Contacts of the strand formed by residues 120 - 129 (chain K) 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 K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26J  PHE*     4.1    12.1    -      +       -      -
     85J  ALA*     2.8    51.0    -      -       +      +
     86J  HIS*     3.2    29.4    +      -       -      -
     87J  SER*     3.9    14.7    +      -       -      -
    112J  ARG*     5.0     7.4    +      -       -      -
    114J  GLN*     3.8    26.1    +      -       -      +
    112K  ARG*     3.7    41.3    -      -       +      +
    113K  VAL      3.2    13.9    -      -       -      +
    114K  GLN*     4.2     2.2    -      -       +      +
    118K  GLY      3.1    20.6    -      -       -      +
    119K  SER*     1.3    78.1    +      -       -      +
    121K  HIS*     1.3    66.4    +      -       -      +
    158K  PHE*     4.7     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 121 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81J  TYR      4.1     7.6    -      -       -      -
     84J  TRP*     3.3    37.0    +      +       -      -
     86J  HIS*     2.9    41.1    -      +       -      +
    112K  ARG*     4.5     1.6    -      -       -      -
    113K  VAL*     2.8    32.6    +      -       -      +
    120K  TYR*     1.3    78.5    -      -       -      +
    122K  GLU*     1.3    60.0    +      -       -      +
    154K  ALA*     3.8    13.9    -      -       -      +
    157K  SER*     3.3    37.2    -      -       -      -
    158K  PHE*     3.3    41.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 122 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86J  HIS*     3.1    31.2    +      -       -      -
     87J  SER*     3.3    19.6    -      -       -      -
     88J  ILE*     2.6    54.1    +      -       +      +
    147J  VAL*     4.9     0.3    -      -       -      +
     89K  THR*     2.9    37.2    +      -       -      +
    110K  PHE*     4.1     5.7    -      -       -      +
    111K  VAL      3.1    16.4    -      -       -      +
    112K  ARG*     3.7    17.1    -      -       +      -
    121K  HIS*     1.3    74.7    -      -       -      +
    123K  ASP*     1.3    65.2    +      -       -      +
    154K  ALA*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 123 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86J  HIS*     4.5     7.8    -      -       +      -
     88J  ILE*     3.6    14.3    -      -       -      +
    147J  VAL*     4.0    10.4    -      -       -      +
    148J  THR*     5.4     0.9    +      -       -      -
    151J  LEU*     6.0     0.5    -      -       -      +
    110K  PHE*     3.3     4.7    -      -       -      -
    111K  VAL      3.0    30.4    +      -       -      -
    122K  GLU*     1.3    75.5    -      -       -      +
    124K  VAL*     1.3    76.6    +      -       -      +
    150K  GLY      4.4     2.5    -      -       -      +
    153K  ARG*     2.9    53.4    +      -       +      +
    154K  ALA*     3.8    23.7    -      -       +      +
    157K  SER*     4.7     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 124 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88J  ILE*     4.1     2.7    -      -       +      -
     91J  GLN*     3.9     9.2    -      -       -      +
    143J  ARG*     3.9    18.2    -      -       +      +
    144J  LYS*     4.5     7.3    -      -       +      -
    147J  VAL*     2.9    38.6    -      -       +      -
    108K  CYS*     4.4     7.2    -      -       +      -
    109K  ALA      3.4     7.0    -      -       -      +
    110K  PHE*     3.5    30.3    -      -       +      +
    123K  ASP*     1.3    78.4    +      -       -      +
    125K  GLY*     1.3    68.1    +      -       -      +
    126K  TYR*     5.8     0.2    -      -       +      -
    150K  GLY*     4.0     2.7    -      -       -      -
    153K  ARG*     2.9    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 125 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144J  LYS*     4.6     2.0    -      -       -      -
    108K  CYS*     3.3     7.3    -      -       -      +
    109K  ALA      2.7    27.5    +      -       -      -
    124K  VAL*     1.3    78.0    -      -       -      +
    126K  TYR*     1.3    61.0    +      -       -      +
    146K  ALA      3.3     9.6    -      -       -      -
    149K  ASP*     3.3    11.7    -      -       -      -
    150K  GLY*     3.3    21.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136J  ALA      3.7    14.8    -      -       -      -
    139J  LEU*     3.3    24.4    -      -       +      +
    140J  GLU*     3.6    45.7    -      -       +      +
    143J  ARG*     3.7    18.8    -      -       +      -
    144J  LYS*     4.0     4.5    -      -       +      -
     94K  ASP*     2.5    35.0    +      -       -      +
     95K  PHE*     4.1     1.2    -      -       -      -
    106K  GLY*     3.6    11.1    -      -       -      -
    107K  VAL      3.3    28.3    -      -       -      -
    108K  CYS*     3.6    12.1    -      -       +      -
    124K  VAL*     5.8     0.2    -      -       +      -
    125K  GLY*     1.3    72.2    -      -       -      -
    127K  GLY*     1.3    71.2    +      -       -      +
    128K  VAL*     3.7    13.8    -      -       +      +
    145K  GLU*     4.1     2.8    -      -       -      +
    146K  ALA*     3.4     8.8    +      -       -      +
    149K  ASP*     2.9    20.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 127 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106K  GLY*     3.6     2.4    -      -       -      -
    107K  VAL      2.8    35.0    +      -       -      +
    126K  TYR*     1.3    75.4    -      -       -      +
    128K  VAL*     1.3    66.1    +      -       -      +
    142K  ALA*     3.2    27.9    -      -       -      +
    145K  GLU*     3.9     7.4    -      -       -      -
    146K  ALA*     3.4     8.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136J  ALA*     3.3    29.2    -      -       +      -
    137J  LEU*     4.7     8.3    -      -       +      -
    140J  GLU*     4.9    11.9    -      -       -      +
    105K  VAL      3.4     6.1    -      -       -      +
    126K  TYR*     3.7    22.4    -      -       +      +
    127K  GLY*     1.3    80.0    -      -       -      +
    129K  SER*     1.3    64.3    +      -       -      +
    130K  GLU*     3.6    23.1    -      -       +      +
    141K  LYS*     2.9    32.0    +      -       -      +
    142K  ALA*     4.1     4.1    -      -       -      +
    145K  GLU*     3.6     7.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 129 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103K  PHE      3.4     3.2    -      -       -      +
    104K  TYR*     3.4     0.2    -      -       -      -
    105K  VAL*     2.8    37.3    +      -       -      +
    128K  VAL*     1.3    77.7    -      -       -      +
    130K  GLU*     1.3    61.8    +      -       -      +
    131K  GLY      4.6     0.5    +      -       -      -
    132K  LEU*     3.7    14.2    -      -       -      +
    138K  SER*     3.1    49.7    +      -       -      -
    141K  LYS*     3.9    13.9    -      -       -      +
    142K  ALA      4.6     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