Contacts of the strand formed by residues 21 - 23 (chain N) in PDB entry 1KYO


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 PRO 21 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19N  ASP      3.3     8.3    -      -       -      +
     20N  SER*     1.3    85.1    +      -       -      +
     22N  GLN*     1.3    67.5    +      -       -      +
     23N  PRO*     4.4     0.2    -      -       -      +
    205N  GLY*     5.3     2.9    -      -       -      -
    218N  ARG*     3.2    38.4    +      -       +      +
     10S  MET*     4.5     9.5    -      -       +      +
     12S  TRP*     3.4    33.2    -      -       +      -
     13S  TRP*     3.7    28.0    -      -       +      +
     16S  MET*     3.9    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 22 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20N  SER*     2.8    37.6    +      -       -      +
     21N  PRO*     1.3    76.7    +      -       -      +
     23N  PRO*     1.3    76.5    -      -       +      +
     26N  ILE*     4.4     7.4    -      -       +      +
    206N  SER*     4.2    16.6    +      -       -      -
    218N  ARG*     3.1    10.3    -      -       -      -
    219N  ILE*     2.9    30.8    +      -       -      +
    221N  MET*     3.1    28.8    -      -       +      +
    225N  PHE*     3.4    41.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 23 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21N  PRO      4.4     0.7    -      -       -      +
     22N  GLN*     1.3    92.9    -      -       +      +
     24N  SER*     1.3    65.7    +      -       -      +
     25N  SER*     3.1     4.8    +      -       -      +
     26N  ILE*     3.3    35.8    +      -       +      +
    206N  SER*     3.8    16.6    -      -       -      +
    207N  SER      3.6    17.5    -      -       -      +
    208N  ASN*     4.0    16.6    -      -       +      +
    214N  GLY*     4.5    11.4    -      -       -      +
    217N  ASP      4.0     2.9    -      -       -      +
    218N  ARG*     3.9    22.2    -      -       -      +
    225N  PHE*     3.8     2.9    -      -       -      -
     79R  HIS*     5.4     2.0    -      -       +      +
----------------------------------------------------------
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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