Contacts of the strand formed by residues 84 - 99 (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 TRP 84 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26F  PHE*     3.9     2.7    -      -       -      -
     72F  ILE*     4.3    11.9    -      -       +      -
     75F  ALA*     3.8    25.1    -      -       +      -
     76F  ASN*     3.0    24.0    +      -       -      +
     79F  PHE*     3.7    19.3    -      +       +      -
     80F  GLY      3.3    16.8    +      -       -      -
     81F  TYR      4.1     3.0    +      -       -      +
     82F  ASN      3.5     0.4    -      -       -      -
     83F  GLY*     1.3    81.4    -      -       -      +
     85F  ALA*     1.3    73.7    +      -       -      +
     86F  HIS*     4.3     3.8    -      +       +      -
    113F  VAL*     3.9    16.4    -      -       +      -
    114F  GLN      3.3     7.9    -      -       -      +
    115F  LEU*     4.0     8.1    -      -       +      -
    151F  LEU*     3.8    38.4    -      -       +      -
    155F  LEU*     4.0    12.3    -      -       +      -
    119G  SER*     3.9     9.7    +      -       -      -
    121G  HIS*     3.2    44.5    +      +       -      -
    157G  SER*     3.7    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26F  PHE*     3.6    16.8    -      -       +      -
     84F  TRP*     1.3    80.7    -      -       -      +
     86F  HIS*     1.3    58.0    +      -       -      +
    113F  VAL*     3.2     6.8    -      -       -      +
    114F  GLN      2.7    35.4    +      -       -      +
    120G  TYR*     2.8    52.5    -      -       +      +
    121G  HIS*     4.0     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84F  TRP*     4.3     4.0    -      +       +      -
     85F  ALA*     1.3    78.1    -      -       -      +
     87F  SER*     1.3    61.4    +      -       -      +
     88F  ILE*     5.7     0.6    -      -       -      +
    111F  VAL*     3.8    20.5    -      -       +      +
    112F  ARG      3.1    11.4    -      -       -      +
    113F  VAL*     4.2     2.9    -      -       +      -
    147F  VAL*     5.2     6.3    -      -       +      -
    151F  LEU*     3.5    39.5    -      -       +      +
    120G  TYR*     3.1    20.4    +      -       -      -
    121G  HIS*     2.8    42.2    -      +       +      +
    122G  GLU      3.2    42.0    +      -       -      -
    123G  ASP*     4.7     7.8    -      -       -      +
    154G  ALA*     6.0     0.2    -      -       -      -
    157G  SER*     3.5    14.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 87 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86F  HIS*     1.3    78.1    -      -       -      +
     88F  ILE*     1.3    67.0    +      -       -      +
     89F  THR*     3.6     2.3    +      -       -      -
    111F  VAL*     3.5     5.9    -      -       -      +
    112F  ARG*     2.9    44.6    +      -       -      +
    112G  ARG*     5.0     6.7    -      -       -      -
    120G  TYR*     3.8    17.7    +      -       -      -
    122G  GLU*     3.4    18.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86F  HIS*     5.7     0.2    -      -       -      +
     87F  SER*     1.3    74.5    -      -       -      +
     89F  THR*     1.3    68.3    +      -       -      +
     90F  GLN*     3.7    22.8    -      -       -      +
     91F  GLN*     4.4     3.4    -      -       +      -
    109F  ALA*     4.8     0.7    -      -       +      -
    110F  PHE      3.5    11.2    -      -       -      +
    111F  VAL*     4.6     6.7    -      -       +      +
    147F  VAL*     3.5    37.0    -      -       +      -
    110G  PHE*     3.7    33.7    -      -       +      -
    122G  GLU*     2.8    34.2    +      -       +      +
    123G  ASP*     3.9    22.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 89 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88E  ILE      5.7     2.5    -      -       -      +
     87F  SER*     3.6     4.7    +      -       -      -
     88F  ILE*     1.3    74.3    -      -       -      +
     90F  GLN*     1.3    67.4    +      -       +      +
    110F  PHE*     2.8    17.7    +      -       +      -
    112F  ARG*     3.9    17.2    -      -       -      +
    122F  GLU*     2.7    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 90 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88F  ILE*     3.2     8.0    -      -       -      +
     89F  THR*     1.3    90.1    -      -       +      +
     91F  GLN*     1.3    71.6    +      -       -      +
     92F  ASN*     4.6     9.0    -      -       +      +
    109F  ALA*     3.4     0.5    -      -       -      -
    110F  PHE*     2.7    53.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 91 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88F  ILE*     4.3     2.1    -      -       +      +
     90F  GLN*     1.3    80.7    -      -       -      +
