Contacts of the strand formed by residues 239 - 241 (chain C) in PDB entry 5HP1


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 TRP 239 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  HIS*     3.9    27.8    -      +       -      -
     97C  PRO*     3.7    20.7    -      -       +      +
     98C  ALA*     4.3     4.4    -      -       +      +
    232C  TYR*     3.7    24.0    -      +       -      -
    233C  GLU      3.5    10.5    -      -       -      +
    234C  LEU*     4.0     9.9    -      -       +      -
    235C  HIS*     4.5     1.3    -      -       -      -
    238C  LYS*     1.3    72.6    -      -       -      +
    240C  THR*     1.3    95.3    +      -       -      +
    241C  VAL*     4.4     1.6    -      -       -      -
    269C  GLN*     4.7     5.6    -      -       -      -
    270C  ILE*     4.2    26.5    -      -       +      -
    315C  HIS*     3.3     5.7    -      -       -      +
    316C  GLY*     2.8    50.9    +      -       -      -
    317C  VAL      2.8    31.7    +      -       -      -
    318C  TYR*     3.4    28.9    -      +       +      +
    349C  LEU      3.0    24.6    +      -       -      -
    350C  LYS*     4.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 240 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232C  TYR*     3.3     8.1    -      -       -      +
    233C  GLU*     2.7    59.8    +      -       +      +
    235C  HIS*     4.1    11.2    -      -       +      -
    239C  TRP*     1.3    91.4    -      -       -      +
    241C  VAL*     1.3    71.9    +      -       -      +
    270C  ILE*     5.2     2.0    -      -       -      +
    271C  TYR*     5.4     1.0    +      -       -      -
    314C  VAL*     2.7    27.6    +      -       -      +
    315C  HIS*     4.1     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 241 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231C  GLY      4.0     7.0    -      -       -      +
    232C  TYR*     4.2    13.2    -      -       +      -
    233C  GLU*     3.7    11.5    -      -       -      +
    239C  TRP*     4.4     1.6    -      -       +      -
    240C  THR*     1.3    89.2    +      -       -      +
    242C  GLN*     1.3    72.4    +      -       -      +
    243C  PRO*     3.7     2.4    -      -       +      +
    244C  ILE*     3.8    12.8    -      -       +      -
    266C  TRP*     3.4    35.9    -      -       +      +
    267C  ALA*     6.1     0.7    -      -       -      -
    269C  GLN*     4.9     3.6    -      -       -      +
    270C  ILE*     3.9    16.6    -      -       +      +
    271C  TYR*     3.9    30.3    -      -       +      +
----------------------------------------------------------
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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