Contacts of the strand formed by residues 23 - 27 (chain H) in PDB entry 3EXG


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 23 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154G  TYR*     4.2     0.2    -      -       -      -
     16H  GLU*     4.6     2.7    -      -       -      +
     17H  LEU*     3.1    30.2    -      -       +      +
     20H  ASP*     3.6    29.8    -      -       +      +
     21H  GLU      3.2     3.0    -      -       -      -
     22H  LYS*     1.3    77.6    -      -       -      +
     24H  PHE*     1.3    64.0    +      -       -      +
     51H  ARG*     2.8    28.9    +      -       -      +
     75H  ARG*     3.4    31.9    -      -       +      +
     77H  ILE*     3.8    18.6    -      -       +      -
    161H  ILE*     4.3    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 24 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150G  LEU*     3.7    30.7    -      -       +      -
    154G  TYR*     3.9    22.2    -      +       -      +
     17H  LEU*     4.1     2.5    -      -       -      -
     22H  LYS      4.2     6.5    -      -       -      -
     23H  VAL*     1.3    77.8    -      -       -      +
     25H  LEU*     1.3    62.1    +      -       -      +
     26H  LEU*     4.1    15.7    -      -       +      -
     50H  LYS      4.3     1.6    -      -       -      +
     51H  ARG*     3.3    19.3    -      -       -      +
     53H  ILE*     3.5    22.9    -      -       +      -
     66H  ALA*     5.2     1.1    -      -       -      -
     69H  ALA*     3.8     8.5    -      -       +      -
     74H  LEU*     4.0    24.5    -      -       +      -
     75H  ARG      3.5     2.4    +      -       -      -
     76H  PRO*     3.4    31.9    -      -       +      +
     77H  ILE*     2.6    40.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 25 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13H  MET*     4.5    13.2    -      -       +      -
     17H  LEU*     5.3     4.0    -      -       +      -
     24H  PHE*     1.3    75.5    -      -       -      +
     26H  LEU*     1.3    69.7    +      -       -      +
     30H  VAL*     3.8    28.2    -      -       +      +
     40H  SER*     3.9    20.6    -      -       -      -
     43H  LEU*     4.6     5.2    -      -       +      -
     51H  ARG      2.8     8.8    +      -       -      +
     52H  ILE*     3.7    23.2    -      -       +      +
     53H  ILE*     3.1    25.1    +      -       -      +
     77H  ILE*     3.3    38.8    -      -       +      +
     79H  GLU*     4.3    14.4    -      -       +      +
    115H  ARG*     4.5     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 26 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150G  LEU*     5.2     1.1    -      -       +      -
    185G  TRP*     4.8     7.4    -      -       +      -
     24H  PHE*     4.1    24.2    -      -       +      -
     25H  LEU*     1.3    77.1    -      -       -      +
     27H  GLY*     1.3    57.2    -      -       -      +
     30H  VAL*     4.3     5.4    -      -       -      -
     53H  ILE*     3.4    21.8    -      -       +      +
     55H  THR*     4.2    14.6    -      -       +      -
     62H  PHE*     4.3    22.0    -      -       +      +
     65H  ILE*     4.5    17.3    -      -       +      -
     66H  ALA*     3.9    11.2    -      -       +      -
     76H  PRO*     4.7     1.1    -      -       +      -
     77H  ILE      2.9    21.5    +      -       -      +
     78H  CYS*     3.6    18.9    -      -       +      -
     79H  GLU*     2.8    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 27 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26H  LEU*     1.3    77.1    -      -       -      +
     28H  GLU*     1.3    66.6    +      -       -      -
     29H  GLU      3.6     1.0    +      -       -      -
     30H  VAL*     3.6    14.3    -      -       -      +
     53H  ILE      3.3     7.7    +      -       -      +
     54H  ASP*     3.6     0.7    -      -       -      -
     55H  THR*     2.9    31.2    +      -       -      +
     62H  PHE*     4.3     5.4    -      -       -      -
     79H  GLU      3.7    14.8    -      -       -      -
----------------------------------------------------------
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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