Contacts of the strand formed by residues 169 - 176 (chain A) in PDB entry 4EWE


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 169 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  PHE*     4.0    19.6    -      -       +      -
     92A  TRP*     3.8    28.9    -      -       +      -
    116A  LEU*     4.8     3.6    -      -       +      -
    118A  VAL*     3.9    16.7    -      -       +      +
    153A  SER*     2.8    22.8    +      -       -      +
    154A  GLY*     3.7     8.2    +      -       -      -
    165A  THR*     3.5    10.3    +      -       -      +
    167A  THR*     2.8    20.7    +      -       -      +
    168A  PRO*     1.3    71.7    +      -       -      +
    170A  LEU*     1.3    66.6    +      -       -      +
    171A  TYR*     4.6     4.3    -      -       +      -
    190A  TRP*     4.0     5.8    -      -       -      -
    241A  ILE*     4.6     2.9    -      -       +      -
    242A  ALA      3.2    12.1    -      -       -      +
    243A  GLY*     4.5     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  SER      3.5    16.4    -      -       -      +
    154A  GLY*     3.8     2.7    -      -       -      -
    155A  GLU      3.6    31.4    -      -       -      +
    169A  THR*     1.3    74.4    -      -       -      +
    171A  TYR*     1.3    62.4    +      -       -      +
    172A  LEU*     3.7    21.1    -      -       +      -
    184A  GLN*     4.3     1.6    -      -       +      +
    185A  PRO      4.1    19.7    -      -       -      +
    186A  ILE*     4.4     6.7    -      -       +      -
    187A  PRO*     5.0     4.0    -      -       +      -
    190A  TRP*     3.8    12.2    -      -       +      -
    240A  LEU*     3.9    24.7    -      -       +      -
    241A  ILE*     3.3     4.9    -      -       -      -
    242A  ALA*     2.8    44.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     4.2     4.5    -      -       -      -
     64A  VAL*     3.9    24.8    +      -       +      -
     66A  TYR*     3.9    17.1    -      +       +      +
     92A  TRP*     4.4     3.4    -      +       -      -
    114A  LEU*     3.7    32.1    +      -       -      +
    116A  LEU*     4.1    29.0    -      -       +      +
    152A  ILE*     2.9    54.7    +      -       +      +
    153A  SER*     3.0    24.7    +      -       -      +
    169A  THR*     4.6     2.7    -      -       +      -
    170A  LEU*     1.3    75.6    -      -       -      +
    172A  LEU*     1.3    66.1    +      -       -      +
    239A  VAL*     3.9    22.7    -      -       +      -
    240A  LEU      3.5     2.9    -      -       -      -
    241A  ILE*     3.9    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  VAL*     3.6    10.1    -      -       +      -
    150A  ALA      3.4     2.9    -      -       -      -
    151A  VAL*     3.9    22.4    -      -       +      -
    153A  SER      4.1     0.2    -      -       -      +
    155A  GLU      4.3     0.2    -      -       -      +
    156A  ALA*     3.7    22.9    -      -       +      -
    170A  LEU*     3.7    31.2    -      -       +      -
    171A  TYR*     1.3    88.2    -      -       -      +
    173A  ASP*     1.3    60.9    +      -       -      +
    174A  PHE*     3.7    23.3    +      -       +      -
    184A  GLN*     3.7    35.2    -      -       +      +
    239A  VAL*     3.2     6.2    -      -       -      +
    240A  LEU*     2.8    41.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  TYR*     2.8    44.0    +      -       +      +
     68A  LEU*     4.6     1.3    -      -       -      +
    149A  VAL*     3.2     4.2    -      -       -      -
    150A  ALA*     2.8    38.9    +      -       +      +
    152A  ILE*     4.2     3.1    -      -       +      +
    171A  TYR*     5.5     0.2    -      -       +      -
    172A  LEU*     1.3    71.6    -      -       -      +
    174A  PHE*     1.3    59.7    +      -       -      +
    175A  LYS*     3.5    11.6    +      -       -      -
    237A  HIS*     3.0    24.4    +      -       -      -
    238A  PHE      3.9     2.9    -      -       -      -
    239A  VAL*     4.1     9.0    -      -       +      -
   1003A  EDO      2.9    25.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  VAL*     4.0    21.3    -      -       +      -
    148A  THR      3.4     1.6    -      -       -      -
    149A  VAL*     3.9    20.0    -      -       +      -
    172A  LEU*     3.7    41.1    -      -       +      -
    173A  ASP*     1.3    73.5    +      -       -      +
    175A  LYS*     1.4    60.5    +      -       -      +
    176A  LEU*     4.1     8.7    -      -       +      -
    182A  HIS*     3.5    36.3    -      +       -      -
    184A  GLN*     4.0     4.3    -      -       +      -
    228A  VAL*     5.3     3.4    -      -       +      -
    236A  SER      3.8     0.2    -      -       -      +
    237A  HIS*     3.3     8.7    -      -       -      -
    238A  PHE*     2.9    69.8    +      +       +      +
    240A  LEU*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  GLU*     6.2     4.3    -      -       -      -
    146A  GLY      3.7     3.1    -      -       -      +
    148A  THR*     2.9    39.8    +      -       -      +
    173A  ASP*     3.3     5.1    +      -       -      -
    174A  PHE*     1.4    75.9    -      -       -      +
    176A  LEU*     1.3    63.0    +      -       -      +
    177A  ASP*     4.2     1.9    +      -       -      +
    235A  ARG*     3.0    46.2    -      -       -      +
    236A  SER      3.2     3.4    -      -       -      -
    237A  HIS*     3.1    31.9    +      -       +      -
   1003A  EDO      2.1    56.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  GLY      3.6     3.1    -      -       -      -
    147A  VAL*     4.0    26.9    -      -       +      -
    174A  PHE*     4.1    14.8    -      -       +      -
    175A  LYS*     1.3    78.0    -      -       -      +
    177A  ASP*     1.3    66.7    +      -       -      +
    180A  ALA*     4.2    10.5    -      -       +      +
    182A  HIS*     5.0     0.2    -      -       +      -
    201A  VAL*     4.2     1.8    -      -       +      -
    228A  VAL*     4.0    20.0    -      -       +      +
    229A  GLU*     4.0     8.3    -      -       -      +
    230A  ASN*     3.0    37.3    +      -       +      +
    235A  ARG*     3.4     5.8    -      -       -      -
    236A  SER*     2.9    36.6    +      -       -      +
    238A  PHE*     3.7    28.7    -      -       +      -
----------------------------------------------------------
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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