Contacts of the strand formed by residues 223 - 229 (chain G) in PDB entry 8GCH


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 SER 223 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171G  TYR*     3.4    21.1    +      -       -      -
    185G  ALA*     3.8    13.7    -      -       -      +
    221G  SER*     3.0    12.9    +      -       -      -
    222G  THR*     1.3    80.8    +      -       -      +
    224G  THR*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 224 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  TRP*     5.5     0.7    -      -       -      -
    171G  TYR*     4.3     8.1    -      -       +      -
    172G  TRP*     4.2     8.4    -      -       +      -
    185G  ALA*     3.6    11.2    +      -       -      -
    188G  VAL      5.1     1.4    -      -       -      +
    189G  SER*     4.9     3.1    +      -       -      -
    217G  SER*     3.1    28.5    +      -       -      -
    221G  SER*     3.5    32.4    +      -       -      +
    222G  THR      4.5     0.3    -      -       -      -
    223G  SER*     1.3    85.9    -      -       -      +
    225G  PRO*     1.3    77.3    +      -       -      +
    226G  GLY      3.6     1.4    +      -       -      -
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Residues in contact with PRO 225 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  TRP*     4.9     0.2    -      -       -      -
    163G  LEU*     3.8    20.0    -      -       +      -
    168G  CYS*     3.9    12.3    -      -       -      -
    171G  TYR*     3.3    47.3    -      -       +      -
    172G  TRP*     2.8    38.6    +      -       -      +
    182G  CYS*     4.0    12.8    -      -       +      -
    183G  ALA      3.7     7.9    -      -       -      +
    185G  ALA*     3.6     9.4    -      -       +      -
    216G  GLY*     4.4     1.7    -      -       -      -
    224G  THR*     1.3    88.4    +      -       -      +
    226G  GLY*     1.3    62.6    +      -       -      +
    227G  VAL*     4.0     0.5    +      -       -      +
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Residues in contact with GLY 226 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  TRP*     3.4    30.1    -      -       -      -
    182G  CYS*     3.1     6.9    -      -       -      +
    183G  ALA      2.8    35.9    +      -       -      -
    184G  GLY*     4.8     0.2    -      -       -      -
    190G  SER      5.9     0.2    -      -       -      -
    215G  TRP      3.9     0.2    -      -       -      -
    224G  THR      3.6     3.2    +      -       -      -
    225G  PRO*     1.3    74.7    -      -       -      +
    227G  VAL*     1.3    59.8    -      -       -      -
    228G  TYR*     3.4    11.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 227 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  TRP*     4.1     1.1    -      -       -      -
    172G  TRP*     3.8    28.7    -      -       +      +
    176G  ILE*     4.0     8.3    -      -       +      -
    180G  MET*     3.8    27.1    -      -       +      -
    181G  ILE      3.8     4.3    -      -       -      +
    182G  CYS*     4.2     4.3    -      -       -      +
    214G  SER*     3.1     7.6    +      -       -      -
    215G  TRP*     2.7    92.3    +      -       +      +
    225G  PRO      4.0     0.7    -      -       -      +
    226G  GLY*     1.3    75.5    -      -       -      +
    228G  TYR*     1.3    66.0    +      -       -      +
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Residues in contact with TYR 228 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  TRP*     4.6     2.2    -      +       -      -
    138F  THR*     4.1     4.0    -      -       -      +
    160G  LEU*     3.5    22.3    -      -       +      +
    180G  MET*     3.4     8.6    -      -       -      +
    181G  ILE*     2.8    45.1    +      -       +      +
    183G  ALA*     3.7    21.5    +      -       +      -
    190G  SER*     2.8    35.7    +      -       -      -
    199G  LEU*     3.8    27.8    -      -       +      -
    211G  GLY*     4.0     8.3    -      -       -      -
    212G  ILE      3.2    15.0    -      -       -      +
    213G  VAL*     3.6    32.8    -      -       +      -
    214G  SER*     3.9     3.4    -      -       -      -
    226G  GLY*     3.4    24.7    -      -       -      -
    227G  VAL*     1.3    77.3    -      -       -      +
    229G  ALA*     1.3    61.1    +      -       -      +
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Residues in contact with ALA 229 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102F  ASP*     3.5    37.0    -      -       +      +
    179G  ALA      3.8     5.4    -      -       -      +
    180G  MET*     4.8     2.2    -      -       -      +
    211G  GLY*     3.2    19.2    -      -       -      -
    212G  ILE*     2.9    24.5    +      -       +      +
    214G  SER*     3.9     3.5    -      -       -      -
    228G  TYR*     1.3    69.9    -      -       -      +
    230G  ARG*     1.3    59.1    -      -       -      +
    231G  VAL*     3.1     9.7    +      -       -      +
    234G  LEU*     3.8    18.4    -      -       +      -
----------------------------------------------------------
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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