Contacts of the strand formed by residues 120 - 129 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  ARG*     3.6    42.8    -      -       -      +
    113A  VAL      3.1    13.9    -      -       -      +
    114A  GLN*     4.2     1.6    -      -       +      -
    118A  GLY      3.2    21.1    -      -       -      +
    119A  SER*     1.3    77.7    +      -       -      +
    121A  HIS*     1.3    66.3    +      -       -      +
    158A  PHE*     4.7     2.5    -      -       -      -
     26K  PHE*     4.1     3.8    -      +       -      -
     85K  ALA*     2.8    50.5    +      -       +      +
     86K  HIS      3.1    31.9    +      -       -      -
     87K  SER*     3.7    16.2    +      -       -      -
    112K  ARG*     4.9     9.0    +      -       -      -
    114K  GLN*     3.5    34.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  ARG*     3.6     1.7    -      -       -      -
    113A  VAL*     2.8    33.6    +      -       -      +
    119A  SER*     5.1     0.2    -      -       -      -
    120A  TYR*     1.3    80.1    -      -       -      +
    122A  GLU*     1.3    59.4    +      -       -      +
    154A  ALA*     3.8    12.9    -      -       -      +
    157A  SER*     3.4    31.1    -      -       -      -
    158A  PHE*     3.3    47.3    -      +       +      -
     81K  TYR      4.1     4.9    -      -       -      -
     84K  TRP*     3.3    39.8    +      +       -      -
     86K  HIS*     2.9    43.1    -      +       -      +
----------------------------------------------------------
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Residues in contact with GLU 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  THR*     2.9    36.9    +      -       -      +
    110A  PHE*     4.1     5.6    -      -       +      +
    111A  VAL      3.1    17.3    -      -       -      +
    112A  ARG*     3.7    17.0    -      -       +      -
    121A  HIS*     1.3    76.6    -      -       -      +
    123A  ASP*     1.3    67.2    +      -       -      +
    154A  ALA*     4.5     1.1    -      -       -      -
     86K  HIS*     3.1    29.1    +      -       -      -
     87K  SER*     3.4    17.9    -      -       -      -
     88K  ILE*     2.6    57.4    +      -       +      +
    147K  VAL*     4.7     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  PHE*     3.3     5.0    -      -       -      -
    111A  VAL*     2.9    32.3    +      -       -      +
    122A  GLU*     1.3    75.9    -      -       -      +
    124A  VAL*     1.3    77.4    +      -       -      +
    150A  GLY      4.4     3.1    -      -       -      +
    153A  ARG*     3.1    49.5    +      -       +      +
    154A  ALA*     3.8    23.9    -      -       +      +
    157A  SER*     4.7     3.5    +      -       -      -
     86K  HIS*     4.5     7.3    -      -       +      -
     88K  ILE*     3.7    12.7    -      -       -      +
    147K  VAL*     3.8    11.5    -      -       -      +
    148K  THR*     5.4     1.2    +      -       -      -
    151K  LEU*     6.0     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  CYS*     4.4     7.0    -      -       +      -
    109A  ALA      3.2     7.4    -      -       -      +
    110A  PHE*     3.4    30.7    -      -       +      -
    123A  ASP*     1.3    85.5    +      -       -      +
    125A  GLY*     1.3    68.0    +      -       -      +
    126A  TYR*     5.9     0.2    -      -       +      -
    150A  GLY*     4.0     2.5    -      -       -      -
    153A  ARG*     2.9    29.3    +      -       -      +
     88K  ILE*     4.2     2.2    -      -       +      -
     91K  GLN*     3.9     9.2    -      -       -      +
    143K  ARG*     3.9    17.5    -      -       +      +
    144K  LYS*     4.4     8.1    -      -       +      -
    147K  VAL*     3.0    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  CYS*     3.3     7.3    -      -       -      +
    109A  ALA      2.7    28.5    +      -       -      -
    124A  VAL*     1.3    78.0    -      -       -      +
    126A  TYR*     1.3    61.2    +      -       -      +
    146A  ALA      3.3     9.6    -      -       -      -
    149A  ASP*     3.4     6.3    -      -       -      -
    150A  GLY*     3.3    26.8    -      -       -      -
    144K  LYS*     4.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ASP*     2.6    35.4    +      -       -      +
     95A  PHE*     4.0     1.2    -      -       -      -
    106A  GLY*     3.6    11.4    -      -       -      -
    107A  VAL      3.3    16.2    -      -       -      -
    108A  CYS*     3.6    17.0    -      -       +      -
    124A  VAL*     5.9     0.2    -      -       +      -
    125A  GLY*     1.3    72.8    -      -       -      -
    127A  GLY*     1.3    80.0    +      -       -      +
    128A  VAL*     3.7    14.0    +      -       +      +
    145A  GLU*     4.1     3.1    -      -       -      +
    146A  ALA*     3.5     7.9    +      -       -      +
    149A  ASP*     2.9    21.4    +      -       -      +
    136K  ALA      3.5    15.7    -      -       -      -
    139K  LEU*     3.4    21.7    -      -       +      +
    140K  GLU*     3.5    49.2    -      -       +      +
    143K  ARG*     3.8    12.6    -      -       +      -
    144K  LYS*     4.0     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  GLY*     3.7     0.5    -      -       -      -
    107A  VAL      2.7    37.2    +      -       -      +
    126A  TYR*     1.3    74.2    -      -       -      +
    128A  VAL*     1.3    67.6    +      -       -      +
    142A  ALA*     3.2    27.7    -      -       -      +
    145A  GLU*     3.9     7.0    -      -       -      -
    146A  ALA*     3.4     8.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  VAL      3.5     4.9    -      -       -      +
    126A  TYR*     3.7    23.8    -      -       +      +
    127A  GLY*     1.3    80.7    -      -       -      +
    129A  SER*     1.3    63.9    +      -       -      +
    130A  GLU*     3.5    28.5    -      -       +      +
    141A  LYS*     2.9    32.4    +      -       -      +
    142A  ALA*     3.8     4.5    -      -       -      +
    145A  GLU*     3.7     7.1    +      -       -      +
    136K  ALA*     3.6    21.1    -      -       +      -
    137K  LEU*     4.7     8.5    -      -       +      -
    140K  GLU*     4.8    11.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  PHE      3.4     1.6    -      -       -      +
    104A  TYR*     3.4     1.9    -      -       -      -
    105A  VAL*     2.7    39.2    +      -       -      +
    128A  VAL*     1.3    78.4    -      -       -      +
    130A  GLU*     1.3    61.2    +      -       -      +
    131A  GLY      4.6     0.2    +      -       -      -
    132A  LEU*     3.7    14.7    -      -       -      +
    138A  SER*     3.2    49.6    +      -       -      -
    141A  LYS*     3.9    13.2    -      -       -      +
    142A  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