Contacts of the strand formed by residues 94 - 104 (chain C) in PDB entry 3KDH


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 SER 94 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  VAL      3.5     0.2    -      -       -      +
     86C  THR*     3.3     6.9    -      -       -      +
     87C  VAL*     2.8    41.4    +      -       -      +
     89C  SER*     5.6     1.2    +      -       -      -
     92C  PRO      4.0     6.7    +      -       -      -
     93C  ALA*     1.3    76.2    -      -       -      +
     95C  THR*     1.3    67.5    +      -       -      +
    119C  HIS*     5.1     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  GLU*     3.9    40.5    +      -       +      +
     85C  VAL      3.3     6.3    -      -       -      +
     86C  THR*     4.6     7.8    +      -       -      +
     87C  VAL*     5.5     0.2    -      -       -      -
     94C  SER*     1.3    76.5    +      -       -      +
     96C  SER*     1.3    62.6    +      -       -      +
     97C  THR*     4.0    11.6    +      -       -      +
    119C  HIS*     3.0    20.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83C  ARG      3.6     1.2    -      -       -      +
     84C  GLU*     3.5     1.0    -      -       -      -
     85C  VAL*     2.8    45.6    +      -       -      +
     87C  VAL*     4.3    15.5    -      -       -      +
     94C  SER      4.1     0.4    +      -       -      -
     95C  THR*     1.3    74.3    -      -       -      +
     97C  THR*     1.3    62.7    +      -       -      +
     98C  GLU*     2.8    30.7    +      -       -      +
    114C  VAL*     4.0    13.7    -      -       -      +
    119C  HIS*     3.8    12.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  PRO*     6.0     1.3    -      -       +      -
     48A  SER*     5.9     1.6    -      -       -      +
     73C  ILE*     4.2    10.5    -      -       +      -
     82C  VAL*     3.4    28.3    -      -       +      -
     83C  ARG      3.4     5.4    -      -       -      +
     84C  GLU*     4.1     8.2    +      -       +      +
     95C  THR*     4.0    14.1    +      -       -      +
     96C  SER*     1.3    71.3    +      -       -      +
     98C  GLU*     1.3    55.9    +      -       -      +
    114C  VAL*     3.4     8.3    -      -       -      +
    115C  VAL*     2.8    56.3    +      -       +      +
    119C  HIS*     4.8     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  PHE*     3.6     5.1    -      -       -      -
     64C  LYS*     4.6     3.2    +      -       -      -
     82C  VAL*     3.3     4.8    -      -       -      -
     83C  ARG*     2.8    79.8    +      -       +      +
     85C  VAL*     3.7    14.4    -      -       -      +
     87C  VAL*     5.9     0.3    -      -       -      +
     96C  SER*     2.8    26.7    +      -       -      +
     97C  THR*     1.3    81.2    -      -       -      +
     99C  ARG*     1.3    60.9    +      -       -      +
    112C  PHE*     3.7    22.1    -      -       +      -
    113C  ARG      3.3     6.3    -      -       -      +
    114C  VAL*     4.0    14.7    -      -       +      +
    115C  VAL*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  VAL*     3.7    26.6    -      -       -      +
    180A  ALA      3.7     2.0    +      -       -      -
    181A  ALA      2.9    27.7    +      -       -      -
    183A  SER      3.8     3.2    -      -       -      +
    184A  ALA      2.8    31.7    +      -       -      -
    186A  MET*     3.5    22.7    -      -       -      +
     57C  PHE*     3.8     3.4    -      -       -      -
     79C  VAL*     6.1     0.2    -      -       -      +
     80C  GLY*     3.7    24.3    +      -       -      +
     81C  SER      3.3    11.0    -      -       -      +
     82C  VAL*     3.9     8.9    -      -       +      +
     98C  GLU*     1.3    73.0    -      -       -      +
    100C  LEU*     1.3    69.4    +      -       -      +
    101C  GLU*     2.9    38.6    +      -       -      +
    112C  PHE*     3.2     5.5    -      -       -      -
    113C  ARG      2.9    30.2    +      -       -      +
    115C  VAL*     3.9    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 100 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55C  ARG*     4.2     5.2    -      -       -      +
     57C  PHE*     3.5    31.3    -      -       +      -
     77C  GLY      3.7    13.7    -      -       -      +
     78C  ASP      3.6    26.2    -      -       -      +
     79C  VAL*     3.6     4.1    -      -       -      +
     80C  GLY*     2.8    34.2    +      -       -      +
     81C  SER      2.9    15.0    +      -       -      +
     99C  ARG*     1.3    71.1    +      -       -      +
    101C  GLU*     1.3    60.5    +      -       -      +
    102C  PHE      3.9     0.4    -      -       -      +
    103C  VAL*     3.5    36.1    -      -       +      -
    110C  LEU*     3.5    29.2    -      -       +      -
    111C  SER      3.6    11.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  PRO*     3.3    30.8    -      -       +      +
    186A  MET*     2.7    27.5    +      -       -      +
     79C  VAL*     3.4    12.4    -      -       -      +
     99C  ARG*     2.9    54.4    +      -       -      +
    100C  LEU*     1.3    74.3    -      -       -      +
    102C  PHE*     1.3    63.0    +      -       +      +
    111C  SER*     2.8    22.5    +      -       -      +
    112C  PHE      4.2     1.1    -      -       -      -
    113C  ARG*     3.3    38.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  PRO*     5.8     3.8    -      -       +      -
     25C  TYR*     4.3    15.9    -      +       -      -
     79C  VAL*     4.0     6.2    -      -       -      +
    100C  LEU      3.6     1.0    -      -       -      -
    101C  GLU*     1.3    82.7    -      -       +      +
    103C  VAL*     1.3    77.1    +      -       -      +
    104C  ASP*     3.9    35.2    -      -       +      -
    109C  VAL*     4.1    24.5    -      -       +      -
    110C  LEU*     3.4     0.7    -      -       -      -
    111C  SER*     2.8    42.4    +      -       -      +
    127C  VAL*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 103 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  TRP*     3.9     3.8    -      -       +      -
     55C  ARG*     3.3    24.7    -      -       -      +
     79C  VAL*     4.7    12.4    -      -       +      +
    100C  LEU*     3.5    36.6    -      -       +      -
    102C  PHE*     1.3    91.1    -      -       -      +
    104C  ASP*     1.3    65.4    +      -       -      +
    105C  ASP*     3.2    27.6    -      -       -      +
    109C  VAL      3.3     8.5    -      -       -      +
    110C  LEU*     4.1     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 104 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25C  TYR*     4.3     4.3    +      -       -      +
     51C  TRP*     3.8     0.7    -      -       -      -
    102C  PHE*     3.9    21.7    -      -       +      -
    103C  VAL*     1.3    76.9    -      -       -      +
    105C  ASP*     1.3    59.2    +      -       -      +
    106C  ASP*     2.9    23.4    +      -       -      +
    107C  HIS*     2.9    35.5    +      -       +      +
    108C  ARG*     2.8    24.6    +      -       -      -
    109C  VAL*     2.9    19.9    +      -       +      +
----------------------------------------------------------
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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