Contacts of the strand formed by residues 134 - 137 (chain B) in PDB entry 3EWS


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 134 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  ALA*     3.9    22.4    -      -       +      +
    125B  LEU*     3.4    22.2    -      -       +      -
    126B  MET*     3.5    34.1    -      -       +      -
    132B  GLN      4.7     0.7    -      -       -      +
    133B  ASN*     1.3    78.7    -      -       -      +
    135B  ILE*     1.3    75.1    +      -       -      +
    136B  ALA*     4.0    15.3    -      -       +      +
    270B  MET      3.3     9.1    +      -       -      +
    271B  LEU*     3.8    14.6    -      -       +      +
    272B  LEU      3.4    20.1    +      -       -      -
    273B  PHE*     4.7     3.6    -      -       +      -
    289B  VAL*     4.1     1.6    -      -       -      +
    293B  ASN*     3.5    12.8    -      -       +      +
    295B  ILE*     3.4    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  LEU*     1.3    82.1    -      -       -      +
    136B  ALA*     1.3    60.8    +      -       -      +
    137B  GLN*     3.8     0.8    +      -       +      +
    272B  LEU*     3.4    18.8    -      -       +      +
    277B  PHE*     4.6    20.9    -      -       +      -
    282B  TRP*     4.7    12.6    -      -       +      -
    285B  ALA*     3.6    39.7    -      -       +      +
    286B  GLN*     5.3     1.1    -      -       +      -
    289B  VAL*     4.1    14.4    -      -       +      -
    292B  PRO*     4.1    18.8    -      -       +      -
    293B  ASN      2.8    18.0    +      -       -      +
    294B  VAL*     3.5     7.8    -      -       +      +
    295B  ILE      2.8    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118B  ILE*     4.7    15.5    -      -       +      -
    122B  ALA*     5.0     2.7    -      -       +      -
    134B  LEU*     4.0    11.5    -      -       +      +
    135B  ILE*     1.3    73.6    -      -       -      +
    137B  GLN*     1.3    61.1    +      -       -      +
    138B  SER*     4.2     1.8    -      -       -      +
    144B  LYS*     4.2     0.9    -      -       -      +
    272B  LEU*     3.2     7.1    +      -       -      +
    273B  PHE*     3.3    34.5    -      -       +      +
    274B  SER*     3.2    22.0    +      -       -      +
    295B  ILE*     3.6    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118B  ILE*     4.1     2.4    -      -       -      +
    135B  ILE*     3.8     0.6    +      -       +      -
    136B  ALA*     1.3    73.6    -      -       -      +
    138B  SER*     1.3    67.5    +      -       -      +
    274B  SER*     3.0    11.9    -      -       -      +
    275B  ALA      2.9    26.1    +      -       -      +
    276B  THR      5.3     0.2    -      -       -      +
    277B  PHE*     3.3    55.4    +      -       +      -
    295B  ILE      2.8    16.3    +      -       -      +
    296B  LYS*     3.9     4.2    -      -       -      -
    297B  LEU*     2.7    47.3    +      -       -      +
    298B  LYS*     3.1    22.5    -      -       -      +
    299B  ARG      5.3     0.4    -      -       -      +
----------------------------------------------------------
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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