Contacts of the helix formed by residues 72 - 87 (chain A) in PDB entry 1KYZ


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 ASP 72 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  ASN*     2.9    19.2    +      -       -      +
     71A  PRO*     1.3    84.1    -      -       -      +
     73A  ALA*     1.3    66.5    +      -       -      +
     74A  PRO*     3.3     2.8    -      -       -      -
     75A  VAL*     3.4    10.1    +      -       +      +
     76A  MET*     3.1    32.2    +      -       +      +
    150E  GLY*     5.4     3.3    -      -       -      -
    151E  GLY      5.7     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ALA*     4.1    13.2    -      -       +      -
     66A  LEU*     4.8     0.4    -      -       +      -
     68A  THR*     4.6     9.6    -      -       +      -
     70A  ASN*     3.1    25.2    +      -       +      +
     72A  ASP*     1.3    76.8    -      -       -      +
     74A  PRO*     1.3    69.1    -      -       +      +
     76A  MET*     3.3     4.3    +      -       -      +
     77A  LEU*     2.9    30.0    +      -       +      +
    147E  VAL*     4.1    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  PRO*     3.3    21.7    -      -       +      +
     60A  ILE*     3.9    36.6    -      -       +      +
     63A  ALA*     3.7    16.1    -      -       +      -
     70A  ASN      4.1     1.6    -      -       -      +
     71A  PRO*     3.4    15.3    -      -       +      +
     72A  ASP      3.4     4.3    -      -       -      -
     73A  ALA*     1.3    93.8    -      -       +      +
     75A  VAL*     1.3    60.2    +      -       +      +
     77A  LEU*     3.1     2.5    +      -       +      +
     78A  ASP*     2.8    25.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  ASP*     3.4    11.3    +      -       +      +
     74A  PRO*     1.3    77.3    -      -       +      +
     76A  MET*     1.3    64.3    +      -       +      +
     78A  ASP*     3.2     8.9    +      -       +      +
     79A  ARG*     3.2    38.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  ASN*     4.2     9.0    -      -       -      -
     72A  ASP*     3.1    24.7    -      -       +      +
     73A  ALA*     3.3     6.0    +      -       -      +
     75A  VAL*     1.3    77.8    -      -       +      +
     77A  LEU*     1.3    62.9    +      -       -      +
     79A  ARG*     3.3     3.6    +      -       -      +
     80A  MET*     3.2    26.6    +      -       -      +
    143E  LEU*     4.6     4.5    -      -       +      -
    146E  ALA*     3.8    43.7    -      -       +      +
    147E  VAL*     4.1    21.8    -      -       +      +
    150E  GLY*     5.6     0.7    -      -       -      -
    151E  GLY      4.1     9.4    -      -       -      +
    153E  PRO*     5.1     2.9    -      -       +      -
    321E  LEU*     3.6    36.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  LEU*     4.2     8.7    -      -       +      -
     44A  LEU*     3.8    33.0    -      -       +      -
     59A  PRO*     4.0     5.6    -      -       +      +
     62A  ILE*     4.2     8.5    -      -       +      -
     63A  ALA*     3.7    27.6    -      -       +      +
     66A  LEU*     3.6    22.2    -      -       +      -
     73A  ALA      2.9    21.7    +      -       -      +
     74A  PRO*     3.5     3.1    -      -       +      +
     76A  MET*     1.3    74.4    -      -       -      +
     78A  ASP*     1.3    58.3    +      -       -      +
     80A  MET*     3.1     9.4    +      -       -      -
     81A  LEU*     2.8    50.0    +      -       +      +
    147E  VAL*     4.2    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  PRO*     3.6    21.6    -      -       +      +
     74A  PRO      2.8    13.5    +      -       -      +
     75A  VAL*     3.2    14.8    +      -       +      +
     77A  LEU*     1.3    75.2    -      -       -      +
