Contacts of the strand formed by residues 226 - 230 (chain H) in PDB entry 1AVG


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 GLY 226 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182H  CYS*     2.9    23.7    -      -       -      -
    183H  ALA      3.0    15.6    +      -       -      -
    189H  ASP*     3.9    20.2    +      -       -      -
    190H  ALA*     6.4     0.2    -      -       -      -
    215H  TRP      3.9     7.0    -      -       -      -
    216H  GLY*     5.1     1.1    -      -       -      -
    225H  TYR*     1.3    74.0    -      -       -      +
    227H  PHE*     1.3    60.3    +      -       -      -
    228H  TYR*     3.3    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 227 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168H  CYS*     3.6    30.1    -      -       +      -
    171H  SER*     4.3     3.8    -      -       -      -
    172H  THR*     4.2     7.2    -      -       +      -
    176H  ILE*     3.3    34.3    -      -       +      -
    180H  MET*     4.3    13.7    -      -       +      -
    181H  PHE      3.2     9.6    -      -       -      -
    182H  CYS*     3.4    27.6    -      -       +      -
    213H  VAL*     5.3     0.5    -      -       -      +
    214H  SER*     3.1    22.8    +      -       -      -
    215H  TRP*     2.9    65.7    +      +       +      +
    225H  TYR*     3.6    20.2    -      -       +      -
    226H  GLY*     1.3    75.0    -      -       -      -
    228H  TYR*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 228 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138H  VAL*     3.7    14.9    -      -       +      +
    160H  LEU*     3.5    24.4    -      -       +      +
    180H  MET*     3.2     6.4    -      -       -      -
    181H  PHE*     2.8    63.8    +      +       +      +
    183H  ALA*     4.1    15.9    -      -       +      -
    189H  ASP*     4.3     5.0    +      -       -      -
    190H  ALA*     4.1    14.1    -      -       +      +
    199H  PHE*     3.8    21.5    -      +       +      -
    212H  ILE      3.0    13.5    -      -       -      +
    213H  VAL*     3.6    42.2    -      -       +      -
    214H  SER*     4.4     1.6    -      -       -      -
    226H  GLY*     3.3    28.2    -      -       -      -
    227H  PHE*     1.3    74.6    -      -       -      +
    229H  THR*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 229 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101H  ARG*     4.9     0.4    -      -       -      -
    102H  ASP*     3.0    48.4    +      -       -      +
    103H  ILE*     4.4     9.2    -      -       +      -
    179H  ASN      3.6    12.3    -      -       -      +
    180H  MET*     4.5     1.1    -      -       -      +
    211H  GLY*     3.1    20.3    -      -       -      -
    212H  ILE*     2.8    25.5    +      -       +      +
    214H  SER*     3.8     9.5    -      -       -      -
    228H  TYR*     1.3    70.2    -      -       -      +
    230H  HIS*     1.3    62.7    +      -       -      +
    231H  VAL*     2.9     9.8    +      -       -      +
    234H  LEU*     4.0    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 230 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130H  LEU*     3.6    31.9    -      -       +      +
    165H  ARG*     4.4    13.2    +      -       -      -
    178H  ASP      3.8    12.8    -      -       -      +
    179H  ASN      3.0    28.0    +      -       -      -
    180H  MET*     3.8     1.8    -      -       -      +
    181H  PHE*     3.8    26.5    -      +       +      -
    210H  MET      5.0     1.3    +      -       -      -
    228H  TYR      3.4     2.2    +      -       -      -
    229H  THR*     1.3    67.7    -      -       -      +
    231H  VAL*     1.3    66.0    +      -       -      +
    232H  PHE*     3.8    16.4    +      +       +      -
    233H  ARG*     3.2    50.5    +      -       +      +
    234H  LEU*     3.0    22.0    -      -       -      +
----------------------------------------------------------
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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