Contacts of the strand formed by residues 188 - 194 (chain A) in PDB entry 4H3E


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 ARG 188 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  TYR*     3.2    61.9    -      -       +      +
     22A  THR*     4.7     0.7    -      -       -      -
    162A  CYS*     4.0     1.8    -      -       -      -
    163A  VAL*     2.8    41.1    +      -       +      +
    165A  PRO*     3.8    30.3    -      -       +      +
    169A  ASN*     5.7     0.4    +      -       -      -
    186A  GLY      4.3     4.6    +      -       -      +
    187A  LEU*     1.3    74.5    -      -       -      +
    189A  PRO*     1.3    70.8    -      -       -      +
    190A  VAL*     3.5     2.6    +      -       -      +
    230A  GLN      4.7     1.0    +      -       -      -
    231A  ALA*     2.8    52.1    +      -       +      -
    233A  LYS*     5.1     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  TYR*     5.7     1.0    +      -       -      -
     22A  THR*     3.6    24.9    +      -       +      +
    108A  PHE*     4.2    20.2    -      -       +      -
    112A  PHE*     3.5    16.5    -      -       +      -
    160A  TRP*     3.6    34.8    -      -       +      -
    161A  LEU      3.8     0.2    -      -       -      +
    162A  CYS*     3.8    12.6    -      -       -      -
    182A  PRO*     4.6     9.0    -      -       +      -
    183A  LEU*     5.1     6.1    -      -       +      +
    187A  LEU      3.6     9.2    -      -       -      +
    188A  ARG*     1.3    86.8    -      -       -      +
    190A  VAL*     1.3    61.6    +      -       -      +
    191A  LEU      4.8     0.2    -      -       -      +
    227A  MET*     4.0     6.8    -      -       -      +
    231A  ALA*     5.5     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  PHE*     3.6    10.9    -      -       -      -
    116A  CYS*     4.3     0.9    -      -       -      -
    128A  PHE*     4.5     3.4    -      -       +      -
    161A  LEU*     2.8    45.8    +      -       +      +
    163A  VAL*     4.0    15.3    -      -       +      +
    171A  LEU*     4.4     6.7    -      -       +      -
    188A  ARG      3.9     8.1    -      -       -      +
    189A  PRO*     1.3    77.0    -      -       -      +
    191A  LEU*     1.3    58.0    +      -       -      +
    224A  VAL*     3.2    46.0    -      -       +      +
    227A  MET*     3.8     9.1    -      -       -      +
    228A  HIS*     3.6    31.0    -      -       +      +
    231A  ALA*     4.7     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  PHE*     3.7     7.1    -      -       -      -
    116A  CYS*     3.9    19.3    -      -       +      -
    142A  PHE*     4.3     8.5    -      -       +      -
    146A  PHE*     4.0    26.5    -      -       +      -
    160A  TRP*     3.2     9.9    -      -       -      +
    161A  LEU*     3.0    37.6    +      -       +      +
    190A  VAL*     1.3    79.9    -      -       -      +
    192A  ALA*     1.3    76.4    +      -       -      +
    193A  VAL*     4.4     1.6    -      -       +      -
    216A  TRP*     4.1    11.4    -      -       +      -
    219A  ILE*     3.9    19.3    -      -       +      -
    221A  TRP*     4.1    25.4    -      -       +      -
    224A  VAL*     4.1    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  ASN      4.8     0.2    -      -       -      +
    112A  PHE*     3.8    11.2    -      -       +      -
    113A  TYR*     3.3    24.6    -      -       +      +
    116A  CYS*     3.6    12.9    -      -       -      +
    158A  TRP*     4.5    10.5    -      -       +      -
    159A  THR      3.6     4.3    -      -       -      -
    160A  TRP*     3.4    35.7    -      -       +      -
    191A  LEU*     1.3    79.1    -      -       -      +
    193A  VAL*     1.3    70.3    +      -       -      +
    219A  ILE*     5.4     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  TYR*     3.8     2.2    -      -       -      -
    146A  PHE*     3.7    30.5    -      -       +      -
    158A  TRP*     3.5     3.9    -      -       -      -
    159A  THR*     2.8    36.3    +      -       -      +
    191A  LEU*     4.4    11.4    -      -       +      -
    192A  ALA*     1.3    79.9    -      -       -      +
    194A  ASP*     1.3    67.1    +      -       -      +
    195A  VAL*     3.5     2.6    +      -       +      +
    211A  TYR*     3.6    19.3    -      -       +      +
    212A  LEU*     3.6    27.8    -      -       +      -
    215A  ILE*     4.2    24.9    -      -       +      -
    216A  TRP*     5.7     1.3    -      -       +      -
    219A  ILE*     4.7     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  HIS*     2.8    12.0    +      -       -      -
    110A  HIS*     3.5     1.6    +      -       -      -
    113A  TYR*     3.5    20.3    -      -       +      -
    157A  GLY      3.4     0.5    -      -       -      +
    158A  TRP*     3.4    27.7    -      -       +      -
    193A  VAL*     1.3    69.9    -      -       -      +
    195A  VAL*     1.3    58.7    +      -       -      +
    196A  TRP*     3.1    36.5    +      -       -      +
    198A  HIS*     3.7     0.3    +      -       -      -
    199A  ALA*     3.8    16.3    -      -       +      +
    211A  TYR*     2.7    32.4    +      -       -      -
    301A  FE2      2.0    31.2    -      -       -      -
----------------------------------------------------------
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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