Contacts of the strand formed by residues 114 - 118 (chain O) in PDB entry 3KYM


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 114 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112O  ALA      3.5     2.6    +      -       -      -
    113O  PRO*     1.3    72.3    -      -       -      +
    115O  VAL*     1.3    59.0    +      -       -      +
    116O  PHE*     3.2    32.8    -      -       -      -
    135O  LEU      3.4     0.5    -      -       -      +
    137O  ASN*     3.1    32.8    +      -       -      +
    141P  THR*     5.1     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 115 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113O  PRO*     3.9     8.5    +      -       +      +
    114O  SER*     1.3    70.8    -      -       -      +
    116O  PHE*     1.3    81.2    +      -       -      +
    134O  CYS*     3.7    26.9    -      -       -      -
    135O  LEU      3.4     6.3    -      -       -      +
    136O  LEU*     4.5     8.3    -      -       +      -
    194O  CYS*     4.8     2.5    -      -       +      +
    196O  VAL*     3.8    34.1    -      -       +      -
    201O  LEU*     5.4     0.4    -      -       +      -
    205O  VAL*     3.9    19.5    -      -       +      +
    207O  LYS*     3.8    42.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 116 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114O  SER*     3.2    31.6    -      -       -      -
    115O  VAL*     1.3    85.8    -      -       -      +
    117O  ILE*     1.3    61.8    +      -       -      +
    118O  PHE*     4.2    18.8    -      -       +      -
    133O  VAL      3.9     0.4    -      -       -      +
    134O  CYS*     3.3     6.1    -      -       -      -
    135O  LEU*     2.8    56.3    +      -       +      +
    137O  ASN*     4.0    12.3    -      -       +      -
    207O  LYS*     5.1     4.0    -      -       -      -
    132P  PRO*     6.3     3.6    -      -       +      -
    141P  THR*     3.8    33.2    -      -       +      -
    142P  ALA*     5.5     0.2    -      -       -      -
    143P  ALA*     3.7    27.4    -      -       +      -
    189P  THR*     4.4     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 117 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116O  PHE*     1.3    76.0    -      -       -      +
    118O  PHE*     1.3    70.2    +      -       -      +
    119O  PRO*     3.9     6.4    -      -       -      +
    132O  VAL*     4.3     1.3    -      -       +      -
    133O  VAL      3.4     8.7    -      -       -      +
    148O  TRP*     3.5    34.3    -      -       +      -
    192O  TYR      4.0    11.9    -      -       -      +
    194O  CYS*     4.0    19.1    -      -       +      +
    207O  LYS*     4.0    25.7    -      -       +      +
    208O  SER*     4.0    11.7    -      -       -      +
    209O  PHE*     3.7    31.6    -      -       +      -
    132P  PRO*     4.2    11.4    -      -       -      +
    133P  CYS*     5.1     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 118 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116O  PHE*     4.2    11.2    -      -       +      -
    117O  ILE*     1.3    76.6    -      -       -      +
    119O  PRO*     1.3    70.4    -      -       +      +
    131O  SER      4.2     0.3    -      -       -      +
    132O  VAL*     3.4     8.4    -      -       -      +
    133O  VAL*     2.7    54.0    +      -       +      +
    135O  LEU*     3.9    27.4    -      -       +      -
    209O  PHE*     4.5     0.2    -      -       -      -
    130P  LEU*     3.6    35.5    -      -       +      +
    131P  ALA      3.5    22.9    -      -       -      +
    132P  PRO*     3.8     8.1    -      -       +      -
    143P  ALA*     3.4    42.6    -      -       +      -
    144P  LEU*     3.8    15.5    -      -       -      -
    187P  VAL*     4.9     2.2    -      -       +      -
----------------------------------------------------------
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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