Contacts of the strand formed by residues 227 - 229 (chain A) in PDB entry 1SID


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 227 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP*     3.2    20.9    +      -       +      -
    162A  TYR*     4.6     2.4    +      -       -      -
    174A  LEU*     3.2    36.8    -      -       +      -
    176A  GLY*     3.3    29.2    -      -       -      -
    191A  VAL*     2.9    21.1    +      -       +      -
    192A  THR*     3.6     3.4    -      -       -      -
    193A  ILE*     3.5    29.8    -      -       +      -
    196A  ILE*     3.4    29.4    -      -       +      -
    212A  SER*     4.0     9.0    -      -       -      -
    214A  ALA*     3.5    24.9    -      -       +      -
    222A  TYR*     3.1    33.9    -      +       +      +
    223A  PRO*     3.1    19.6    +      -       +      +
    224A  VAL      3.5     8.8    -      -       -      +
    226A  ILE*     1.3    84.5    -      -       +      +
    228A  HIS*     1.3    69.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP*     4.9     0.9    -      -       -      +
    162A  TYR*     4.3     2.2    +      -       -      -
    172A  LEU*     5.3     0.4    -      -       -      -
    174A  LEU*     2.8     8.2    -      -       -      +
    175A  GLN*     2.5    48.2    +      -       +      +
    177A  LEU*     3.2    29.0    +      -       +      -
    224A  VAL      4.2     6.0    +      -       -      -
    225A  GLU      4.7     0.2    +      -       -      -
    226A  ILE      3.4    14.9    +      -       -      -
    227A  TRP*     1.3    80.1    +      -       -      +
    229A  PRO*     1.3    65.4    -      -       +      +
    230A  ASP*     2.6     9.6    +      -       -      -
    130E  VAL*     5.2     5.4    -      -       +      -
    131E  GLY*     3.3    30.2    +      -       -      +
    133E  GLY*     3.3    39.6    +      -       -      -
    134E  SER*     3.5     5.2    +      -       -      -
    255E  PHE*     4.0     8.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP*     4.5    17.6    -      -       +      -
    162A  TYR*     4.9     1.8    -      -       -      +
    164A  VAL*     5.2     4.3    -      -       +      -
    172A  LEU*     4.5    14.6    -      -       +      -
    173A  ASP      3.9     8.3    -      -       -      +
    174A  LEU*     4.2     2.2    -      -       +      -
    227A  TRP      4.7     0.2    -      -       -      +
    228A  HIS*     1.3    87.8    -      -       +      +
    230A  ASP*     1.3    63.0    +      -       -      +
    231A  PRO*     3.1    14.0    -      -       -      +
    239A  TYR*     3.4    42.5    +      -       +      -
    128E  GLU*     4.2     1.7    -      -       -      +
    130E  VAL*     4.6     2.6    -      -       -      +
    255E  PHE*     3.9    27.4    -      -       +      -
----------------------------------------------------------
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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