     79A  ARG*     1.3    58.8    +      -       +      +
     81A  LEU*     4.3     1.6    -      -       -      -
     82A  ARG*     2.9    30.9    +      -       -      +
    103A  GLN*     6.0     0.2    -      -       -      -
    104A  ARG*     2.6    40.4    +      -       -      +
    106A  TYR*     2.8    35.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  VAL*     3.2    29.6    +      -       +      +
     76A  MET*     3.6     6.1    -      -       -      +
     77A  LEU      3.2     0.2    -      -       -      -
     78A  ASP*     1.3    78.8    -      -       +      +
     80A  MET*     1.3    61.1    +      -       -      +
     82A  ARG*     3.7    19.0    +      -       -      +
     83A  LEU      3.5    10.2    +      -       -      -
    314E  VAL*     4.8     0.7    -      -       -      +
    317E  ASP*     2.8    60.6    +      -       -      +
    318E  VAL*     3.5    18.6    -      -       +      +
    320E  MET*     3.7     0.4    -      -       -      +
    321E  LEU*     3.5    41.2    -      -       +      +
    324E  ASN      5.7     1.0    +      -       -      -
    326E  GLY      5.8     0.8    -      -       -      -
    327E  GLY      3.0    27.4    +      -       -      -
    328E  LYS*     3.5    12.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ILE*     3.8    26.7    -      -       +      +
     38A  SER*     3.8    19.5    -      -       -      -
     39A  ALA*     4.1    14.4    -      -       +      +
     42A  LEU*     4.2    10.8    -      -       +      -
     44A  LEU*     4.7     5.8    -      -       +      -
     76A  MET      3.2    15.6    +      -       -      +
     77A  LEU*     3.1    22.3    +      -       -      +
     79A  ARG*     1.3    74.1    -      -       -      +
     81A  LEU*     1.3    67.7    +      -       +      +
     83A  LEU*     3.1    15.1    +      -       -      +
     84A  LEU*     3.3    15.5    +      -       +      +
    143E  LEU*     3.8    29.8    -      -       +      -
    147E  VAL*     4.2    11.9    -      -       -      -
    318E  VAL*     4.6     4.3    -      -       -      -
    321E  LEU*     3.9    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     4.0    26.5    -      -       +      -
     45A  LEU*     6.3     0.7    -      -       +      -
     48A  ILE*     4.5     5.6    -      -       +      -
     59A  PRO*     4.3     5.8    -      -       +      -
     62A  ILE*     3.9    26.5    -      -       +      -
     77A  LEU*     2.8    40.7    +      -       +      +
     78A  ASP      4.2     0.7    -      -       -      +
     80A  MET*     1.3    68.9    -      -       -      +
     82A  ARG*     1.3    59.9    +      -       -      +
     84A  LEU*     3.0     9.7    +      -       +      +
     85A  ALA*     2.8    29.3    +      -       -      +
     90A  LEU*     3.4    25.6    -      -       +      +
    106A  TYR*     3.5    39.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  ASP*     2.9    18.5    +      -       -      +
     79A  ARG*     3.8    21.9    +      -       -      +
     81A  LEU*     1.3    75.3    -      -       -      +
     83A  LEU*     1.3    63.8    +      -       -      +
     85A  ALA*     3.2     3.5    +      -       -      +
     86A  CYS*     3.0    23.0    +      -       -      -
    104A  ARG*     3.8    38.0    -      -       -      +
    106A  TYR*     3.3    15.8    +      -       -      +
    300E  LEU*     3.4    35.3    -      -       -      +
    301E  PRO      5.1     5.8    +      -       -      -
    302E  VAL      5.4     1.1    -      -       -      -
    303E  ALA      6.0     0.4    -      -       -      -
    304E  PRO*     4.1    16.6    -      -       +      +
    314E  VAL*     4.2    22.2    -      -       +      +
    317E  ASP*     3.1    32.9    +      -       -      -
    329E  GLU      5.4     0.4    +      -       -      -
