Contacts of the strand formed by residues 158 - 162 (chain A) in PDB entry 5FWU


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 PHE 158 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  LEU*     3.4    33.7    -      -       +      -
    132A  LEU*     3.8    14.8    -      -       +      -
    151A  CYS*     4.1     1.2    -      -       -      -
    156A  PHE*     3.5     2.3    -      -       -      +
    157A  LYS*     1.3   121.2    -      -       +      +
    159A  ALA*     1.3    62.6    +      -       -      +
    169A  CYS*     3.4     6.1    -      -       -      +
    170A  GLY      3.0    41.5    +      -       -      +
    171A  ASN      4.1     2.7    -      -       -      -
    172A  ASN      3.4    30.1    -      -       -      -
    173A  PRO*     4.3     5.8    -      -       +      -
    175A  TYR*     3.8    18.4    -      +       +      -
    206A  LEU*     5.3     2.7    -      -       +      -
    207A  PHE      3.7     4.0    -      -       -      -
    208A  ASP*     4.6     5.8    -      -       +      -
    209A  THR*     3.8     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  LEU*     3.7     5.4    -      -       -      -
    147A  CYS*     4.3    13.0    -      -       -      +
    148A  ILE*     4.4     9.6    -      -       +      -
    151A  CYS*     3.5    26.5    -      -       +      -
    158A  PHE*     1.3    74.7    -      -       -      +
    160A  GLY*     1.3    58.3    +      -       -      +
    161A  MET*     4.4     7.4    -      -       +      +
    168A  PHE      3.2     5.4    -      -       -      -
    206A  LEU*     3.3     7.4    -      -       -      +
    207A  PHE      2.9    36.9    +      -       -      +
    209A  THR*     4.2     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  LEU*     3.6     3.5    -      -       -      +
    147A  CYS*     3.3     2.3    -      -       -      -
    159A  ALA*     1.3    74.4    -      -       -      +
    161A  MET*     1.3    65.8    +      -       -      -
    166A  ALA      3.4     0.5    -      -       -      +
    167A  CYS*     3.3     6.4    -      -       -      -
    168A  PHE*     2.7    39.8    +      -       -      -
    204A  ILE*     3.7    21.8    -      -       -      -
    205A  ILE      3.2     9.9    -      -       -      -
    206A  LEU*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  LEU*     4.4     4.3    -      -       +      -
    144A  ILE*     3.2    44.2    -      -       +      +
    147A  CYS*     3.4    28.0    -      -       +      -
    148A  ILE*     4.0     9.6    -      -       +      +
    159A  ALA*     4.4     7.6    -      -       +      -
    160A  GLY*     1.3    77.7    -      -       -      +
    162A  GLU*     1.3    60.0    +      -       -      +
    166A  ALA      3.1     5.6    -      -       -      +
    198A  CYS*     2.9    43.3    -      -       +      +
    199A  GLY*     3.8     0.3    -      -       -      -
    204A  ILE*     3.4     5.0    -      -       -      +
    205A  ILE*     3.1    36.8    +      -       +      +
    207A  PHE*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ASP*     2.3    43.4    -      -       -      +
    161A  MET*     1.3    69.3    -      -       -      +
    163A  SER*     1.3    66.8    +      -       -      +
    164A  GLY      2.9    11.1    +      -       -      +
    165A  TYR      3.2     0.2    +      -       -      -
    166A  ALA*     2.9    31.5    +      -       +      +
    168A  PHE*     3.9    23.0    -      -       +      -
    198A  CYS      3.1     2.1    +      -       -      -
    201A  ASP*     3.9     6.2    -      -       -      +
    202A  GLY*     3.4    19.9    +      -       -      -
    203A  ARG      3.2    20.0    -      -       -      +
    204A  ILE*     3.6    20.3    -      -       +      +
----------------------------------------------------------
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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