3.6    31.0    -      -       -      -
    120F  VAL*     3.7    36.1    -      -       +      -
    123F  ALA*     4.0    11.4    -      -       +      -
----------------------------------------------------------
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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