Contacts of the strand formed by residues 26 - 33 (chain A) in PDB entry 2WEA


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 THR 26 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  VAL      3.5     1.0    -      -       -      +
     22A  THR*     3.4     0.6    -      -       -      -
     23A  ILE      2.8    34.7    +      -       -      +
     24A  GLY      3.3     4.6    +      -       -      -
     25A  GLY*     1.3    77.9    -      -       -      +
     27A  THR*     1.3    66.4    +      -       -      +
     28A  LEU*     3.5    26.6    +      -       +      +
     55A  SER*     5.0     3.1    -      -       -      -
     56A  VAL      3.8    18.9    +      -       -      +
     57A  TYR*     5.3     3.8    -      -       -      -
     58A  ASN*     5.3     6.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PRO*     3.7    30.5    -      -       +      -
     21A  VAL      3.3     9.2    -      -       -      +
     22A  THR*     2.8    23.8    +      -       -      +
     25A  GLY      4.0     2.0    +      -       -      -
     26A  THR*     1.3    73.5    -      -       -      +
     28A  LEU*     1.3    67.4    +      -       -      +
     29A  ASN*     5.1     2.0    -      -       -      +
     55A  SER*     3.7    14.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PRO*     3.3     3.3    -      -       -      +
     21A  VAL*     2.8    36.0    +      -       -      +
     23A  ILE*     4.5     7.6    -      -       +      -
     26A  THR*     3.5    37.5    -      -       +      +
     27A  THR*     1.3    75.2    -      -       -      +
     29A  ASN*     1.3    63.6    +      -       -      +
     30A  LEU*     3.6    15.2    +      -       +      -
     41A  VAL*     3.7    35.4    -      -       +      -
     42A  PHE      4.2     0.4    -      -       -      +
     55A  SER*     3.9    19.3    -      -       -      +
     56A  VAL      4.2     7.0    -      -       -      -
     57A  TYR*     4.1    17.7    -      -       +      +
    119A  ASP*     3.7    15.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ILE*     3.9    32.1    -      -       +      +
     19A  THR      3.9     3.3    -      -       -      -
     20A  PRO*     3.9    20.3    -      -       -      +
     27A  THR*     5.1     2.1    -      -       -      +
     28A  LEU*     1.3    74.1    -      -       -      +
     30A  LEU*     1.3    59.2    +      -       -      +
    117A  ASN      4.1     7.5    +      -       -      +
    118A  ASN*     3.3     5.9    -      -       -      -
    119A  ASP*     2.7    46.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ILE*     3.4     6.5    -      -       -      -
     19A  THR*     2.9    35.9    +      -       -      +
     21A  VAL*     3.9    33.0    -      -       +      -
     23A  ILE*     4.4     2.9    -      -       +      -
     28A  LEU*     3.8    14.8    -      -       +      -
     29A  ASN*     1.3    77.8    -      -       -      +
     31A  ASN*     1.3    61.7    +      -       -      +
     32A  PHE*     3.6     4.8    +      -       +      -
     39A  LEU*     4.0    27.4    -      -       +      -
     41A  VAL*     4.1     8.5    -      -       +      -
    119A  ASP      3.5    32.3    -      -       -      +
    120A  GLY*     3.5    10.1    -      -       -      +
    121A  LEU      4.4     2.5    -      -       -      +
    122A  LEU*     4.0    17.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  GLU*     3.4    35.8    +      -       -      +
     17A  TYR*     3.6    17.4    +      -       -      +
     29A  ASN      4.3     0.4    +      -       -      -
     30A  LEU*     1.3    72.2    -      -       -      +
     32A  PHE*     1.3    73.0    +      -       -      +
     33A  ASP*     3.4     1.8    +      -       -      -
    118A  ASN*     4.1     7.9    -      -       +      +
    120A  GLY      3.0    15.1    +      -       -      +
    121A  LEU*     3.3    25.3    -      -       +      +
    122A  LEU      3.1    17.4    +      -       -      -
    214A  THR      4.5     2.9    -      -       -      +
    215A  GLY*     4.4    20.2    +      -       -      -
    326A  PP6      5.5     5.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TYR      4.1     4.8    +      -       -      +
     19A  THR*     3.5    36.8    +      -       +      +
     21A  VAL*     3.5    30.5    -      -       +      -
     30A  LEU*     3.6     6.2    +      -       +      -
     31A  ASN*     1.3    79.5    +      -       -      +
     33A  ASP*     1.3    53.1    +      -       -      +
     92A  VAL*     3.8    24.5    -      -       +      -
    122A  LEU*     3.4    28.7    -      -       +      +
    124A  LEU*     3.9    15.9    -      -       +      -
    165A  TYR*     3.5    47.8    +      +       +      +
    167A  PHE*     4.1    13.5    -      +       -      -
    214A  THR*     2.8    24.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ASN*     3.9     9.2    -      -       -      +
     32A  PHE*     1.3    75.6    -      -       -      +
     34A  THR*     1.3    58.4    +      -       -      +
     35A  GLY*     2.8    24.1    +      -       -      -
     36A  SER*     3.2    25.4    +      -       -      +
    121A  LEU*     3.7    20.8    -      -       +      +
    122A  LEU      2.8    12.4    +      -       -      +
    123A  GLY*     3.4     0.5    -      -       -      -
    124A  LEU*     2.9    23.1    +      -       -      +
    213A  ASP*     3.1    14.9    -      -       -      +
    214A  THR*     3.3     1.8    -      -       -      -
    215A  GLY*     3.4    12.6    -      -       -      +
    326A  PP6      2.5    26.5    +      -       -      +
----------------------------------------------------------
 Back to top of page


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