Contacts of the strand formed by residues 221 - 225 (chain N) in PDB entry 6DZT


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 221 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206N  ILE*     4.1     6.3    -      -       -      +
    210N  THR      5.3     1.6    -      -       -      -
    212N  LEU*     5.3     0.7    -      -       -      -
    218N  SER      5.0     4.3    -      -       -      -
    219N  ARG      4.7     2.1    +      -       -      -
    220N  PHE*     1.3    77.1    -      -       -      +
    222N  GLY*     1.3    64.4    +      -       -      +
    223N  SER*     5.0     2.4    +      -       -      -
    230N  SER      4.0     0.2    -      -       -      +
    231N  LEU*     3.8     3.8    -      -       -      +
    232N  THR*     2.9    49.9    +      -       -      +
    234N  ASN*     4.7     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 222 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193N  TRP*     5.3     0.9    -      -       -      -
    206N  ILE*     3.7    22.1    -      -       -      +
    209N  ALA      3.2    16.6    -      -       -      -
    210N  THR*     4.0    15.7    +      -       -      +
    221N  SER*     1.3    78.6    -      -       -      +
    223N  SER*     1.3    69.7    +      -       -      -
    230N  SER      3.4     9.2    -      -       -      -
    231N  LEU*     4.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 223 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193N  TRP*     5.5     0.5    +      -       -      -
    209N  ALA      3.1     9.8    +      -       -      +
    210N  THR*     4.3     6.1    -      -       -      -
    221N  SER*     5.0     2.8    +      -       -      -
    222N  GLY*     1.3    81.2    +      -       -      -
    224N  GLY*     1.3    64.7    +      -       -      +
    229N  PHE*     3.5     7.6    -      -       -      +
    230N  SER*     3.1    40.0    +      -       -      +
    232N  THR*     5.7     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 224 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189N  SER*     4.7     1.9    +      -       -      -
    209N  ALA*     3.9     8.7    -      -       -      +
    210N  THR*     4.9     6.8    -      -       -      +
    223N  SER*     1.3    80.7    -      -       -      +
    225N  SER*     1.3    63.8    +      -       -      -
    228N  ASP      3.3    15.3    -      -       -      -
    229N  PHE*     3.7    12.0    -      -       -      -
    230N  SER*     5.7     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 225 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188N  ARG*     4.9     4.7    -      -       -      +
    189N  SER*     3.8    18.4    +      -       -      -
    224N  GLY*     1.3    76.9    -      -       -      -
    226N  GLY*     1.3    64.3    +      -       -      +
    227N  GLN      3.2     7.1    +      -       -      -
    228N  ASP*     3.5    11.2    +      -       -      +
    229N  PHE*     3.7    11.4    -      -       -      -
----------------------------------------------------------
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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