Contacts of the helix formed by residues 2026 - 2034 (chain B) in PDB entry 1F5T


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 LEU2026 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2018B  LEU*     4.2     0.2    -      -       -      +
   2024B  THR*     2.8    21.2    +      -       +      +
   2025B  PRO*     1.3    78.3    -      -       -      +
   2027B  ARG*     1.3    57.9    +      -       -      +
   2028B  ALA*     4.3     2.2    -      -       +      +
   2029B  ARG*     2.8    49.2    +      -       +      +
   2030B  ILE*     3.3     6.1    +      -       -      +
   2059B  ASP      4.2     7.9    -      -       -      +
   2060B  ARG*     3.0    52.7    -      -       +      +
   2061B  SER*     3.9     3.4    -      -       -      +
   2062B  LEU*     3.6     4.0    -      -       -      -
    408F    G      4.4    24.0    -      -       -      +
    409F    C      3.8    13.2    -      -       -      +
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Residues in contact with ARG2027 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2026B  LEU*     1.3    75.1    -      -       -      +
   2028B  ALA*     1.3    63.1    +      -       -      +
   2029B  ARG      3.2     0.2    +      -       -      -
   2030B  ILE*     3.3     6.9    +      -       +      +
   2031B  ALA*     3.0    23.3    +      -       -      +
   2038B  GLY      6.1     0.2    -      -       -      +
   2041B  VAL*     3.8    13.9    -      -       +      +
   2042B  SER*     4.1    27.5    +      -       -      +
   2045B  VAL*     4.0    30.4    -      -       +      +
   2056B  VAL*     4.1    29.4    -      -       -      +
   2060B  ARG*     4.1    14.1    +      -       -      +
   2062B  LEU*     3.4    15.9    -      -       +      +
    409F    C      3.4    46.8    +      -       -      +
    410F    T      3.3    28.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA2028 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2026B  LEU*     3.1     2.7    -      -       +      -
   2027B  ARG*     1.3    74.5    -      -       -      +
   2029B  ARG*     1.3    81.2    +      -       -      +
   2031B  ALA*     3.3     8.8    -      -       -      +
   2032B  GLU*     3.1    28.1    +      -       -      +
    408F    G      3.8    24.5    -      -       +      +
    409F    C      2.8    22.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG2029 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2018B  LEU*     3.8    22.4    -      -       +      -
   2023B  VAL*     4.0    22.9    -      -       -      -
   2024B  THR      3.7     5.4    -      -       -      +
   2026B  LEU*     2.8    37.1    +      -       +      +
   2028B  ALA*     1.3    79.8    -      -       -      +
   2030B  ILE*     1.3    56.2    +      -       -      +
   2031B  ALA      3.1     0.9    -      -       -      -
   2032B  GLU*     2.4    52.4    +      -       -      +
   2033B  ARG*     2.7    41.7    +      -       +      +
    408F    G      2.8    42.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE2030 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2011B  TYR*     4.1    19.3    -      -       +      +
   2014B  THR*     3.7    25.1    -      -       +      -
   2015B  ILE*     3.8    31.9    -      -       +      -
   2018B  LEU*     4.7     4.9    -      -       +      -
   2026B  LEU      3.3     6.7    +      -       -      +
   2027B  ARG*     3.3    10.9    +      -       -      +
   2029B  ARG*     1.3    75.4    -      -       -      +
   2031B  ALA*     1.3    65.2    +      -       -      +
   2033B  ARG*     4.4     0.2    -      -       -      -
   2034B  LEU*     2.8    48.4    +      -       +      +
   2041B  VAL*     4.1    14.8    -      -       +      -
   2045B  VAL*     4.6    13.2    -      -       +      -
   2062B  LEU*     4.5    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA2031 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2027B  ARG      3.0    13.2    +      -       -      +
   2028B  ALA*     3.3    14.8    -      -       -      +
   2030B  ILE*     1.3    77.4    -      -       -      +
   2032B  GLU*     1.3    62.6    +      -       -      +
   2035B  GLU*     3.1     3.3    +      -       -      -
   2036B  GLN*     3.0    39.8    +      -       -      +
   2038B  GLY*     4.6    12.8    -      -       -      +
   2041B  VAL*     3.6    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU2032 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2028B  ALA*     3.1     9.5    -      -       -      +
   2029B  ARG*     2.4    52.0    +      -       -      +
   2031B  ALA*     1.3    76.6    -      -       -      +
   2033B  ARG*     1.3    71.8    +      -       +      +
   2035B  GLU*     3.5    15.7    +      -       -      +
    408F    G      4.9     2.6    +      -       -      -
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Residues in contact with ARG2033 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2014B  THR*     4.4    24.3    +      -       +      +
   2017B  GLU*     5.2     6.7    +      -       -      +
   2018B  LEU*     3.0    38.8    -      -       -      +
   2021B  GLU*     3.3    31.5    +      -       -      -
   2023B  VAL*     4.4     7.9    -      -       -      +
   2029B  ARG*     2.7    32.0    +      -       +      +
   2030B  ILE      3.8     2.7    -      -       -      +
   2032B  GLU*     1.3    79.5    +      -       +      +
   2034B  LEU*     1.3    64.6    +      -       +      +
   2035B  GLU*     3.6     6.2    +      -       -      +
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Residues in contact with LEU2034 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2004B  LEU*     4.6    21.2    -      -       +      +
   2010B  MET*     4.0    36.3    -      -       +      +
   2011B  TYR*     3.4    39.5    -      -       +      -
   2014B  THR*     3.8    18.2    -      -       -      +
   2030B  ILE*     2.8    28.6    +      -       +      +
   2033B  ARG*     1.3    75.4    -      -       +      +
   2035B  GLU*     1.3    74.5    +      -       -      +
   2036B  GLN*     3.1    21.0    +      -       +      +
----------------------------------------------------------
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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