Contacts of the strand formed by residues 185 - 189 (chain A) in PDB entry 5EAA


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 VAL 185 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  LEU*     3.7    20.9    -      -       +      -
    125A  VAL*     3.6    31.0    -      -       +      -
    129A  ARG      3.2    12.1    +      -       -      +
    133A  VAL*     3.3    14.1    -      -       +      +
    134A  TRP*     3.0    26.3    +      -       -      -
    184A  ASP*     1.3    70.4    -      -       -      +
    186A  VAL*     1.3    62.1    +      -       -      +
    218A  LEU*     3.1    25.8    -      -       +      +
    220A  LEU*     3.6    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  TRP*     4.0    12.6    -      -       +      +
    158A  TYR*     4.0    15.5    -      -       +      -
    177A  LEU*     4.3    17.7    -      -       +      -
    180A  ALA*     5.0     0.2    -      -       +      -
    184A  ASP      3.8     1.0    +      -       -      +
    185A  VAL*     1.3    77.5    -      -       -      +
    187A  LEU*     1.3    63.4    +      -       -      +
    188A  PHE*     3.4    41.2    +      -       +      -
    212A  SER*     5.4     0.4    -      -       -      +
    217A  TRP*     3.8    40.6    -      -       +      -
    218A  LEU      2.9     7.8    +      -       -      +
    219A  PRO*     3.5     4.6    -      -       +      +
    220A  LEU*     2.8    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  LEU*     4.7     4.7    -      -       +      -
    133A  VAL*     4.5     7.2    -      -       +      -
    134A  TRP      2.9    19.7    +      -       -      +
    135A  VAL*     4.5    11.7    -      -       +      -
    136A  SER      4.3     0.8    +      -       -      +
    143A  HIS*     3.7    40.4    -      -       +      +
    147A  PHE*     3.7    30.1    -      -       +      -
    158A  TYR*     2.7    28.8    +      -       -      -
    185A  VAL      4.0     0.4    +      -       -      -
    186A  VAL*     1.3    72.8    -      -       -      +
    188A  PHE*     1.3    61.1    -      -       -      +
    189A  HIS*     4.0    17.4    +      -       +      +
    220A  LEU*     3.2    21.8    -      -       +      +
    222A  ASP*     4.8     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  TYR*     3.2    28.3    -      +       -      -
    160A  TYR*     6.2     2.2    -      +       -      -
    173A  LEU*     5.4     0.4    -      -       +      -
    177A  LEU*     4.5    10.8    -      -       +      -
    186A  VAL*     3.4    32.8    -      -       +      -
    187A  LEU*     1.3    74.3    -      -       -      +
    189A  HIS*     1.3    57.5    +      -       -      +
    190A  GLY      3.7     0.2    -      -       -      -
    205A  TRP*     3.8    24.5    -      +       +      -
    208A  LEU*     4.2    25.6    -      -       +      -
    212A  SER*     4.9     4.5    -      -       -      -
    217A  TRP*     5.3     3.8    -      +       -      -
    219A  PRO*     5.1     3.8    -      -       +      -
    220A  LEU      2.9     7.1    +      -       -      +
    221A  PHE*     3.2    18.2    -      +       +      -
    222A  ASP*     2.7    32.4    +      -       -      +
    243A  PHE*     3.4    42.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with HIS 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  SER*     4.1     5.2    +      -       -      -
    139A  SER*     3.1    28.0    +      -       -      -
    140A  TRP      4.3     2.0    +      -       -      -
    143A  HIS*     3.8    17.4    -      +       -      -
    158A  TYR*     5.2     0.4    +      -       -      -
    160A  TYR*     6.0     0.4    -      -       -      +
    187A  LEU*     4.0    11.0    +      -       +      +
    188A  PHE*     1.3    72.2    -      -       -      +
    190A  GLY*     1.3    65.3    +      -       -      +
    191A  SER*     3.2     5.7    +      -       -      +
    192A  CYS      4.7     1.8    -      -       -      -
    193A  HIS*     3.7    37.6    +      +       +      -
    194A  ASN*     3.3    41.0    +      -       +      +
    195A  PRO*     4.4     0.4    -      -       -      +
    199A  ASP*     5.2     2.6    -      -       -      +
    200A  PRO*     5.3     2.1    -      -       -      +
    205A  TRP*     3.5    16.2    -      -       -      -
    222A  ASP*     3.5    11.2    -      -       +      +
    458A  PLP      4.2    11.6    -      -       +      +
----------------------------------------------------------
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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