Contacts of the strand formed by residues 85 - 89 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  PHE*     6.0     0.4    -      -       +      -
      8B  LEU*     5.6     0.2    -      -       +      -
     12B  LYS*     4.2    22.7    -      -       +      -
     13B  HIS      3.3     2.8    +      -       -      -
     14B  ILE*     3.6    15.6    -      -       +      +
     15B  ALA      3.0    26.2    +      -       -      +
     83B  ILE*     3.6     7.2    -      -       -      +
     84B  ASP*     1.3    86.7    -      -       +      +
     86B  LEU*     1.3    63.8    +      -       -      +
     87B  ILE*     4.0    23.1    -      -       +      -
    114B  ILE*     4.3     0.7    -      -       -      -
    115B  PRO*     3.5    27.1    -      -       +      +
    126B  ILE*     4.5     5.6    -      -       +      -
    132B  PHE*     4.1    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ALA*     3.9    23.1    -      -       +      +
     17B  VAL*     4.4    10.3    -      -       +      -
     74B  VAL*     4.4     9.9    -      -       +      -
     78B  ILE*     4.3     4.9    -      -       +      -
     83B  ILE*     5.3     0.4    -      -       +      -
     85B  VAL*     1.3    74.0    -      -       -      +
     87B  ILE*     1.3    68.0    +      -       -      +
     88B  PHE*     4.2    17.0    -      -       +      -
    105B  LEU*     4.2    20.6    -      -       +      -
    106B  LEU*     4.4     6.1    -      -       +      -
    109B  ALA*     3.9    17.5    -      -       +      -
    114B  ILE*     4.0    15.2    -      -       +      +
    115B  PRO      2.9     9.8    +      -       -      +
    116B  VAL*     3.3    23.4    -      -       +      -
    117B  ALA      2.8    31.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ILE*     4.0    10.5    -      -       +      -
     15B  ALA      3.0     8.6    +      -       -      +
     16B  LEU*     3.6    30.7    -      -       +      -
     17B  VAL*     2.9    26.2    +      -       -      +
     26B  LEU*     4.3    11.4    -      -       +      +
     29B  TRP*     4.4    22.9    -      -       +      -
     85B  VAL*     4.0    15.9    -      -       +      -
     86B  LEU*     1.3    79.9    -      -       -      +
     88B  PHE*     1.3    60.9    +      -       -      +
     89B  PHE*     4.0    28.0    -      -       +      -
    117B  ALA*     3.6    16.4    -      -       +      +
    123B  ALA*     4.5     7.4    -      -       +      +
    126B  ILE*     5.4     4.0    -      -       +      -
    132B  PHE*     6.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  VAL*     3.3    37.2    -      -       +      -
     18B  ALA      4.4     0.4    -      -       -      -
     19B  HIS*     4.0    23.3    -      +       -      -
     71B  ASP*     4.5     3.6    -      -       -      -
     86B  LEU*     3.9    16.5    -      -       +      -
     87B  ILE*     1.3    74.5    -      -       -      +
     89B  PHE*     1.3    63.2    +      -       -      +
     90B  TRP*     3.3    22.0    +      +       +      -
    102B  VAL*     3.8    34.5    -      -       +      -
    105B  LEU*     3.9    24.9    -      -       +      -
    106B  LEU*     4.1    24.0    -      -       +      -
    117B  ALA      2.8    12.3    +      -       -      +
    118B  THR*     3.2    22.5    -      -       -      -
    202B  PGA      4.0    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  VAL      2.9    12.1    +      -       -      +
     18B  ALA*     3.4     3.9    -      -       +      -
     19B  HIS      3.0    23.7    +      -       -      -
     22B  CYS*     3.3    21.9    -      -       +      +
     25B  MET*     4.2    14.1    -      -       -      -
     26B  LEU*     3.9    42.0    -      -       +      -
     29B  TRP*     4.5     7.9    -      +       +      -
     87B  ILE*     4.0    22.0    -      -       +      -
     88B  PHE*     1.3    75.1    -      -       -      +
     90B  TRP*     1.3    62.0    +      -       -      +
    117B  ALA      4.5     1.8    -      -       -      -
    118B  THR      3.8    13.5    -      -       -      -
    119B  ASN*     3.3    37.9    -      -       -      -
    120B  VAL*     3.7    23.1    -      -       +      -
    123B  ALA*     4.2     6.3    -      -       +      -
----------------------------------------------------------
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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