Contacts of the strand formed by residues 65 - 68 (chain E) in PDB entry 1ACB


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 65 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32E  SER      3.6     0.2    -      -       -      +
     33E  LEU*     3.5     6.4    -      -       -      +
     34E  GLN*     2.8    61.3    +      -       +      +
     35E  ASP      4.5     6.3    -      -       -      +
     36E  LYS*     6.1     0.7    -      -       -      -
     63E  SER      5.4     0.4    -      -       -      +
     64E  ASP*     1.3    76.5    -      -       -      +
     66E  VAL*     1.4    62.5    +      -       -      +
     67E  VAL*     3.7    15.3    -      -       +      -
     82E  LYS*     4.3    24.7    -      -       +      -
     83E  LEU      3.6    18.4    -      -       -      +
     84E  LYS*     4.6    15.5    -      -       -      +
     85E  ILE*     4.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 66 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  VAL*     4.0    27.8    -      -       +      -
     32E  SER      3.8     2.7    -      -       -      -
     33E  LEU*     4.4    11.7    -      -       +      -
     52E  VAL*     4.1    14.8    -      -       +      -
     65E  VAL*     1.4    73.0    -      -       -      +
     67E  VAL*     1.3    61.0    +      -       -      +
     68E  ALA      3.8     0.3    +      -       -      -
     81E  GLN      3.3     3.3    -      -       -      +
     82E  LYS*     3.5     0.7    -      -       -      -
     83E  LEU*     2.8    60.8    +      -       +      +
     85E  ILE*     3.8    20.9    -      -       +      -
    106E  LEU*     4.4     9.4    -      -       +      -
    108E  LEU*     3.5    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 67 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  GLN      4.6     0.2    -      -       -      +
     31E  VAL*     3.3     7.1    -      -       -      -
     32E  SER*     2.8    49.8    +      -       -      +
     34E  GLN*     3.7    30.3    -      -       -      +
     65E  VAL*     3.7    14.6    -      -       +      -
     66E  VAL*     1.3    73.0    -      -       -      +
     68E  ALA*     1.3    68.9    +      -       -      +
     70E  GLU*     3.9    25.1    -      -       +      +
     80E  ILE*     4.4    15.7    -      -       +      -
     81E  GLN      3.4     6.7    -      -       -      +
     82E  LYS*     4.1    20.9    -      -       +      -
    141E  TRP*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 68 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  GLN      4.8     0.4    -      -       -      -
     31E  VAL*     4.0    18.8    -      -       +      +
     46E  LEU*     4.5     2.2    -      -       +      -
     66E  VAL      3.8     0.4    +      -       -      -
     67E  VAL*     1.3    76.8    -      -       -      +
     69E  GLY*     1.3    59.0    +      -       -      +
     70E  GLU*     3.2     7.1    +      -       -      -
     80E  ILE*     3.6     4.9    -      -       -      +
     81E  GLN*     2.9    41.0    +      -       +      +
     83E  LEU*     4.4    16.8    -      -       +      -
    118E  VAL*     4.2    22.2    -      -       +      -
----------------------------------------------------------
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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