Contacts of the strand formed by residues 25 - 30 (chain A) in PDB entry 2EXG


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 LEU 25 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  VAL*     4.8     6.5    -      -       +      -
     23A  MET*     4.1     4.9    -      -       +      +
     24A  GLY*     1.3    83.3    -      -       -      +
     26A  SER*     1.3    61.5    +      -       -      +
     42A  VAL*     5.8     0.4    -      -       +      -
     44A  SER      3.9     4.0    -      -       -      +
     45A  VAL*     3.8    27.6    -      -       +      -
     46A  VAL*     3.2    12.2    -      -       -      +
     51A  ALA*     3.7    26.9    -      -       +      +
     52A  ASP      3.8    11.7    -      -       -      +
     57A  LEU*     3.9    24.5    -      -       +      -
     90A  VAL*     4.8     0.7    -      -       +      -
    102A  STF      3.0    68.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU*     1.3    76.8    -      -       -      +
     27A  ILE*     1.3    60.4    +      -       -      +
     28A  VAL*     5.6     0.3    -      -       -      +
     42A  VAL*     3.4     6.8    -      -       -      +
     43A  LYS*     2.8    42.0    +      -       -      +
     44A  SER*     2.8    38.9    +      -       -      +
     46A  VAL*     4.1     7.6    -      -       -      -
    102A  STF      4.1     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  SER*     1.3    78.6    +      -       -      +
     28A  VAL*     1.3    72.9    -      -       -      +
     40A  ILE*     4.9     7.4    -      -       +      -
     41A  TYR      3.2    13.5    -      -       -      +
     42A  VAL*     3.9     6.7    -      -       +      -
     43A  LYS      4.1     0.4    -      -       -      +
     63A  LEU*     3.8    18.8    -      -       +      -
     76A  GLN*     4.2    25.1    -      -       +      +
     80A  ALA*     4.4     6.1    -      -       +      -
     83A  MET*     3.9    17.0    -      -       +      -
    102A  STF      3.4    51.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  SER*     5.6     0.7    -      -       -      +
     27A  ILE*     1.3    80.8    -      -       -      +
     29A  ALA*     1.3    73.2    +      -       -      +
     40A  ILE*     3.4     5.3    -      -       -      -
     41A  TYR*     2.9    41.5    +      -       +      +
     43A  LYS*     3.9    31.9    -      -       +      +
     76A  GLN*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ILE      4.4     0.2    -      -       -      -
     28A  VAL*     1.3    88.5    -      -       -      +
     30A  ALA*     1.3    62.2    +      -       -      +
     39A  GLY      3.4    12.3    -      -       -      +
     40A  ILE*     4.0     7.3    -      -       +      +
     41A  TYR*     5.8     1.1    -      -       -      -
     75A  SER*     4.0     8.5    -      -       -      -
     76A  GLN*     3.3    49.4    -      -       +      +
     77A  GLU*     4.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  ALA*     1.3    74.3    -      -       -      +
     31A  LYS*     1.3    60.5    +      -       -      +
     37A  LYS*     5.1     5.6    -      -       +      -
     38A  LEU*     3.5    33.0    -      -       -      +
     39A  GLY      2.8    13.6    +      -       -      +
     41A  TYR*     5.5     5.4    -      -       +      -
     75A  SER*     2.7    27.0    +      -       -      -
----------------------------------------------------------
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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