Contacts of the strand formed by residues 120 - 129 (chain J) 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 J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26I  PHE*     4.2    12.3    -      +       -      -
     85I  ALA*     2.7    48.5    +      -       +      +
     86I  HIS*     3.2    28.3    +      -       -      -
     87I  SER*     3.8    16.8    +      -       -      -
    112I  ARG*     5.1     7.3    +      -       -      -
    114I  GLN*     3.6    26.6    +      -       -      +
    112J  ARG*     3.8    42.2    -      -       +      +
    113J  VAL      3.2    13.5    -      -       -      +
    114J  GLN*     4.1     1.8    -      -       +      -
    118J  GLY      3.2    21.5    -      -       -      +
    119J  SER*     1.3    78.7    +      -       -      +
    121J  HIS*     1.3    66.6    +      -       -      +
    158J  PHE*     4.8     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 121 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81I  TYR      4.2     3.8    -      -       -      -
     84I  TRP*     3.4    40.7    +      +       -      -
     86I  HIS*     2.9    39.9    -      +       -      +
    112J  ARG*     4.5     1.6    -      -       -      -
    113J  VAL*     2.8    32.9    +      -       -      +
    119J  SER*     5.2     0.4    -      -       -      -
    120J  TYR*     1.3    79.8    -      -       -      +
    122J  GLU*     1.3    61.7    +      -       -      +
    154J  ALA*     3.8    14.8    -      -       -      +
    157J  SER*     3.4    32.9    -      -       -      -
    158J  PHE*     3.3    44.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 122 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86I  HIS*     3.2    28.9    +      -       -      +
     87I  SER*     3.3    18.1    -      -       -      -
     88I  ILE*     2.7    56.6    +      -       +      +
    147I  VAL*     4.9     0.3    -      -       -      +
     89J  THR*     2.8    36.8    +      -       -      +
    110J  PHE*     4.2     6.2    -      -       +      +
    111J  VAL      3.1    14.8    -      -       -      +
    112J  ARG*     3.7    17.0    -      -       +      +
    121J  HIS*     1.3    75.6    -      -       -      +
    123J  ASP*     1.3    65.6    +      -       -      +
    154J  ALA*     4.6     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 123 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86I  HIS*     4.5     8.0    -      -       +      -
     88I  ILE*     3.8    10.3    -      -       -      -
    147I  VAL*     3.7    16.3    -      -       -      +
    148I  THR*     5.3     1.4    +      -       -      -
    151I  LEU*     5.9     0.7    -      -       -      +
    110J  PHE*     3.3     5.2    -      -       -      +
    111J  VAL*     2.9    33.6    +      -       -      +
    122J  GLU*     1.3    76.3    -      -       -      +
    124J  VAL*     1.3    73.5    +      -       -      +
    150J  GLY*     4.3     2.6    -      -       -      +
    153J  ARG*     3.1    50.2    +      -       +      +
    154J  ALA*     3.9    23.4    -      -       +      +
    157J  SER*     4.7     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 124 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88I  ILE*     4.1     3.6    -      -       +      -
     91I  GLN*     3.8     9.0    -      -       -      +
    143I  ARG*     4.0    17.5    -      -       +      +
    144I  LYS*     4.3     7.4    -      -       +      -
    147I  VAL*     3.0    37.9    -      -       +      -
    108J  CYS*     4.4     7.4    -      -       +      -
    109J  ALA      3.2     6.5    -      -       -      +
    110J  PHE*     3.4    32.3    -      -       +      -
    123J  ASP*     1.3    83.8    +      -       -      +
    125J  GLY*     1.3    68.1    +      -       -      +
    126J  TYR*     5.9     0.4    -      -       +      -
    150J  GLY*     4.0     2.9    -      -       -      -
    153J  ARG*     2.9    28.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 125 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144I  LYS*     4.6     1.8    -      -       -      -
    108J  CYS*     3.3     8.3    -      -       -      +
    109J  ALA      2.6    28.2    +      -       -      -
    124J  VAL*     1.3    77.9    -      -       -      +
    126J  TYR*     1.3    62.4    +      -       -      +
    146J  ALA      3.4     9.4    -      -       -      -
    149J  ASP*     3.2    10.8    -      -       -      -
    150J  GLY*     3.2    22.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136I  ALA*     3.7    15.0    -      -       -      -
    139I  LEU*     3.3    24.5    -      -       +      +
    140I  GLU*     3.6    44.4    -      -       +      +
    143I  ARG*     3.9    13.9    -      -       +      -
    144I  LYS*     4.2     4.7    -      -       +      -
     94J  ASP*     2.6    35.4    +      -       -      +
     95J  PHE*     4.1     1.6    -      -       -      -
    106J  GLY*     3.6    10.9    -      -       -      -
    107J  VAL      3.2    18.8    -      -       -      -
    108J  CYS*     3.6    16.8    -      -       +      -
    124J  VAL*     5.9     0.2    -      -       +      -
    125J  GLY*     1.3    72.8    -      -       -      -
    127J  GLY*     1.3    81.5    +      -       -      +
    128J  VAL*     3.7    14.0    +      -       +      +
    145J  GLU*     4.3     2.8    -      -       -      +
    146J  ALA*     3.6     5.8    +      -       -      +
    149J  ASP*     2.8    23.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 127 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105J  VAL      3.8     0.2    -      -       -      +
    106J  GLY*     3.6     1.7    -      -       -      -
    107J  VAL      2.7    35.3    +      -       -      +
    126J  TYR*     1.3    74.5    -      -       -      +
    128J  VAL*     1.3    69.3    +      -       -      +
    142J  ALA*     3.3    30.0    -      -       -      +
    145J  GLU*     4.0     5.8    -      -       -      -
    146J  ALA*     3.4     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136I  ALA*     3.4    27.4    -      -       +      -
    137I  LEU*     4.8     7.9    -      -       +      -
    140I  GLU*     4.9    10.8    -      -       -      +
    105J  VAL      3.4     6.1    -      -       -      +
    126J  TYR*     3.7    22.9    -      -       +      +
    127J  GLY*     1.3    82.0    -      -       -      +
    129J  SER*     1.3    65.3    +      -       -      +
    130J  GLU*     3.5    23.8    -      -       +      +
    141J  LYS*     2.8    32.8    +      -       -      +
    142J  ALA*     4.1     3.8    -      -       -      +
    145J  GLU*     3.8     5.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 129 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103J  PHE      3.2     5.2    +      -       -      +
    105J  VAL*     2.8    35.7    +      -       -      -
    128J  VAL*     1.3    78.3    -      -       -      +
    130J  GLU*     1.3    60.4    +      -       -      +
    131J  GLY      4.5     0.7    +      -       -      -
    132J  LEU*     4.0    11.4    -      -       -      +
    138J  SER*     3.1    49.9    +      -       -      -
    141J  LYS*     3.9    15.8    -      -       -      +
    142J  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