Contacts of the strand formed by residues 120 - 129 (chain F) in PDB entry 1KN0


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 TYR 120 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26E  PHE*     4.2    11.7    -      +       -      -
     85E  ALA*     2.8    48.6    -      -       +      +
     86E  HIS      3.1    29.1    +      -       -      -
     87E  SER*     3.8    15.5    +      -       -      -
    112E  ARG*     4.9     7.8    +      -       -      -
    114E  GLN*     3.8    28.8    +      -       -      +
    112F  ARG*     3.8    41.7    -      -       +      +
    113F  VAL      3.1    13.2    -      -       -      +
    114F  GLN*     4.1     2.2    -      -       +      -
    118F  GLY      3.2    20.0    -      -       -      +
    119F  SER*     1.3    79.6    +      -       -      +
    121F  HIS*     1.3    68.4    +      -       -      +
    158F  PHE*     4.7     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 121 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81E  TYR      4.0     5.8    -      -       -      -
     84E  TRP*     3.2    46.3    +      +       -      -
     86E  HIS*     3.0    39.0    -      +       -      +
    111F  VAL      4.1     0.2    -      -       -      +
    112F  ARG*     3.5     2.3    -      -       -      -
    113F  VAL*     2.7    37.5    +      -       -      +
    119F  SER*     4.8     0.2    -      -       -      -
    120F  TYR*     1.3    76.6    -      -       -      +
    122F  GLU*     1.3    58.8    +      -       -      +
    154F  ALA*     3.7    20.3    -      -       -      +
    157F  SER*     3.4    20.8    -      -       -      -
    158F  PHE*     3.2    47.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 122 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86E  HIS*     3.2    28.3    +      -       -      +
     87E  SER*     3.3    18.6    -      -       -      -
     88E  ILE*     2.5    56.8    +      -       +      +
    147E  VAL*     4.9     0.2    -      -       -      +
     89F  THR*     2.7    37.3    +      -       -      +
    110F  PHE*     4.2     5.5    -      -       +      +
    111F  VAL      3.1    15.7    -      -       -      +
    112F  ARG*     3.7    16.1    -      -       +      -
    121F  HIS*     1.3    75.2    -      -       -      +
    123F  ASP*     1.3    65.5    +      -       -      +
    154F  ALA*     4.7     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 123 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86E  HIS*     4.5     8.4    -      -       +      -
     88E  ILE*     3.8    10.5    -      -       -      -
    147E  VAL*     3.6    18.6    -      -       -      +
    148E  THR*     5.1     2.3    +      -       -      -
    151E  LEU*     5.9     0.5    -      -       -      +
    110F  PHE*     3.5     2.8    -      -       -      +
    111F  VAL*     2.9    33.6    +      -       -      +
    122F  GLU*     1.3    76.1    -      -       -      +
    124F  VAL*     1.3    75.1    +      -       -      +
    150F  GLY      4.4     2.9    -      -       -      +
    153F  ARG*     3.1    66.9    +      -       +      +
    154F  ALA*     3.9     5.4    -      -       -      +
    157F  SER*     4.7     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 124 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88E  ILE*     4.1     3.6    -      -       +      -
     91E  GLN*     3.8     8.1    -      -       -      +
    143E  ARG*     4.0    17.0    -      -       +      +
    144E  LYS*     4.4     8.5    -      -       +      -
    147E  VAL*     3.0    36.3    -      -       +      -
    108F  CYS*     4.3     7.4    -      -       +      -
    109F  ALA      3.2     9.0    -      -       -      +
    110F  PHE*     3.6    29.2    -      -       +      -
    123F  ASP*     1.3    82.3    +      -       -      +
    125F  GLY*     1.3    69.5    +      -       -      +
    126F  TYR*     5.8     0.2    -      -       +      -
    150F  GLY*     4.0     3.6    -      -       -      -
    153F  ARG*     2.8    29.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 125 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144E  LYS*     4.5     1.1    -      -       -      -
    108F  CYS*     3.3     7.6    -      -       -      +
    109F  ALA      2.6    28.3    +      -       -      -
    124F  VAL*     1.3    79.1    -      -       -      +
    126F  TYR*     1.3    61.1    +      -       -      +
    146F  ALA*     3.2    22.4    -      -       -      -
    149F  ASP*     3.4     4.9    -      -       -      -
    150F  GLY*     3.3    14.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136E  ALA      3.5    15.6    +      -       -      -
    139E  LEU*     3.2    22.7    -      -       +      +
    140E  GLU*     3.3    50.7    -      -       +      +
    143E  ARG*     3.8    13.7    -      -       +      -
    144E  LYS*     3.9     4.5    -      -       +      -
     94F  ASP*     2.6    34.1    +      -       -      +
     95F  PHE*     4.1     0.9    -      -       -      -
    106F  GLY*     3.7     9.5    -      -       -      -
    107F  VAL      3.1    23.1    -      -       -      -
    108F  CYS*     3.6    16.4    -      -       +      -
    124F  VAL*     5.8     0.4    -      -       +      -
    125F  GLY*     1.3    72.8    -      -       -      -
    127F  GLY*     1.3    76.9    -      -       -      +
    128F  VAL*     3.6    13.2    -      -       +      +
    145F  GLU*     4.2     2.6    -      -       -      +
    146F  ALA*     3.4     7.3    +      -       -      +
    149F  ASP*     2.9    21.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 127 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105F  VAL      3.9     0.2    -      -       -      +
    106F  GLY*     3.8     0.5    -      -       -      -
    107F  VAL      2.7    32.3    +      -       -      +
    126F  TYR*     1.3    74.6    -      -       -      +
    128F  VAL*     1.3    68.6    +      -       -      +
    142F  ALA*     3.2    27.5    -      -       -      +
    145F  GLU*     3.9     7.4    -      -       -      -
    146F  ALA*     3.2     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136E  ALA*     3.4    27.4    -      -       +      -
    137E  LEU*     4.6    11.4    -      -       +      -
    140E  GLU*     4.8     7.6    -      -       -      +
    105F  VAL      3.5     6.1    -      -       -      +
    126F  TYR*     3.6    23.3    -      -       +      +
    127F  GLY*     1.3    81.9    -      -       -      +
    129F  SER*     1.3    60.6    +      -       -      +
    130F  GLU*     3.5    23.3    -      -       +      +
    141F  LYS*     2.8    38.0    +      -       -      +
    142F  ALA*     3.9     4.1    -      -       -      +
    145F  GLU*     3.9     7.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 129 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103F  PHE      3.2     3.9    -      -       -      +
    104F  TYR*     3.4     0.2    -      -       -      -
    105F  VAL*     2.8    35.8    +      -       -      -
    128F  VAL*     1.3    78.6    -      -       -      +
    130F  GLU*     1.3    62.4    +      -       -      +
    131F  GLY      4.5     0.5    +      -       -      -
    132F  LEU*     3.7    14.9    -      -       -      +
    138F  SER*     3.3    49.6    +      -       -      -
    141F  LYS*     4.0    14.4    -      -       -      +
    142F  ALA*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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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