Contacts of the strand formed by residues 114 - 120 (chain P) 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 LYS 114 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169C  PHE*     4.1    28.5    +      -       +      +
    170C  SER*     5.2     3.6    -      -       -      -
    263C  LEU*     4.4     1.1    -      -       -      -
    110P  LYS*     3.9     0.7    -      -       -      -
    111P  TRP*     3.0    47.3    +      -       -      +
    112P  GLN*     3.0    42.3    +      -       +      +
    113P  GLY*     1.3    79.0    -      -       -      +
    115P  PRO*     1.3    69.7    -      -       +      +
    116P  VAL*     3.7     1.1    +      -       -      +
    156P  LEU*     4.6    22.6    -      -       +      +
    158P  ILE*     4.5    17.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 115 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262C  PRO      4.2     6.1    -      -       -      +
    263C  LEU*     3.6    26.0    -      -       +      -
    108P  VAL*     4.0    15.0    -      -       +      -
    109P  VAL      3.7     6.1    -      -       -      +
    113P  GLY      3.9     6.1    -      -       -      +
    114P  LYS*     1.3    84.3    -      -       -      +
    116P  VAL*     1.3    60.1    +      -       -      +
    117P  PHE*     5.0     0.7    -      -       +      -
    156P  LEU*     3.8     7.3    -      -       -      +
    157P  GLY*     2.9    49.9    +      -       -      +
    158P  ILE*     3.6    15.0    -      -       +      -
    165P  VAL*     3.7    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 116 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107P  VAL      3.6     0.7    -      -       -      +
    108P  VAL*     3.5     4.9    -      -       -      +
    109P  VAL*     2.7    47.2    +      -       +      +
    111P  TRP*     3.7    32.1    -      -       +      -
    114P  LYS      4.2     0.7    -      -       -      +
    115P  PRO*     1.3    75.0    -      -       -      +
    117P  PHE*     1.3    65.8    +      -       -      +
    118P  ILE*     3.8     7.6    +      -       +      +
    154P  ILE*     3.9    24.7    -      -       +      -
    155P  MET      3.6     9.9    -      -       -      +
    156P  LEU*     3.7    19.5    -      -       +      -
    203P  PRO*     4.8     1.6    -      -       +      -
    214P  VAL*     4.4    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 117 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106P  ASN*     6.4     1.8    -      -       +      -
    107P  VAL      3.7     2.7    -      -       -      -
    108P  VAL*     3.9    33.9    -      -       +      -
    115P  PRO*     4.0     1.7    +      -       +      -
    116P  VAL*     1.3    72.8    -      -       -      +
    118P  ILE*     1.3    64.7    +      -       -      +
    153P  LEU      3.5     1.4    -      -       -      +
    154P  ILE*     3.4     1.7    -      -       -      +
    155P  MET*     2.9    57.6    +      -       +      +
    157P  GLY*     3.7    24.5    -      -       -      -
    165P  VAL*     3.4    23.8    -      -       +      -
    166P  PRO*     3.3    29.6    -      -       +      -
    168P  GLY      5.6     0.4    -      -       -      -
    176P  TRP*     3.6    38.6    -      +       +      -
    200P  LEU*     4.3     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 118 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96P  VAL*     3.9    37.5    -      -       +      -
     98P  LEU*     4.1    13.9    -      -       +      -
    101P  ILE*     4.0    18.6    -      -       +      +
    105P  LYS      3.9     1.4    -      -       -      +
    106P  ASN*     3.6     2.8    -      -       -      +
    107P  VAL*     2.9    45.5    +      -       +      +
    109P  VAL*     4.5     5.4    -      -       +      -
    116P  VAL*     4.1    13.5    -      -       +      +
    117P  PHE*     1.3    80.7    -      -       -      +
    119P  ARG*     1.3    62.5    +      -       -      +
    152P  TRP*     4.1     8.5    -      -       +      -
    153P  LEU      3.2     2.9    -      -       -      +
    154P  ILE*     3.8    30.1    -      -       +      -
    212P  VAL*     4.6     8.1    -      -       +      -
    214P  VAL*     5.0     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 119 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104P  GLY*     3.8    17.5    +      -       -      -
    105P  LYS      3.5    10.8    -      -       -      +
    106P  ASN*     2.8    56.4    +      -       -      +
    117P  PHE*     5.7     0.2    -      -       -      +
    118P  ILE*     1.3    73.7    -      -       -      +
    120P  HIS*     1.3    68.5    +      -       -      +
    121P  ARG*     3.4    17.5    -      -       +      +
    122P  THR*     5.5     0.6    -      -       -      +
    125P  GLU*     2.8    40.3    +      -       -      -
    151P  GLN      3.3     4.0    -      -       -      +
    152P  TRP*     3.5     9.0    -      -       -      -
    153P  LEU*     2.9    38.7    +      -       +      -
    169P  GLU*     3.4    29.3    +      -       -      +
    176P  TRP*     4.1    19.0    -      -       +      -
    187P  ILE*     4.3     9.0    -      -       -      +
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Residues in contact with HIS 120 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101P  ILE*     3.4    11.8    +      -       +      +
    102P  PRO      2.8    29.9    +      -       -      +
    103P  LEU*     2.4    60.2    -      -       +      +
    104P  GLY*     4.1     4.0    -      -       -      -
    105P  LYS      3.2     5.8    +      -       -      +
    118P  ILE      4.3     0.2    +      -       -      -
    119P  ARG*     1.3    76.4    +      -       -      +
    121P  ARG*     1.3    59.2    +      -       -      +
    122P  THR      3.6     0.5    +      -       -      -
    151P  GLN*     3.3    46.0    +      -       +      +
    152P  TRP*     3.3    32.4    -      +       +      -
----------------------------------------------------------
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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