Contacts of the strand formed by residues 145 - 147 (chain B) in PDB entry 1EFA


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 ALA 145 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  LEU*     3.4     9.9    -      -       +      +
    124B  ILE*     4.9     2.5    -      -       +      -
    137B  GLU*     4.1    14.6    +      -       -      +
    140B  CYS*     4.0    27.4    -      -       +      -
    143B  VAL      3.7     0.8    +      -       -      -
    144B  PRO*     1.3    75.6    -      -       -      +
    146B  LEU*     1.3    59.9    +      -       -      +
    147B  PHE*     3.7    26.0    -      -       +      -
    157B  ASN*     3.4    27.8    +      -       -      +
    304B  LEU*     4.7     1.6    -      -       -      -
    307B  LEU*     4.4     1.6    -      -       -      +
    314B  LYS*     5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  LEU      2.9    12.2    +      -       -      +
    123B  ILE*     3.4     8.3    -      -       +      +
    124B  ILE*     2.8    26.2    +      -       -      +
    145B  ALA*     1.3    74.5    -      -       -      +
    147B  PHE*     1.3    63.5    +      -       -      +
    148B  LEU*     4.6     4.3    -      -       +      -
    157B  ASN*     3.5    10.8    -      -       +      -
    158B  SER*     3.5    35.2    -      -       -      +
    159B  ILE*     3.8    16.6    -      -       +      -
    300B  SER*     3.5    31.9    -      -       -      +
    303B  ARG*     3.5    30.5    -      -       +      -
    304B  LEU*     4.1    12.1    -      -       +      +
    307B  LEU*     4.5     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  ILE*     3.5    26.2    -      -       +      -
    126B  TYR      5.6     0.4    -      -       -      -
    128B  LEU*     3.7    24.9    -      -       +      -
    133B  ALA*     3.6    22.9    -      -       -      -
    136B  VAL*     4.0     7.6    -      -       +      -
    137B  GLU*     3.9    23.8    -      -       +      -
    145B  ALA*     3.7    22.4    -      -       +      -
    146B  LEU*     1.3    78.1    -      -       -      +
    148B  LEU*     1.3    63.8    +      -       -      +
    149B  ASP      4.7     0.4    -      -       -      +
    150B  VAL*     3.8    30.5    -      -       +      -
    156B  ILE*     3.4    20.9    -      -       +      -
    157B  ASN      2.8    23.2    +      -       -      +
    158B  SER*     3.0     6.6    -      -       -      -
    159B  ILE      2.9    25.5    +      -       -      -
    160B  ILE*     4.7     0.2    -      -       -      +
----------------------------------------------------------
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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