Contacts of the strand formed by residues 115 - 119 (chain A) in PDB entry 3EYF


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 SER 115 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  ALA      4.0     0.6    +      -       -      -
    114A  PRO*     1.3    73.3    -      -       -      +
    116A  VAL*     1.3    59.7    +      -       -      +
    117A  PHE*     3.6    26.5    -      -       -      -
    136A  LEU      3.3     4.0    -      -       -      +
    137A  LEU*     3.4     1.7    -      -       -      -
    138A  ASN*     2.9    40.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  PRO*     3.9    21.7    +      -       +      +
    115A  SER*     1.3    77.2    -      -       -      +
    117A  PHE*     1.3    72.7    +      -       -      +
    135A  CYS*     3.9    20.0    -      -       -      -
    136A  LEU      3.3     8.1    -      -       -      +
    137A  LEU*     4.4     2.9    -      -       +      -
    195A  CYS*     4.6     3.1    -      -       -      +
    197A  VAL*     3.9    30.1    -      -       +      -
    206A  VAL*     4.3    18.6    -      -       +      +
    208A  LYS*     3.7    38.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  SER*     3.6    37.0    -      -       -      -
    116A  VAL*     1.3    80.3    -      -       -      +
    118A  ILE*     1.3    61.9    +      -       -      +
    119A  PHE*     4.1    19.2    -      +       +      -
    134A  VAL      3.9     0.2    -      -       -      +
    135A  CYS*     3.3     7.5    -      -       -      -
    136A  LEU*     2.8    48.0    +      -       +      +
    138A  ASN*     4.0    17.3    -      -       -      -
    208A  LYS*     4.7     5.6    -      -       -      +
    147B  THR*     5.0    11.0    -      -       +      -
    148B  ALA*     5.1     0.9    -      -       -      -
    149B  ALA*     3.9    28.0    -      -       +      -
    195B  THR*     4.9     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  PHE*     1.3    77.9    -      -       -      +
    119A  PHE*     1.3    73.5    +      -       -      +
    120A  PRO*     3.9     5.0    -      -       +      +
    133A  VAL*     4.3     2.7    -      -       +      -
    134A  VAL      3.4     7.6    -      -       -      +
    149A  TRP*     3.9    23.3    -      -       +      -
    193A  TYR      3.7    18.4    -      -       -      +
    195A  CYS*     4.1     8.3    -      -       +      +
    208A  LYS*     3.6    40.4    -      -       +      +
    209A  SER      4.1    12.6    -      -       -      +
    210A  PHE*     3.8    30.7    -      -       +      -
    139B  SER*     5.2     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  PHE*     4.1    14.8    -      +       +      -
    118A  ILE*     1.3    79.4    -      -       -      +
    120A  PRO*     1.3    69.5    -      -       -      +
    133A  VAL*     3.2    10.1    -      -       -      +
    134A  VAL*     2.7    46.7    +      -       +      +
    136A  LEU*     4.1    22.9    -      -       +      -
    210A  PHE*     4.3     0.4    -      -       -      -
    136B  LEU*     3.5    50.9    -      -       +      -
    137B  ALA      3.4    26.9    -      -       -      -
    138B  PRO*     4.7     0.4    -      -       +      -
    139B  SER*     5.6     1.1    -      -       -      -
    149B  ALA*     3.6    39.5    -      -       +      -
    150B  LEU*     4.1     4.7    -      -       -      -
    193B  VAL*     5.1     4.9    -      -       +      -
----------------------------------------------------------
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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