Contacts of the strand formed by residues 121 - 125 (chain C) 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 GLY 121 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63C  LEU      3.9     0.8    +      -       -      -
     64C  ILE      3.8     1.0    -      -       -      -
     65C  GLY      2.8    25.5    +      -       -      -
    119C  VAL*     3.2     4.9    +      -       -      +
    120C  SER*     1.3    82.6    +      -       -      +
    122C  LEU*     1.3    67.4    +      -       -      +
    143C  VAL*     4.4     4.3    -      -       -      -
    144C  PRO*     3.5    13.5    -      -       -      -
    304C  LEU*     3.6    20.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 122 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  GLY*     3.5     3.8    -      -       -      -
    111C  VAL*     3.4    38.1    -      -       +      -
    114C  LEU*     3.6    27.1    -      -       +      -
    115C  LEU*     4.1     9.0    -      -       +      -
    119C  VAL*     3.3    23.1    -      -       +      -
    121C  GLY*     1.3    84.6    -      -       -      +
    123C  ILE*     1.3    63.4    +      -       -      +
    124C  ILE*     3.9    19.7    -      -       +      -
    140C  CYS*     3.6    15.0    -      -       -      -
    143C  VAL*     4.9     2.5    -      -       +      -
    144C  PRO      2.9    12.0    +      -       -      +
    145C  ALA*     3.5     7.1    -      -       +      -
    146C  LEU      3.0    23.1    +      -       -      -
    304C  LEU*     3.3    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 123 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  ILE*     4.1    16.8    -      -       +      -
     65C  GLY      3.0    10.1    +      -       -      +
     66C  VAL*     3.3     9.1    -      -       +      +
     67C  ALA      3.0    25.5    +      -       -      +
     83C  ILE*     4.1    27.1    -      -       +      -
    122C  LEU*     1.3    77.4    -      -       -      +
    124C  ILE*     1.3    64.0    +      -       -      +
    125C  ASN*     4.8     1.6    -      -       +      +
    146C  LEU*     3.4    11.2    -      -       +      +
    148C  LEU*     4.0    30.7    -      -       +      -
    300C  SER*     3.9    32.1    -      -       -      +
    301C  VAL*     4.3     3.4    -      -       -      +
    304C  LEU*     3.8    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 124 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67C  ALA*     3.5    14.8    -      -       +      +
    107C  CYS*     3.9    24.5    -      -       -      -
    111C  VAL*     3.7    27.8    -      -       +      -
    122C  LEU*     3.9    20.4    -      -       +      -
    123C  ILE*     1.3    74.6    -      -       -      +
    125C  ASN*     1.3    58.8    +      -       -      +
    126C  TYR*     3.6    11.2    +      -       +      +
    128C  LEU*     4.0    16.8    -      -       +      -
    136C  VAL*     4.2     4.5    -      -       +      -
    140C  CYS*     5.3     0.4    -      -       -      -
    145C  ALA*     4.9     2.9    -      -       +      -
    146C  LEU      2.8    12.3    +      -       -      +
    147C  PHE*     3.5    31.7    -      -       +      +
    148C  LEU      3.0    25.4    +      -       -      -
    149C  ASP      4.1     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  VAL*     5.4     2.7    -      -       +      -
     67C  ALA      2.7    13.5    +      -       -      +
     68C  THR*     3.2    15.7    +      -       -      +
     69C  SER*     3.1    26.6    +      -       -      -
     76C  PRO*     4.0    13.5    -      -       -      +
     79C  ILE*     3.8    26.3    -      -       +      +
     80C  VAL*     5.9     0.7    -      -       +      +
     83C  ILE*     6.1     0.2    -      -       +      -
    123C  ILE*     3.7     4.6    +      -       +      +
    124C  ILE*     1.3    70.7    -      -       -      +
    126C  TYR*     1.3    58.6    +      -       -      +
    148C  LEU*     4.1    24.0    -      -       +      +
    149C  ASP*     4.1     5.3    +      -       -      +
    903C  NPF      3.8    28.9    +      -       -      -
----------------------------------------------------------
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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