    331E  THR*     6.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  VAL*     3.6    30.5    -      -       +      +
     32A  LEU*     4.0    12.1    -      -       -      -
     35A  ILE*     3.7    24.2    -      -       +      -
     79A  ARG      3.5     1.8    +      -       -      -
     80A  MET      3.1    10.3    +      -       -      +
     82A  ARG*     1.3    81.7    -      -       -      +
     84A  LEU*     1.3    64.9    +      -       +      +
     86A  CYS*     3.2     4.9    +      -       +      +
     87A  TYR*     3.2    34.5    +      -       +      -
    311E  LYS*     5.9     0.2    -      -       -      -
    314E  VAL*     3.6    25.1    -      -       +      +
    315E  HIS*     3.7    30.7    -      -       +      +
    318E  VAL*     4.1    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     4.4     7.6    -      -       +      -
     35A  ILE*     4.0    18.4    -      -       +      -
     36A  LEU*     4.0    21.5    -      -       +      +
     39A  ALA*     3.9    26.7    -      -       +      -
     44A  LEU*     5.7     0.2    -      -       +      -
     45A  LEU*     5.3     3.4    -      -       +      -
     80A  MET*     3.7    13.9    -      -       +      +
     81A  LEU*     3.0    12.9    +      -       +      +
     83A  LEU*     1.3    75.7    -      -       +      +
     85A  ALA*     1.3    63.6    +      -       -      +
     87A  TYR*     3.2     2.8    +      -       -      +
     88A  ILE      3.1     4.3    +      -       -      -
     89A  ILE*     2.9    56.1    +      -       +      +
     90A  LEU*     3.9    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  LEU      2.8    15.7    +      -       -      +
     82A  ARG      3.5     5.2    -      -       -      +
     84A  LEU*     1.3    73.9    -      -       -      +
     86A  CYS*     1.3    65.8    +      -       -      +
     88A  ILE*     3.0    23.0    +      -       -      +
     90A  LEU*     3.3    20.4    -      -       -      +
     92A  CYS*     4.0    11.0    -      -       +      -
    106A  TYR*     3.9    20.6    -      -       +      -
    304E  PRO*     3.9    16.3    -      -       +      -
    305E  ASP      5.5     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ARG      3.0    17.7    +      -       -      -
     83A  LEU*     3.2    10.3    +      -       +      +
     85A  ALA*     1.3    77.8    -      -       -      +
     87A  TYR*     1.3    58.0    +      -       +      +
     88A  ILE*     3.4     3.1    +      -       -      +
    304E  PRO*     3.9    15.7    -      -       -      -
    305E  ASP      3.4    24.0    -      -       -      +
    306E  SER*     3.4    18.2    +      -       -      -
    310E  THR*     4.0     8.1    -      -       -      -
    311E  LYS*     3.4    30.4    -      -       +      -
    314E  VAL*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  GLN*     2.9    32.5    +      -       -      +
     32A  LEU*     3.9    45.7    -      -       +      +
     83A  LEU*     3.2    34.2    +      -       +      +
     84A  LEU      3.2     7.4    +      -       -      +
     85A  ALA      3.1     0.6    -      -       -      -
     86A  CYS*     1.3    80.4    -      -       +      +
     88A  ILE*     1.3    70.7    +      -       -      +
     89A  ILE*     3.4     7.6    +      -       +      +
      9E  ILE*     4.0     6.1    -      -       +      +
     10E  THR*     3.4    25.2    +      -       -      -
     11E  PRO      4.7     4.3    -      -       -      +
     22E  PHE*     4.0    18.0    -      +       +      -
     26E  LEU*     6.0     0.2    -      -       +      -
    311E  LYS*     3.7    22.6    -      -       +      +
    315E  HIS*     2.6    36.9    +      -       -      -
----------------------------------------------------------
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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