Contacts of the strand formed by residues 230 - 235 (chain C) in PDB entry 1QDU


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
----------------------------------------------------------
    164C  TYR*     3.6    18.4    -      -       +      -
    166C  LEU*     3.2    36.8    -      -       +      -
    198C  PHE*     4.6     0.2    -      -       -      -
    218C  TYR*     4.0    13.7    -      +       +      -
    224C  HIS*     3.8    14.4    -      +       -      +
    229C  CYS*     1.3    81.6    -      -       -      +
    231C  ILE*     1.3    63.4    +      -       -      +
    232C  CYS*     4.2    21.1    -      -       +      -
    265C  PHE*     3.3    50.0    -      +       -      -
    273C  LEU*     4.1    23.8    -      -       +      -
    277C  PRO      3.1     5.8    +      -       -      +
    278C  LYS*     3.4    11.7    -      -       +      -
    279C  VAL      2.8    27.2    +      -       -      +
    280C  PHE*     4.7     4.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 231 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164C  TYR      3.1     7.4    +      -       -      +
    165C  CYS*     3.2    22.9    -      -       -      -
    166C  LEU*     2.9    24.3    +      -       -      +
    193C  PHE*     3.3    31.6    -      -       +      -
    198C  PHE*     3.4    33.7    -      -       +      -
    229C  CYS*     4.1     3.6    -      -       -      -
    230C  PHE*     1.3    82.2    -      -       -      +
    232C  CYS*     1.3    64.1    +      -       -      +
    233C  CYS*     3.9    13.5    -      -       -      -
    279C  VAL*     3.3    16.4    -      -       +      +
    281C  PHE*     4.1    17.5    -      -       +      -
    400D  PHE*     3.8    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 232 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166C  LEU*     3.4    15.7    -      -       +      -
    168C  ILE*     5.4     2.2    -      -       -      -
    215C  LEU*     4.0    21.8    -      -       -      -
    230C  PHE*     4.2    13.7    -      -       +      -
    231C  ILE*     1.3    76.4    -      -       -      +
    233C  CYS*     1.3    63.5    +      -       -      +
    234C  ILE*     4.1    19.7    -      -       -      -
    279C  VAL      2.8    10.1    +      -       -      +
    280C  PHE*     3.2    36.2    -      -       +      +
    281C  PHE      3.0    22.6    +      -       -      +
    282C  ILE*     4.8     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 233 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165C  CYS*     4.1     7.6    -      -       -      -
    166C  LEU      2.7    18.7    +      -       -      +
    167C  ILE*     3.4     9.1    -      -       +      -
    168C  ILE*     2.7    28.1    +      -       -      +
    189C  LEU*     3.6    32.8    -      -       +      -
    193C  PHE*     4.8     0.2    -      -       -      -
    231C  ILE*     3.9    19.3    -      -       -      -
    232C  CYS*     1.3    78.9    -      -       -      +
    234C  ILE*     1.3    63.9    +      -       -      +
    235C  LEU*     4.2    11.4    -      -       +      -
    281C  PHE*     3.3    17.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 234 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168C  ILE*     3.3    29.2    -      -       +      +
    170C  ASN*     5.6     0.2    -      -       -      +
    211C  ILE*     5.3     4.3    -      -       +      -
    215C  LEU*     5.7     1.3    -      -       +      -
    232C  CYS*     4.1    21.1    -      -       -      +
    233C  CYS*     1.3    80.4    -      -       -      +
    235C  LEU*     1.3    61.8    +      -       -      +
    236C  SER*     4.4    16.4    -      -       -      -
    243C  ILE*     4.4    22.9    -      -       +      -
    261C  LEU*     3.6    33.7    -      -       +      -
    280C  PHE*     5.1     1.1    -      -       +      -
    281C  PHE      2.9     7.1    +      -       -      -
    282C  ILE*     3.5    21.5    -      -       +      +
    283C  GLN      2.7    32.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 235 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167C  ILE*     4.7     3.6    -      -       +      -
    168C  ILE      3.0    11.9    +      -       -      +
    169C  ASN*     3.5    30.3    -      -       +      +
    170C  ASN      3.0    26.2    +      -       -      -
    179C  ARG*     3.0     8.9    +      -       -      +
    182C  THR*     3.5    15.3    -      -       +      -
    185C  ASP*     3.7    23.6    -      -       +      +
    186C  ALA*     3.9     7.2    -      -       -      +
    189C  LEU*     4.0    21.8    -      -       +      -
    233C  CYS*     4.5     5.2    -      -       +      -
    234C  ILE*     1.3    84.4    -      -       -      +
    236C  SER*     1.3    65.8    +      -       -      +
    281C  PHE      5.2     0.2    -      -       -      +
    283C  GLN*     3.4    20.2    -      -       +      +
    350D  ILE*     4.0    10.3    -      -       +      -
----------------------------------------------------------
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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