Contacts of the strand formed by residues 74 - 79 (chain E) in PDB entry 5A0Q


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 ILE 74 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69E  GLU*     3.9     0.7    -      -       -      -
     70E  ILE*     3.0    42.7    +      -       +      -
     71E  ASP*     3.2    11.9    +      -       -      +
     73E  HIS*     1.3   113.5    +      -       +      +
     75E  GLY*     1.4    72.7    +      -       -      +
    107E  MET      3.7     2.0    -      -       -      +
    109E  VAL*     3.8    19.5    -      -       +      -
    112E  VAL*     3.5    36.8    -      -       +      -
    143E  PHE*     4.0    16.8    -      -       +      -
    144E  GLY      3.3    10.8    -      -       -      +
    145E  GLY      4.4     0.4    -      -       -      +
    226E  PHE*     5.2     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 75 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48E  LEU*     3.8    14.1    -      -       -      -
     68E  VAL      3.8     5.8    -      -       -      -
     73E  HIS      4.1     0.8    +      -       -      -
     74E  ILE*     1.4    83.1    -      -       -      +
     76E  CYS*     1.4    60.0    +      -       -      -
    143E  PHE*     3.3     1.4    -      -       -      -
    144E  GLY      2.6    32.1    +      -       -      -
    220E  VAL*     5.2     1.2    -      -       -      +
    226E  PHE*     4.3    27.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 76 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48E  LEU*     3.9     1.8    -      -       -      +
     66E  LYS      4.3     0.5    -      -       -      +
     67E  ILE*     3.6     5.0    -      -       -      +
     68E  VAL*     2.8    33.4    +      -       +      +
     70E  ILE*     2.9    35.7    -      -       +      -
     75E  GLY*     1.4    71.3    -      -       -      +
     77E  ALA*     1.3    71.4    +      -       -      +
     78E  MET*     4.1     0.7    +      -       -      +
     89E  ILE*     4.0    14.8    -      -       -      -
    141E  LEU*     4.0    21.1    -      -       -      -
    142E  LEU      3.5     5.8    -      -       -      -
    143E  PHE*     4.1    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 77 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  ALA*     5.1     3.4    -      -       +      -
     48E  LEU*     4.0     7.7    -      -       +      +
     49E  ALA      5.2     1.3    -      -       -      +
     50E  VAL*     5.1    14.1    -      -       +      -
     66E  LYS      4.1     5.6    -      -       -      +
     67E  ILE*     3.9    21.3    -      -       +      +
     76E  CYS*     1.3    78.5    -      -       -      +
     78E  MET*     1.4    62.4    +      -       -      +
    141E  LEU*     3.5     3.3    -      -       -      -
    142E  LEU*     3.0    53.1    +      -       +      +
    170E  ILE*     5.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 78 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35E  SER      5.2     0.3    -      -       -      +
     37E  ALA*     5.0     1.2    -      -       -      +
     50E  VAL*     4.5    15.4    -      -       -      +
     65E  GLU      5.3     1.8    -      -       -      +
     66E  LYS*     3.0    44.8    +      -       +      +
     68E  VAL*     4.0    22.0    -      -       +      -
     76E  CYS      4.6     0.2    -      -       -      +
     77E  ALA*     1.4    75.7    -      -       -      +
     79E  SER*     1.4    64.3    +      -       -      +
     82E  ILE*     4.0    28.3    -      -       +      +
     85E  ALA*     3.8    31.4    -      -       +      -
     86E  LYS*     5.0    11.4    -      -       -      -
     89E  ILE*     3.5    22.4    -      -       +      -
    140E  ALA      3.5     7.0    -      -       -      +
    141E  LEU*     4.1     8.7    -      -       +      -
    170E  ILE*     4.5     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 79 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  ILE*     4.3     2.3    +      -       -      +
     34E  GLY*     3.8     1.2    -      -       -      -
     35E  SER*     2.8    33.6    +      -       -      +
     37E  ALA*     5.1     0.4    -      -       -      -
     66E  LYS*     5.8     1.3    -      -       -      +
     78E  MET*     1.4    77.3    -      -       -      +
     80E  GLY*     1.3    68.3    +      -       -      +
     81E  LEU      4.8     1.5    -      -       -      +
     82E  ILE*     5.5     3.8    -      -       -      -
     85E  ALA*     5.5     0.2    -      -       -      +
    139E  VAL*     3.3    12.3    -      -       -      +
    140E  ALA*     3.0    29.9    +      -       -      -
    170E  ILE*     3.6    24.7    -      -       -      -
    171E  GLY*     3.6    12.1    -      -       -      -
----------------------------------------------------------
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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