Contacts of the strand formed by residues 228 - 232 (chain B) in PDB entry 1O9S


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 GLU 228 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  VAL*     3.6    21.0    -      -       +      +
    219B  ALA*     3.4    16.1    -      -       -      +
    220B  GLU*     4.3     2.7    -      -       -      +
    221B  SER      3.9     0.9    -      -       -      +
    227B  GLY*     1.3    75.8    -      -       -      -
    229B  GLY*     1.3    59.2    +      -       -      +
    283B  HIS*     5.7     0.3    -      -       -      -
    284B  VAL*     4.7     6.9    +      -       -      +
    294B  LYS*     2.7    35.5    +      -       +      +
    296B  ASN*     2.9     9.9    +      -       -      -
   1367B  SAH      2.9    39.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 229 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  VAL*     3.4     8.5    -      -       -      +
    219B  ALA      2.7    32.4    +      -       -      -
    221B  SER*     3.8     1.7    -      -       -      +
    228B  GLU*     1.3    76.0    -      -       -      +
    230B  LEU*     1.3    59.2    +      -       -      -
    231B  PHE*     3.6     6.2    -      -       -      -
    294B  LYS*     3.3    15.0    -      -       -      -
    296B  ASN*     3.8     1.8    -      -       -      -
    330B  GLU*     3.7    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 230 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216B  VAL*     3.7    24.7    -      -       +      -
    217B  TYR      3.5    17.0    -      -       -      +
    218B  VAL*     4.3     6.5    -      -       +      -
    229B  GLY*     1.3    71.8    -      -       -      -
    231B  PHE*     1.3    58.2    +      -       -      +
    243B  SER*     3.7    28.9    -      -       -      +
    291B  LEU*     4.0    26.5    -      -       +      +
    292B  GLY*     4.7     1.3    -      -       -      -
    294B  LYS*     3.4     3.1    +      -       +      -
    295B  ALA*     3.9    33.9    -      -       +      +
    319B  ILE*     4.7     2.7    -      -       +      -
    330B  GLU*     3.5     8.2    +      -       -      +
    331B  LEU*     2.7    48.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 231 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216B  VAL*     3.1     6.2    -      -       -      +
    217B  TYR*     2.8    61.6    +      +       +      +
    219B  ALA*     3.6    29.2    -      -       +      -
    220B  GLU      3.2    27.8    -      -       -      -
    222B  LEU*     3.9    22.0    -      -       +      -
    229B  GLY*     3.6    15.9    -      -       -      -
    230B  LEU*     1.3    77.4    -      -       -      +
    232B  SER*     1.3    61.5    +      -       -      +
    328B  ASP      3.7    16.4    -      -       -      -
    329B  GLU      3.4     5.2    -      -       -      +
    330B  GLU*     3.6    37.0    -      -       +      -
    331B  LEU*     4.3     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 232 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  ARG      3.3     5.8    -      -       -      -
    216B  VAL*     4.5     0.2    -      -       -      +
    217B  TYR*     3.5     4.9    -      -       -      -
    231B  PHE*     1.3    71.6    -      -       -      +
    233B  LYS*     1.3    57.8    +      -       -      +
    234B  VAL      3.6    14.6    -      -       -      -
    242B  MET*     3.7    19.7    -      -       -      -
    325B  VAL*     3.3    12.7    -      -       -      +
    326B  GLU      2.7    26.7    +      -       -      -
    328B  ASP*     2.7    32.1    +      -       -      -
    329B  GLU      3.0    16.6    +      -       -      -
    331B  LEU*     4.1     5.2    -      -       -      +
----------------------------------------------------------
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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