Contacts of the strand formed by residues 223 - 226 (chain H) in PDB entry 5U07


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 223 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201H  VAL*     4.0    19.3    -      -       +      -
    202H  ASP      3.6    10.3    -      -       -      +
    203H  PHE*     4.2    19.4    -      -       +      +
    204H  PHE*     3.8     2.2    -      -       -      -
    222H  ASN*     1.3    73.9    -      -       -      +
    224H  GLY*     1.3    57.4    +      -       -      +
    225H  GLN*     4.4     1.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 224 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201H  VAL*     4.9     0.7    -      -       -      -
    202H  ASP*     2.8    42.7    +      -       -      +
    204H  PHE*     3.2    21.5    -      -       -      -
    223H  ALA*     1.3    72.6    -      -       -      +
    225H  GLN*     1.3    63.4    +      -       -      -
    226H  PHE*     3.6     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 225 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16H  ASN*     3.0    22.0    +      -       -      -
     22H  LEU*     4.7     4.6    -      -       -      +
     23H  GLY*     4.1    13.1    +      -       -      +
     24H  SER*     3.0    34.7    +      -       -      -
     25H  PRO*     5.0     0.4    -      -       -      -
    199H  VAL*     3.8    18.8    -      -       +      -
    200H  GLU      3.8     3.6    -      -       -      -
    201H  VAL*     4.0    17.7    -      -       +      +
    223H  ALA      4.4     1.3    +      -       -      +
    224H  GLY*     1.3    69.2    -      -       -      -
    226H  PHE*     1.3    73.6    +      -       -      +
    166J  ARG*     3.4    32.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 226 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41G  GLN*     5.7     3.4    -      -       -      -
    190G  HIS*     4.6     7.2    -      +       -      -
     14H  TYR*     3.1    59.9    -      +       +      +
     16H  ASN*     3.4    23.1    -      -       +      +
     25H  PRO*     4.6     2.5    -      -       -      -
    199H  VAL*     3.4     5.7    -      -       -      +
    200H  GLU*     2.9    34.4    +      -       -      +
    202H  ASP*     3.8    12.3    -      -       +      -
    204H  PHE*     5.7     2.7    -      +       -      -
    224H  GLY*     3.6    19.3    -      -       -      -
    225H  GLN*     1.3    87.8    -      -       -      +
    227H  SER*     1.3    63.5    +      -       -      +
    271H  LYS*     3.8    31.0    -      -       -      -
    274H  ALA*     5.9     1.8    -      -       +      -
    275H  THR*     3.8    17.5    -      -       +      -
----------------------------------------------------------
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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