Contacts of the strand formed by residues 17 - 22 (chain O) in PDB entry 3HOU


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 ASN 17 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13O  ALA*     4.6     0.7    -      -       -      -
     14O  SER*     2.8    37.8    +      -       -      +
     16O  ASP*     1.3    96.9    -      -       -      +
     18O  VAL*     1.3    69.7    +      -       -      +
     19O  ASP      4.0     0.9    -      -       -      +
    231O  ASN*     3.5    22.1    +      -       -      +
    232O  VAL      3.4     5.2    -      -       -      +
    233O  GLU*     3.3    32.1    -      -       -      +
    240O  VAL*     3.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 18 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10O  ILE*     4.2     9.4    -      -       +      -
     13O  ALA*     4.3     4.3    -      -       +      +
     17O  ASN*     1.3    81.7    -      -       -      +
     19O  ASP*     1.3    73.3    +      -       -      +
     20O  PHE*     2.9    21.2    -      -       +      -
    231O  ASN*     3.5     3.5    +      -       -      -
    232O  VAL*     3.2    20.8    +      -       +      +
    240O  VAL*     3.4    32.8    -      -       +      +
    241O  ASP*     4.7     0.9    -      -       -      -
    244O  VAL*     5.1     1.1    -      -       +      -
    105W  PHE*     3.9    30.7    -      -       +      -
    109W  TRP*     3.5    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 19 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10O  ILE*     3.4     3.1    -      -       -      +
     11O  ARG*     3.0    50.9    +      -       -      +
     12O  GLU*     2.8    43.8    +      -       +      +
     17O  ASN*     4.0     1.2    -      -       -      +
     18O  VAL*     1.3    74.8    -      -       -      +
     20O  PHE*     1.3    81.9    +      -       -      +
    205O  LYS*     3.3    11.4    +      -       -      -
    229O  TYR      5.5     0.3    -      -       -      -
    230O  MET      3.6    13.6    +      -       -      +
    231O  ASN*     3.4    16.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 20 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8O  VAL*     4.0    10.5    -      -       +      -
     10O  ILE*     3.5    23.1    -      -       +      +
     11O  ARG*     3.6     9.2    -      -       -      +
     18O  VAL*     2.9    30.1    -      -       +      -
     19O  ASP*     1.3    81.4    +      -       -      +
     21O  ILE*     1.3    71.1    +      -       -      +
     22O  LEU*     3.4    39.7    -      -       +      -
     33O  LEU*     5.3     3.4    -      -       +      -
     37O  MET*     5.5     0.4    -      -       +      -
    228O  PHE      3.7     0.2    -      -       -      +
    229O  TYR*     3.9     0.7    -      -       -      -
    230O  MET*     3.1    60.1    +      -       +      +
    232O  VAL*     3.8    24.0    -      -       +      -
    244O  VAL*     4.6    13.7    -      -       +      -
    105W  PHE*     4.2    12.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 21 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8O  VAL*     3.4     4.3    -      -       -      -
      9O  LYS*     3.1    38.4    +      -       +      +
     11O  ARG*     3.1    39.0    -      -       +      +
     20O  PHE*     1.3    82.9    -      -       -      +
     22O  LEU*     1.3    65.7    +      -       -      +
     23O  SER*     3.4    10.6    +      -       -      +
    209O  TYR*     4.1    11.7    -      -       +      -
    227O  THR*     4.1    24.2    -      -       +      -
    228O  PHE      3.6     6.7    -      -       -      +
    229O  TYR*     3.6    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 22 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7O  GLN      3.7     3.1    -      -       -      +
      8O  VAL*     4.1     8.1    -      -       +      +
     20O  PHE*     3.4    24.2    -      -       +      -
     21O  ILE*     1.3    70.2    -      -       -      +
     23O  SER*     1.3    59.5    +      -       -      +
     25O  VAL*     3.5    31.9    -      -       +      -
     30O  ALA*     4.2    15.5    -      -       +      -
     33O  LEU*     4.8     8.3    -      -       +      -
    227O  THR*     3.2     2.4    +      -       -      -
    228O  PHE*     2.7    42.1    +      -       +      +
    230O  MET*     3.3    30.5    -      -       +      -
    244O  VAL*     6.5     0.2    -      -       +      -
    101W  LEU*     3.7    37.9    -      -       +      -
    105W  PHE*     6.0     0.4    -      -       +      -
----------------------------------------------------------
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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