     92F  ASN*     1.3    64.0    +      -       -      +
    107F  VAL*     3.9    11.6    -      -       +      +
    108F  CYS      3.4    12.3    -      -       -      +
    109F  ALA*     4.0     9.5    -      -       +      +
    143F  ARG*     2.8    74.5    +      -       -      +
    147F  VAL*     3.7    11.6    -      -       -      +
    110G  PHE*     3.0    42.4    -      -       +      -
    124G  VAL*     3.7     3.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 92 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143E  ARG*     4.4     7.3    -      -       -      +
     90F  GLN*     4.3    11.6    -      -       +      +
     91F  GLN*     1.3    75.6    -      -       -      +
     93F  VAL*     1.3    69.2    +      -       -      +
     94F  ASP*     3.2    29.1    +      -       -      +
    107F  VAL*     4.4     2.2    -      -       -      -
    108F  CYS*     3.0    44.4    +      -       -      -
    110F  PHE*     5.7     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91F  GLN      4.3     0.2    +      -       -      -
     92F  ASN*     1.3    79.5    +      -       -      +
     94F  ASP*     1.3    64.1    +      -       -      +
     95F  PHE*     4.0     7.4    -      -       -      +
     96F  VAL*     3.8    29.2    -      -       +      -
    106F  GLY      3.9     2.7    -      -       -      -
    107F  VAL*     4.0    21.3    -      -       +      -
    139F  LEU*     4.4     7.4    -      -       +      -
    143F  ARG*     3.6    39.7    -      -       -      +
     94G  ASP*     5.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 94 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93E  VAL*     5.0     1.3    -      -       -      +
    139E  LEU*     3.2    25.2    -      -       +      +
    143E  ARG*     2.5    34.9    +      -       -      -
     92F  ASN*     3.2    20.3    +      -       -      +
     93F  VAL*     1.3    73.0    -      -       -      +
     95F  PHE*     1.3    63.6    +      -       +      +
    106F  GLY      2.8    15.3    +      -       -      +
    108F  CYS*     4.5     0.2    -      -       -      -
    126F  TYR*     2.6    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 95 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135E  LYS*     3.3    44.9    -      -       +      +
    136E  ALA*     3.2    35.7    -      -       +      -
    139E  LEU*     3.7    23.3    -      -       +      -
     93F  VAL*     3.4     2.9    -      -       -      +
     94F  ASP*     1.3    79.4    -      -       +      +
     96F  VAL*     1.3    71.5    +      -       -      +
     97F  ASP*     3.4    18.4    -      -       -      +
    104F  TYR*     3.0    33.2    -      -       +      -
    105F  VAL*     3.4     3.0    -      -       -      +
    106F  GLY*     3.1    40.5    +      -       -      +
    130F  GLU*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93F  VAL*     3.8    12.1    -      -       +      -
     95F  PHE*     1.3    83.0    -      -       -      +
     97F  ASP*     1.3    61.9    +      -       -      +
     98F  LEU*     4.2     0.7    +      -       -      +
    103F  PHE*     4.4    12.0    -      -       +      -
    104F  TYR      3.7     4.0    -      -       -      -
    105F  VAL*     3.8    14.4    -      -       +      -
    135F  LYS*     4.2    27.1    -      -       +      -
    139F  LEU*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 97 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135E  LYS*     2.8    40.2    +      -       -      -
     95F  PHE*     3.4     9.6    -      -       -      +
     96F  VAL*     1.3    79.7    +      -       -      +
     98F  LEU*     1.3    60.4    +      -       -      +
     99F  ASN*     4.1    10.3    -      -       -      +
    102F  LYS      3.7     0.3    -      -       -      +
    103F  PHE*     3.4     9.6    -      -       -      -
    104F  TYR*     2.9    44.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96F  VAL      4.2     0.6    +      -       -      +
     97F  ASP*     1.3    74.5    -      -       -      +
     99F  ASN*     1.3    64.1    +      -       -      +
    100F  ASN      4.0     2.3    +      -       -      +
    101F  GLY*     3.6    18.2    -      -       -      +
    102F  LYS      3.2    31.6    -      -       -      +
    103F  PHE*     3.7    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 99 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97F  ASP*     4.1    10.2    -      -       -      +
     98F  LEU*     1.3    75.9    -      -       -      +
    100F  ASN*     1.3    88.1    +      -       -      +
    102F  LYS*     3.0    21.3    +      -       -      +
    104F  TYR*     3.7    39.3    -      -       +      +
----------------------------------------------------------
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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