Contacts of the strand formed by residues 115 - 119 (chain A) in PDB entry 1KHI


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 115 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  GLN*     2.9    35.4    +      -       -      +
    113A  ASP      3.1     5.9    +      -       -      -
    114A  GLY*     1.3    76.9    -      -       -      +
    116A  ILE*     1.3    69.8    +      -       -      +
    127A  GLN      4.6     1.0    +      -       -      -
    128A  ASN*     3.6    34.6    +      -       -      -
    129A  LEU      3.4    15.5    -      -       -      -
    130A  PRO*     4.5     3.1    -      -       -      -
    138A  TRP*     3.4     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  VAL*     4.0    26.9    -      -       +      -
    110A  ASP      3.4     9.2    -      -       -      +
    111A  MET*     3.8    26.5    -      -       +      +
    112A  GLN      4.6     0.4    -      -       -      +
    115A  SER*     1.3    81.9    -      -       -      +
    117A  VAL*     1.3    65.3    +      -       -      +
    118A  ALA*     3.6     6.0    +      -       +      -
    126A  LYS      3.6     1.2    -      -       -      +
    127A  GLN      3.4     5.8    -      -       -      +
    129A  LEU*     3.0    61.1    +      -       +      +
    131A  VAL*     3.8    13.9    -      -       +      -
    138A  TRP*     3.8    14.1    -      -       +      -
    141A  LEU*     4.2     2.7    -      -       +      -
    154A  VAL*     4.0    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  VAL*     3.7     3.6    -      -       -      +
    109A  LEU*     2.8    43.8    +      -       +      -
    110A  ASP*     2.7    39.6    +      -       +      +
    111A  MET*     5.9     0.2    -      -       -      -
    112A  GLN*     6.0     4.5    -      -       +      -
    116A  ILE*     1.3    74.2    -      -       -      +
    118A  ALA*     1.3    58.9    +      -       -      +
    125A  VAL*     4.0    24.9    -      -       +      -
    126A  LYS      3.4     4.7    -      -       -      +
    127A  GLN*     3.3    39.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  TYR*     4.0    15.7    -      -       +      -
    107A  ARG      3.1    12.1    -      -       -      +
    109A  LEU*     4.6     2.2    -      -       -      -
    116A  ILE*     3.6     6.8    +      -       +      -
    117A  VAL*     1.3    75.3    -      -       -      +
    119A  MET*     1.3    61.9    +      -       -      +
    125A  VAL*     3.5     6.9    -      -       -      +
    126A  LYS*     2.8    38.0    +      -       +      +
    129A  LEU*     3.7    31.9    -      -       +      -
    154A  VAL*     4.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  TYR*     3.5     4.0    -      -       -      -
    107A  ARG*     2.8    56.0    +      -       +      +
    109A  LEU*     3.9    37.0    -      -       +      -
    118A  ALA*     1.3    75.5    -      -       -      +
    120A  THR*     1.3    73.5    +      -       -      +
    121A  GLU      6.0     0.4    -      -       -      +
    123A  GLY*     3.5    37.9    -      -       -      +
    124A  ASP      3.3     5.8    -      -       -      +
    125A  VAL*     4.3     6.1    -      -       +      -
----------------------------------------------------------
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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