Contacts of the strand formed by residues 218 - 226 (chain G) in PDB entry 5DST


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 ARG 218 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349B  ARG*     5.2     3.4    -      -       -      +
    216G  PRO*     4.5     1.7    -      -       -      +
    217G  ASP*     1.3    85.2    +      -       -      +
    219G  ALA*     1.3    64.6    +      -       -      +
    220G  ALA*     3.8    24.8    -      -       -      +
    222G  TYR*     5.1     3.8    +      -       -      -
    274G  LEU*     5.9     0.2    -      -       -      +
    277G  GLU*     3.3    32.7    +      -       -      +
    278G  VAL      3.4     8.5    -      -       -      +
    279G  ASP*     5.1     6.3    -      -       +      +
    280G  ILE*     4.5     3.4    -      -       -      +
    312G  ASN*     5.8     3.6    +      -       -      +
    313G  ILE*     3.7     6.8    -      -       -      +
    314G  GLU*     2.8    73.3    +      -       +      +
    316G  THR*     4.1    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 219 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186G  TRP*     4.2    15.9    -      -       +      -
    191G  LEU*     4.1    19.3    -      -       +      -
    218G  ARG*     1.3    80.2    +      -       -      +
    220G  ALA*     1.3    63.5    +      -       -      +
    276G  LYS      4.6     0.4    -      -       -      -
    277G  GLU*     3.7     3.3    -      -       -      +
    278G  VAL*     2.9    40.5    +      -       +      +
    280G  ILE*     4.8     0.6    -      -       +      +
    312G  ASN      3.4     6.7    -      -       -      -
    313G  ILE*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 220 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191G  LEU*     4.5     2.4    -      -       -      +
    218G  ARG*     3.8    20.6    -      -       -      +
    219G  ALA*     1.3    77.6    -      -       -      +
    221G  LEU*     1.3    60.2    +      -       -      +
    222G  TYR*     3.7    23.2    -      -       +      +
    274G  LEU*     3.8    13.0    -      -       +      -
    276G  LYS      3.3     6.5    -      -       -      +
    277G  GLU*     4.8     1.1    -      -       -      -
    311G  PHE*     3.0     8.4    -      -       -      -
    312G  ASN*     2.8    40.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 221 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190G  CYS*     4.1    22.2    -      -       -      +
    191G  LEU*     4.1    19.5    -      -       +      +
    192G  PHE*     4.2    19.7    -      -       +      -
    220G  ALA*     1.3    74.7    -      -       -      +
    222G  TYR*     1.3    60.1    +      -       -      +
    274G  LEU*     3.7     4.0    -      -       -      +
    275G  ILE*     2.9    50.6    +      -       +      +
    276G  LYS*     2.8    24.6    +      -       +      +
    290G  PHE*     4.7     6.3    -      -       +      -
    309G  THR*     4.2    14.4    -      -       +      -
    310G  TYR      3.5    17.5    -      -       -      +
    311G  PHE*     4.1    11.0    -      -       +      -
    358G  ILE*     5.9     0.9    -      -       +      -
    360G  MET*     5.0     4.0    -      -       -      -
    372G  PHE*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 222 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351B  GLY*     6.0     3.5    -      -       -      -
    218G  ARG*     5.1     3.6    +      -       -      -
    220G  ALA*     3.7    27.5    -      -       +      +
    221G  LEU*     1.3    75.1    -      -       -      +
    223G  VAL*     1.3    62.4    +      -       -      +
    272G  ALA*     4.4     3.8    -      -       +      -
    273G  CYS      3.3    22.4    -      -       -      +
    274G  LEU*     3.5    36.9    -      -       +      +
    275G  ILE*     4.3     3.4    -      -       -      -
    309G  THR*     3.0    32.0    -      -       -      +
    310G  TYR*     2.8    56.2    +      +       +      +
    312G  ASN*     3.2    22.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 223 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222G  TYR*     1.3    72.1    -      -       -      +
    224G  VAL*     1.3    70.7    +      -       -      +
    272G  ALA*     3.4     1.9    -      -       -      +
    273G  CYS*     3.0    40.1    +      -       +      +
    275G  ILE*     3.6    31.2    -      -       +      -
    294G  PHE*     4.1    17.9    -      -       +      -
    296G  LEU*     3.5     9.3    -      -       +      +
    307G  LEU*     4.5    20.6    -      -       +      -
    308G  VAL      3.3     6.3    -      -       -      +
    309G  THR*     3.6    24.9    -      -       +      -
    310G  TYR*     5.2     0.4    -      -       -      -
    340G  PHE*     6.1     0.2    -      -       +      -
    358G  ILE*     4.8     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 224 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223G  VAL*     1.3    81.7    -      -       -      +
    225G  ALA*     1.3    64.3    +      -       -      +
    226G  ILE*     4.0     7.6    -      -       +      -
    268G  VAL*     3.5    39.5    -      -       +      -
    270G  THR*     3.7     4.3    -      -       -      -
    271G  ASN      3.4    18.2    -      -       -      +
    272G  ALA*     3.7    15.5    -      -       +      -
    296G  LEU*     3.8     6.5    -      -       -      -
    307G  LEU*     3.4     6.1    -      -       -      +
    308G  VAL*     2.9    37.9    +      -       +      +
    310G  TYR*     4.3    13.7    -      -       +      -
    328G  PRO*     5.5     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 225 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224G  VAL*     1.3    74.4    -      -       -      +
    226G  ILE*     1.3    65.9    +      -       -      +
    268G  VAL*     3.7     1.6    -      -       -      -
    269G  VAL*     2.9    25.7    +      -       -      +
    270G  THR*     3.1    27.6    +      -       +      -
    296G  LEU*     3.8     5.6    -      -       +      +
    304G  VAL*     3.8    19.1    -      -       +      -
    306G  ALA      3.4    11.0    -      -       -      +
    307G  LEU*     3.9    12.3    -      -       +      -
    354G  ILE*     4.1     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 226 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224G  VAL*     4.0     8.3    -      -       +      -
    225G  ALA*     1.3    79.9    -      -       -      +
    227G  GLU*     1.3    60.3    +      -       -      +
    228G  ASP*     3.8    29.2    -      -       +      +
    263G  VAL*     4.1    20.6    -      -       +      -
    267G  GLN*     3.2    19.3    -      -       -      +
    268G  VAL*     3.9    14.6    -      -       +      -
    269G  VAL*     4.1     4.0    -      -       -      -
    303G  TYR      4.1     3.1    -      -       -      -
    304G  VAL*     3.3     4.1    -      -       -      -
    305G  HIS      2.8    25.1    +      -       -      -
    306G  ALA*     2.9    26.5    +      -       +      +
    308G  VAL*     3.6    34.5    -      -       +      -
    339G  VAL*     4.6     4.7    -      -       +      -
----------------------------------------------------------
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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