Contacts of the strand formed by residues 169 - 174 (chain D) in PDB entry 1EAK


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 ILE 169 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119D  TRP*     4.3     3.6    -      -       +      +
    124D  ILE*     4.1    21.1    -      -       +      -
    125D  THR      2.8     8.8    +      -       -      +
    126D  TYR*     3.2     6.0    -      -       +      +
    127D  ARG      3.1    21.8    +      -       -      -
    148D  PHE*     3.6    33.4    -      -       +      -
    159D  PHE*     4.2     7.9    -      -       +      -
    167D  ALA*     4.1     1.8    -      -       -      -
    168D  ASP*     1.3    80.9    -      -       -      +
    170D  MET*     1.3    60.8    +      -       -      +
    171D  ILE*     3.6    17.0    +      -       +      -
    203D  GLY*     3.2    27.1    -      -       -      +
    205D  SER*     3.7    12.8    -      -       -      +
    405D  PHE*     4.3     0.4    -      -       +      -
    408D  ALA*     3.9    17.9    -      -       +      -
    409D  MET*     4.2     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 170 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127D  ARG*     3.8    11.4    -      -       -      +
    129D  ILE*     3.4    35.4    -      -       +      -
    165D  GLY      4.3     5.8    -      -       -      +
    166D  GLU*     3.0    51.6    -      -       +      +
    167D  ALA*     3.2    24.7    -      -       -      +
    169D  ILE*     1.3    71.0    -      -       -      +
    171D  ILE*     1.3    61.6    +      -       -      +
    172D  ASN      4.0     0.2    +      -       -      -
    204D  ASP*     2.8    35.4    +      -       -      +
    205D  SER      3.1    23.7    +      -       -      +
    206D  HIS*     4.4     4.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 171 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126D  TYR*     3.8    27.4    -      -       +      -
    127D  ARG      2.9    13.3    +      -       -      +
    128D  ILE*     4.1     8.3    -      -       +      -
    129D  ILE*     2.6    35.6    +      -       -      +
    130D  GLY      3.5     1.0    +      -       -      +
    144D  PHE*     3.3    45.1    -      -       +      -
    148D  PHE*     3.8     2.9    -      -       +      -
    169D  ILE*     3.9    11.7    -      -       +      +
    170D  MET*     1.3    74.8    -      -       -      +
    172D  ASN*     1.3    63.8    +      -       -      +
    173D  PHE*     4.9     1.3    -      -       +      -
    205D  SER*     3.6     4.5    -      -       -      +
    207D  PHE*     4.0     7.9    -      -       +      -
    405D  PHE*     3.5    38.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 172 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129D  ILE*     3.5    21.9    +      -       +      +
    130D  GLY*     3.1    28.0    -      -       -      +
    131D  TYR      4.6     0.2    -      -       -      +
    170D  MET*     4.0     0.9    +      -       +      +
    171D  ILE*     1.3    75.1    -      -       -      +
    173D  PHE*     1.3    91.5    +      -       -      +
    205D  SER      3.2     6.3    +      -       -      -
    206D  HIS*     3.3    22.2    -      -       +      +
    207D  PHE*     2.8    27.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 173 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298B  GLN*     4.9     0.5    -      -       -      +
    852B  SO4      5.5     2.4    +      -       -      -
    130D  GLY      4.0     5.2    -      -       -      -
    131D  TYR*     3.7    32.8    -      -       -      +
    132D  THR*     3.1    43.1    -      -       +      -
    140D  VAL*     4.2     2.0    -      -       +      -
    144D  PHE*     3.7    27.4    -      +       -      -
    171D  ILE*     4.9     0.9    -      -       +      -
    172D  ASN*     1.3    99.8    +      -       -      +
    174D  GLY*     1.3    59.9    +      -       -      +
    178D  HIS*     5.7     1.3    -      -       -      -
    207D  PHE*     3.1    22.7    -      -       +      +
    209D  ASP*     3.9    15.2    -      -       -      +
    213D  TRP*     4.2    19.7    -      +       -      -
    397D  LEU*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 174 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298B  GLN*     3.6    11.0    -      -       -      -
    172D  ASN      4.4     0.2    +      -       -      -
    173D  PHE*     1.3    75.5    -      -       -      +
    175D  ARG*     1.3    60.8    +      -       -      -
    178D  HIS*     4.5    17.0    -      -       -      -
    184D  PHE*     2.9    25.7    -      -       -      -
    206D  HIS*     5.8     0.2    -      -       -      +
    207D  PHE      2.9     7.3    +      -       -      -
    209D  ASP*     3.1    20.2    +      -       -      +
----------------------------------------------------------
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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