Contacts of the strand formed by residues 230 - 233 (chain C) in PDB entry 4YLO


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 PHE 230 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228C  VAL*     3.8    16.6    +      -       +      +
    229C  ILE*     1.3    82.2    -      -       -      +
    231C  GLU*     1.3    64.0    +      -       -      +
    232C  ILE*     4.0     4.2    +      -       -      +
    237C  LEU*     4.6     6.3    -      -       +      -
    238C  GLN      3.6     7.9    -      -       -      -
    239C  MET*     3.7    44.9    -      -       +      -
    287C  VAL*     4.3    14.4    -      -       +      -
    291C  TYR*     3.8    23.3    -      +       -      -
    292C  ILE*     3.4    37.2    -      -       +      -
    332C  ARG*     4.2     1.6    -      -       -      -
    333C  ILE*     3.4    37.4    +      -       +      +
    335C  THR*     3.9    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 231 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229C  ILE*     4.1     8.5    -      -       +      +
    230C  PHE*     1.3    74.1    -      -       -      +
    232C  ILE*     1.3    62.8    +      -       -      +
    233C  ARG*     3.1    47.9    +      -       +      +
    237C  LEU*     4.1     5.2    -      -       -      +
    238C  GLN*     2.9    41.5    +      -       +      +
    240C  GLU*     4.1    17.9    -      -       +      +
    284C  LEU*     3.2    28.9    -      -       -      +
    331C  LYS      4.5     4.3    -      -       -      +
    332C  ARG*     4.3    21.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 232 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230C  PHE      4.9     3.6    -      -       -      +
    231C  GLU*     1.3    74.0    -      -       -      +
    233C  ARG*     1.3    69.8    +      -       -      +
    234C  ASP      5.4     4.5    -      -       -      +
    235C  ASN*     6.4     1.6    -      -       -      -
    236C  LYS      4.5     2.9    -      -       -      +
    237C  LEU*     4.6    17.9    -      -       +      -
    322C  LEU*     4.6    12.3    -      -       +      -
    326C  SER*     3.8    29.6    -      -       -      -
    330C  HIS      4.4     0.2    -      -       -      +
    331C  LYS*     3.5    45.8    +      -       +      +
    333C  ILE*     3.9    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 233 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231C  GLU*     3.1    39.5    +      -       +      +
    232C  ILE*     1.3    80.0    -      -       -      +
    234C  ASP*     1.3    71.9    +      -       -      +
    235C  ASN      3.0     4.7    +      -       -      -
    236C  LYS*     3.1    26.2    +      -       -      +
    238C  GLN*     3.8    19.8    +      -       -      +
    284C  LEU*     3.6    22.8    -      -       -      +
----------------------------------------------------------
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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