Contacts of the strand formed by residues 138 - 143 (chain F) in PDB entry 5YUS


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 ALA 138 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7F  VAL*     4.1    12.8    -      -       +      -
      8F  ASP      3.6     8.5    -      -       -      +
      9F  MET*     3.7    23.1    -      -       -      +
     10F  ASP*     3.6     5.4    -      -       -      -
    127F  ARG*     3.0    37.6    +      -       +      +
    130F  ILE*     4.1    18.8    -      -       +      +
    136F  LEU      4.2     0.2    +      -       -      -
    137F  THR*     1.3    75.7    -      -       -      +
    139F  SER*     1.3    59.8    +      -       -      +
    159F  ASN*     3.6     7.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 139 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7F  VAL*     3.6     4.2    -      -       -      +
      8F  ASP*     2.9    34.9    +      -       -      -
     10F  ASP*     2.8    23.2    +      -       -      -
    127F  ARG*     3.8     1.6    -      -       -      +
    138F  ALA*     1.3    73.2    -      -       -      +
    140F  ALA*     1.3    65.7    +      -       -      +
    153F  SER*     3.7    20.2    -      -       -      -
    157F  LYS*     3.3    16.5    -      -       -      +
    159F  ASN      3.0    15.9    +      -       -      -
    160F  GLY      3.1    13.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 140 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5F  ILE*     4.4     6.1    -      -       +      -
      6F  HIS      3.2    10.3    -      -       -      +
      7F  VAL*     4.5     5.6    -      -       +      -
    123F  ALA*     4.1    21.1    -      -       +      +
    127F  ARG*     3.9    16.8    -      -       +      +
    139F  SER*     1.3    79.2    -      -       -      +
    141F  GLY*     1.3    60.2    +      -       -      +
    142F  VAL*     5.3     0.2    -      -       -      -
    153F  SER*     3.5    11.6    -      -       -      -
    160F  GLY      3.0     6.9    +      -       -      -
    161F  GLN*     3.0    31.0    -      -       +      -
    162F  PHE      3.1     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 141 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4F  ILE      3.8     0.5    -      -       -      +
      5F  ILE*     3.3     5.9    -      -       -      +
      6F  HIS      2.9    33.3    +      -       -      -
    140F  ALA*     1.3    73.8    -      -       -      +
    142F  VAL*     1.3    64.2    -      -       -      +
    149F  ALA*     3.4    22.7    -      -       -      +
    152F  ALA*     3.6     0.9    -      -       -      -
    153F  SER*     3.3    10.0    -      -       -      -
    162F  PHE      3.4     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3F  LYS*     5.6     1.3    -      -       +      -
      4F  ILE      3.5     8.5    -      -       -      +
      5F  ILE*     4.2     5.4    -      -       +      -
    119F  ALA*     3.8    42.4    -      -       +      +
    120F  THR*     4.6     1.8    -      -       -      +
    123F  ALA*     4.1    16.8    -      -       +      -
    140F  ALA      5.3     0.9    -      -       -      -
    141F  GLY*     1.3    78.9    -      -       -      +
    143F  ALA*     1.3    64.5    +      -       -      +
    149F  ALA*     4.5     0.2    -      -       -      -
    152F  ALA*     4.0     1.5    -      -       -      +
    161F  GLN*     5.2     2.7    -      -       +      +
    162F  PHE      3.0     7.3    +      -       -      +
    163F  VAL*     3.4    33.8    -      -       +      -
    164F  ILE*     2.7    33.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 143 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2F  ARG      4.0     0.8    -      -       -      +
      3F  LYS*     4.0     1.7    -      -       -      -
      4F  ILE*     3.0    31.5    +      -       -      +
    142F  VAL*     1.3    78.5    -      -       -      +
    144F  PRO*     1.3    74.5    -      -       +      +
    145F  VAL      3.3     3.2    +      -       -      +
    148F  LEU*     3.5    17.3    -      -       +      +
    149F  ALA*     3.2    29.6    -      -       -      +
    164F  ILE*     3.6    11.2    -      -       +      +
----------------------------------------------------------
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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