Contacts of the strand formed by residues 229 - 237 (chain A) in PDB entry 5JKC


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 GLY 229 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  ARG*     4.8     0.4    -      -       -      -
    228A  ALA*     1.3    75.3    -      -       -      +
    230A  SER*     1.3    63.8    +      -       -      -
    231A  TYR*     3.7     7.6    -      -       -      -
    249A  HIS*     3.6     4.5    -      -       -      -
    250A  VAL*     2.8    36.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  ARG*     3.6     7.7    +      -       -      +
    201A  VAL*     2.9    56.8    +      -       -      +
    229A  GLY*     1.3    69.5    -      -       -      -
    231A  TYR*     1.3    70.1    +      -       -      +
    247A  ASN*     5.6     2.9    -      -       -      -
    248A  PHE      3.6     3.6    -      -       -      -
    249A  HIS*     3.0    30.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  MET*     4.0    21.8    -      -       +      +
    180A  LEU*     3.8    23.3    -      -       +      -
    198A  PHE*     5.8     3.8    -      +       +      -
    199A  TYR      3.2    10.3    -      -       -      +
    200A  ARG*     3.5    43.0    +      -       +      +
    201A  VAL*     4.7     1.8    -      -       -      +
    210A  VAL*     5.5     1.3    -      -       +      -
    218A  LEU*     4.7    12.6    -      -       +      -
    220A  LYS*     5.1     6.1    +      -       -      -
    227A  ASP*     2.6    41.6    +      -       -      +
    229A  GLY      3.7    12.3    -      -       -      -
    230A  SER*     1.3    77.2    -      -       -      +
    232A  ARG*     1.3    61.0    +      -       -      +
    247A  ASN*     3.5     8.7    +      -       -      -
    248A  PHE*     2.9    37.4    +      -       +      +
    250A  VAL*     3.7    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  SER      3.6     1.2    -      -       -      +
    198A  PHE*     3.5     6.3    -      -       -      -
    199A  TYR*     2.8    54.0    +      -       +      +
    201A  VAL*     3.7    15.7    -      -       +      +
    207A  GLU*     2.9    43.2    +      -       -      -
    231A  TYR*     1.3    74.2    -      -       -      +
    233A  CYS*     1.3    64.5    +      -       -      +
    234A  GLU*     2.8    29.6    +      -       -      +
    245A  ILE*     3.9    22.9    -      -       +      -
    246A  ILE      3.5     5.4    -      -       -      +
    247A  ASN*     3.8    26.2    -      -       -      +
    248A  PHE*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  CYS*     2.0    49.6    -      -       +      -
    196A  TYR*     3.8    13.9    -      -       -      -
    197A  SER      3.3     8.5    -      -       -      -
    198A  PHE*     3.9    20.0    -      -       +      -
    232A  ARG*     1.3    72.8    -      -       -      +
    234A  GLU*     1.3    71.0    +      -       -      +
    235A  LEU      4.4     0.4    -      -       -      -
    244A  THR      3.6     0.3    -      -       -      +
    245A  ILE*     3.2     8.8    -      -       -      +
    246A  ILE*     2.8    36.7    +      -       +      +
    248A  PHE*     3.9     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  ASP      3.3     3.3    -      -       -      +
    197A  SER*     2.8    49.3    +      -       -      +
    199A  TYR*     3.9    16.5    +      -       +      -
    232A  ARG*     2.8    41.6    +      -       -      +
    233A  CYS*     1.3    81.5    -      -       -      +
    235A  LEU*     1.3    59.2    +      -       -      +
    236A  GLY*     3.7     0.8    +      -       -      -
    242A  PRO*     4.2    19.6    -      -       +      +
    244A  THR      3.4     4.0    -      -       -      +
    245A  ILE*     4.2    15.4    -      -       +      +
     42B  LYS*     5.5     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  HIS*     3.6    37.2    -      -       +      +
    193A  LEU*     3.6    32.8    -      -       +      -
    194A  THR      4.6     2.0    -      -       -      +
    195A  ASP      3.5    20.6    -      -       -      +
    196A  TYR*     3.9    30.1    -      -       +      +
    233A  CYS*     4.2     1.0    -      -       -      -
    234A  GLU*     1.3    72.1    -      -       -      +
    236A  GLY*     1.3    70.3    +      -       -      +
    242A  PRO*     3.6     4.1    -      -       -      +
    243A  ALA*     2.8    35.9    +      -       +      -
    244A  THR*     3.0    25.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  LEU*     3.5     9.4    -      -       -      +
    194A  THR*     2.8    38.6    +      -       -      -
    195A  ASP      2.8    14.9    +      -       -      -
    234A  GLU*     3.7     1.9    +      -       -      -
    235A  LEU*     1.3    77.1    -      -       -      +
    237A  SER*     1.3    56.3    +      -       -      -
    242A  PRO*     4.8     6.1    -      -       -      -
    243A  ALA*     4.8     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU*     3.9    13.5    -      -       -      +
    192A  GLY      3.4    12.3    +      -       -      -
    193A  LEU*     4.4     1.0    -      -       -      +
    194A  THR*     3.5    11.4    +      -       -      +
    236A  GLY*     1.3    74.1    -      -       -      -
    238A  VAL*     1.3    59.8    +      -       -      +
    239A  ASN*     3.0    32.7    +      -       -      +
    240A  SER      4.9     0.9    +      -       -      +
    241A  SER      3.3    24.2    +      -       -      -
    243A  ALA*     4.6    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