Contacts of the strand formed by residues 188 - 194 (chain A) in PDB entry 4E4Z


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 188 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  ILE      3.2    10.8    -      -       -      -
     67A  ARG*     4.2     2.1    -      -       -      +
    100A  ARG*     2.7    39.3    +      -       -      -
    109A  MET*     3.4    22.8    -      -       -      +
    169A  LEU*     3.7     9.4    -      -       -      -
    186A  CYS      3.9     1.0    +      -       -      -
    187A  SER*     1.3    76.8    -      -       -      +
    189A  VAL*     1.3    60.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LEU      3.7     1.4    -      -       -      +
     65A  ASP*     4.6     3.4    -      -       -      -
     66A  ILE*     2.8    38.9    +      -       +      +
     67A  ARG*     4.4     0.8    -      -       -      +
     97A  PHE*     4.1     9.4    -      -       +      -
     98A  LYS      3.6    16.6    -      -       -      +
    100A  ARG*     4.4     1.6    -      -       -      +
    109A  MET*     4.3     9.4    -      -       +      -
    110A  LEU      6.0     0.2    -      -       -      -
    111A  LEU*     4.8     9.6    -      -       +      +
    139A  TYR*     4.0    35.9    -      -       +      -
    169A  LEU*     4.0    19.3    -      -       +      -
    188A  GLY*     1.3    80.6    -      -       -      +
    190A  SER*     1.3    73.1    +      -       -      +
    191A  VAL*     3.9    11.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ALA*     3.8    16.5    -      -       -      +
     64A  LEU      3.5     3.5    +      -       -      -
     65A  ASP*     2.9    30.8    +      -       -      -
     97A  PHE*     3.4     3.3    -      -       -      -
     98A  LYS*     2.7    51.4    +      -       -      +
    100A  ARG*     4.1    22.3    +      -       -      +
    189A  VAL*     1.3    72.5    -      -       -      +
    191A  VAL*     1.3    60.9    +      -       -      +
    192A  HIS      4.1     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ALA*     3.2     5.8    -      -       -      -
     64A  LEU*     2.7    40.6    +      -       +      +
     66A  ILE*     3.4    31.2    -      -       +      -
     94A  VAL*     3.3    38.1    -      -       +      -
     96A  ASP      3.6     2.9    -      -       -      +
     97A  PHE*     4.2     4.5    -      -       +      -
    111A  LEU*     3.8    16.4    -      -       +      -
    167A  PHE*     4.4     5.2    -      -       +      -
    189A  VAL*     4.1    10.1    -      -       +      +
    190A  SER*     1.3    76.3    +      -       -      +
    192A  HIS*     1.3    59.7    +      -       -      +
    193A  LEU*     3.7    20.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LEU*     3.5    28.0    -      -       +      +
     61A  ASP*     2.8    24.8    +      -       -      -
     62A  PHE      3.8     2.5    -      -       -      -
     63A  ALA*     4.5     3.8    -      -       +      +
     94A  VAL*     3.5     4.3    -      -       -      -
     95A  ILE*     2.9    50.8    +      -       +      +
     96A  ASP*     3.0    35.3    +      -       +      +
     98A  LYS*     6.5     0.9    -      -       +      -
    190A  SER      4.1     1.0    +      -       -      -
    191A  VAL*     1.3    70.1    -      -       -      +
    193A  LEU*     1.3    74.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  ASP*     3.2     3.8    -      -       -      -
     62A  PHE*     2.8    58.2    +      -       +      +
     64A  LEU*     3.8    22.4    -      -       +      -
     86A  LEU*     3.8    23.6    -      -       +      -
     92A  ALA*     4.0    13.5    -      -       +      -
     93A  PHE      3.3     4.5    -      -       -      +
     94A  VAL*     4.0    14.6    -      -       +      -
    158A  VAL*     3.9    20.9    -      -       +      -
    167A  PHE*     4.3     5.6    -      -       +      -
    191A  VAL*     3.7    26.7    -      -       +      +
    192A  HIS*     1.3    81.8    -      -       -      +
    194A  THR*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  SER      3.4     6.3    -      -       -      -
     61A  ASP*     2.6    30.1    +      -       -      -
     62A  PHE*     6.0     1.3    -      -       -      -
     92A  ALA*     3.6     6.0    -      -       -      -
     93A  PHE*     2.9    42.5    +      -       +      +
     95A  ILE*     3.9    17.0    -      -       +      -
    193A  LEU*     1.3    75.3    -      -       -      +
    195A  ARG*     1.3    63.1    +      -       -      +
    196A  VAL*     3.0    35.3    +      -       -      +
    198A  GLN*     3.7    13.9    -      -       -      +
----------------------------------------------------------
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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