Contacts of the strand formed by residues 85 - 89 (chain A) in PDB entry 1F15


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 TYR 85 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  ILE*     4.5     6.3    -      -       -      +
     83A  GLY      3.8     8.5    -      -       -      -
     84A  SER*     1.3   102.4    +      -       -      +
     86A  TYR*     1.3    63.1    +      -       -      +
    136A  VAL      4.9     3.0    -      -       -      +
    137A  ALA*     5.0    12.8    -      -       +      +
    139A  ILE*     3.4    22.1    -      -       +      +
    140A  SER*     3.5    40.3    +      -       -      -
    143A  PHE*     3.4    42.9    -      +       +      +
    144A  ALA*     6.1     0.2    -      -       -      +
    187A  VAL      3.5     5.2    -      -       -      +
    188A  TYR*     3.1    37.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  LEU*     3.4    38.5    -      -       +      +
     76A  LYS      4.9     0.3    +      -       -      -
     77A  PRO*     4.3     5.4    -      -       +      -
     78A  PRO*     3.3    40.2    -      -       +      +
     80A  ILE*     3.5    21.1    -      -       +      -
     85A  TYR*     1.3    78.2    -      -       -      +
     87A  GLY*     1.3    80.8    +      -       -      +
     88A  LYS*     3.5    17.6    -      -       +      +
    135A  SER      5.6     0.4    -      -       -      -
    139A  ILE*     3.3     7.7    -      -       -      +
    185A  VAL      5.6     0.2    -      -       -      -
    186A  LEU*     3.3     2.8    -      -       -      -
    187A  VAL*     2.8    37.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  TYR*     1.3    99.9    -      -       -      +
     88A  LYS*     1.3    67.4    +      -       -      +
    135A  SER*     4.3    17.1    +      -       -      -
    139A  ILE*     3.5    11.7    -      -       -      +
    185A  VAL      2.9    14.6    -      -       -      -
    186A  LEU*     4.3     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ILE*     4.7     9.7    -      -       -      +
     74A  THR      4.9     4.2    +      -       -      -
     75A  LEU*     4.1    31.6    -      -       +      +
     86A  TYR*     3.5    24.7    -      -       +      +
     87A  GLY*     1.3    74.0    -      -       -      +
     89A  ARG*     1.3    81.6    +      -       -      +
     90A  LEU*     5.7     0.2    -      -       -      +
     91A  LEU*     3.6    34.4    -      -       +      +
    135A  SER*     4.8     4.3    +      -       -      -
    184A  ALA*     3.2     5.6    -      -       -      +
    185A  VAL*     2.7    36.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LYS*     1.3    94.9    +      -       -      +
     90A  LEU*     1.3    65.4    +      -       -      +
     91A  LEU*     3.3    12.2    -      -       +      +
    128A  VAL*     3.6    35.5    +      -       -      +
    132A  SER*     3.5    42.6    +      -       -      +
    133A  ASP      4.1     0.8    -      -       -      +
    134A  LEU*     4.0    18.8    -      -       -      +
    135A  SER*     4.6     5.8    +      -       -      -
    181A  ARG      3.3    21.7    +      -       -      +
    182A  LYS*     4.4     4.6    +      -       -      +
    183A  TYR      3.2    20.6    -      -       -      +
    184A  ALA*     3.8     6.9    -      -       +      +
----------------------------------------------------------
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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