Contacts of the strand formed by residues 120 - 129 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  PHE*     4.2    11.7    -      +       -      -
     85D  ALA*     2.9    37.5    -      -       +      +
     86D  HIS      3.0    42.0    -      -       -      -
     87D  SER*     3.7    17.0    +      -       -      -
    112D  ARG*     4.7     8.8    +      -       -      -
    114D  GLN*     3.9    26.7    +      -       -      +
    112E  ARG*     3.8    40.4    -      -       +      +
    113E  VAL      3.1    14.4    -      -       -      +
    114E  GLN*     4.2     2.2    -      -       +      +
    118E  GLY      3.3    20.0    -      -       -      +
    119E  SER*     1.3    77.5    +      -       -      +
    121E  HIS*     1.3    74.2    +      -       -      +
    158E  PHE*     4.8     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 121 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81D  TYR      4.1     5.4    -      -       -      -
     84D  TRP*     3.2    52.7    +      +       -      -
     86D  HIS*     2.8    41.5    -      +       -      +
    112E  ARG*     3.5     1.7    -      -       -      -
    113E  VAL*     2.8    33.3    +      -       -      +
    119E  SER*     4.7     0.4    -      -       -      -
    120E  TYR*     1.3    79.9    +      -       -      +
    122E  GLU*     1.3    60.3    +      -       -      +
    154E  ALA*     3.9    13.1    -      -       -      +
    157E  SER*     3.5    24.3    -      -       -      -
    158E  PHE*     3.2    47.0    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 122 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86D  HIS*     3.3    28.2    +      -       -      -
     87D  SER*     3.3    17.9    -      -       -      -
     88D  ILE*     2.6    57.0    +      -       +      +
    147D  VAL*     4.6     0.5    -      -       -      +
     89E  THR*     3.0    37.9    +      -       -      +
    110E  PHE*     4.1     6.3    -      -       +      +
    111E  VAL      3.1    14.8    -      -       -      +
    112E  ARG*     3.6    16.7    -      -       +      +
    121E  HIS*     1.3    75.4    -      -       -      +
    123E  ASP*     1.3    67.3    +      -       -      +
    154E  ALA*     4.6     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 123 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86D  HIS*     4.7     7.1    -      -       -      -
     88D  ILE*     3.9    10.8    -      -       -      -
    147D  VAL*     3.9    11.3    -      -       -      +
    148D  THR*     5.2     1.9    +      -       -      -
    151D  LEU*     5.9     0.5    -      -       -      +
    110E  PHE*     3.5     3.5    -      -       -      +
    111E  VAL*     2.9    33.6    +      -       -      +
    122E  GLU*     1.3    76.5    -      -       -      +
    124E  VAL*     1.3    78.4    +      -       -      +
    125E  GLY      4.0     0.2    +      -       -      -
    150E  GLY*     4.4     1.5    -      -       -      +
    153E  ARG*     2.9    52.7    +      -       +      +
    154E  ALA*     3.8    23.3    -      -       +      +
    157E  SER*     4.7     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 124 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  ILE*     4.1     0.2    -      -       +      -
     91D  GLN*     3.8     7.6    -      -       -      +
    143D  ARG*     3.8    22.2    -      -       +      +
    144D  LYS*     4.4     7.5    -      -       +      -
    147D  VAL*     2.9    36.8    -      -       +      -
    108E  CYS*     4.4     6.1    -      -       +      -
    109E  ALA      3.4     5.6    -      -       -      +
    110E  PHE*     3.3    36.3    -      -       +      -
    123E  ASP*     1.3    84.3    +      -       -      +
    125E  GLY*     1.3    67.7    +      -       -      +
    126E  TYR*     5.8     0.4    -      -       +      -
    150E  GLY*     4.0     3.0    -      -       -      -
    153E  ARG*     2.9    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 125 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144D  LYS*     4.7     0.7    -      -       -      -
    108E  CYS*     3.2     6.9    -      -       -      +
    109E  ALA      2.6    30.0    +      -       -      -
    124E  VAL*     1.3    77.3    -      -       -      +
    126E  TYR*     1.3    60.4    +      -       -      +
    146E  ALA      3.1    22.9    -      -       -      -
    149E  ASP*     3.4     5.2    -      -       -      -
    150E  GLY*     3.3    14.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  ALA      3.3    17.1    +      -       -      -
    139D  LEU*     3.0    25.6    -      -       +      +
    140D  GLU*     3.4    45.7    -      -       +      +
    143D  ARG*     3.7    14.4    -      -       +      -
    144D  LYS*     4.1     4.7    -      -       +      +
     94E  ASP*     2.6    35.2    +      -       -      +
     95E  PHE*     4.2     0.9    -      -       -      -
    106E  GLY*     3.7     9.8    -      -       -      -
    107E  VAL      3.2    23.6    -      -       -      -
    108E  CYS*     3.5    17.3    -      -       +      -
    124E  VAL*     5.8     0.4    -      -       +      -
    125E  GLY*     1.3    71.7    -      -       -      -
    127E  GLY*     1.3    76.1    +      -       -      +
    128E  VAL*     3.7    13.4    +      -       +      +
    145E  GLU*     4.2     1.9    -      -       -      +
    146E  ALA*     3.4     7.5    +      -       -      +
    149E  ASP*     2.8    21.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 127 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106E  GLY*     3.9     0.3    -      -       -      -
    107E  VAL      2.7    35.6    +      -       -      +
    126E  TYR*     1.3    74.3    -      -       -      +
    128E  VAL*     1.3    68.9    +      -       -      +
    142E  ALA*     3.1    27.7    -      -       -      +
    145E  GLU*     3.8     7.2    -      -       -      -
    146E  ALA*     3.3     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  ALA*     3.3    30.5    -      -       +      -
    137D  LEU*     4.7    11.4    -      -       +      -
    140D  GLU*     5.0     7.2    -      -       -      +
    105E  VAL      3.6     6.1    -      -       -      +
    126E  TYR*     3.7    20.4    -      -       +      +
    127E  GLY*     1.3    81.5    -      -       -      +
    129E  SER*     1.3    59.9    +      -       -      +
    130E  GLU*     3.5    24.0    -      -       +      +
    141E  LYS*     2.8    37.9    +      -       -      +
    142E  ALA*     3.9     5.1    -      -       -      +
    145E  GLU*     3.6     6.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 129 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  PHE      3.2     4.0    +      -       -      +
    105E  VAL*     2.9    31.2    +      -       -      -
    128E  VAL*     1.3    78.8    -      -       -      +
    130E  GLU*     1.3    62.4    +      -       -      +
    132E  LEU*     3.9    12.6    -      -       -      +
    138E  SER*     2.9    51.6    +      -       -      -
    141E  LYS*     3.9    14.4    -      -       -      +
----------------------------------------------------------
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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