Contacts of the strand formed by residues 115 - 124 (chain F) in PDB entry 2HU4


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 115 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105F  SER*     5.4     0.9    +      -       -      -
    113F  ASP      4.3     0.4    +      -       -      -
    114F  VAL*     1.3    83.4    -      -       -      +
    116F  VAL*     1.3    62.7    +      -       -      +
    117F  ILE*     3.5    24.3    +      -       +      +
    133F  PHE*     4.2     6.5    -      +       -      -
    135F  THR*     3.8    22.4    -      -       +      -
    137F  GLY*     5.2     1.8    -      -       -      -
    138F  ALA      3.4    17.7    -      -       -      -
    139F  LEU*     3.7    10.5    -      -       +      +
    140F  LEU*     4.4     2.8    -      -       -      +
    159F  MET*     3.6    32.3    -      -       +      -
    167F  PRO*     3.0    15.2    +      -       +      +
    168F  SER*     3.7    20.4    -      -       -      -
    169F  PRO*     3.6    27.4    -      -       +      -
    171F  SER*     4.3     1.8    -      -       -      -
    440F  SER*     4.1     3.5    +      -       -      -
    108G  ILE*     3.4    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 116 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114F  VAL      3.6     1.6    +      -       -      -
    115F  PHE*     1.3    71.8    -      -       -      +
    117F  ILE*     1.3    65.5    +      -       -      +
    135F  THR*     3.5     1.7    -      -       -      -
    136F  GLN*     3.3    39.6    +      -       +      +
    138F  ALA*     3.1    34.5    +      -       +      +
    139F  LEU      4.2     1.3    -      -       -      +
    140F  LEU*     4.5    16.4    -      -       +      +
    145F  SER*     5.1     6.5    -      -       -      +
    148F  THR*     3.8    22.2    -      -       +      +
    438F  TRP*     5.4     0.7    -      -       +      -
    439F  THR      3.2    27.1    -      -       -      +
    440F  SER*     3.6    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 117 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103F  ASP*     6.0     1.8    -      -       -      +
    105F  SER*     5.2     0.7    -      -       -      +
    115F  PHE*     3.5    25.3    +      -       +      +
    116F  VAL*     1.3    82.9    -      -       -      +
    118F  ARG*     1.3    76.1    +      -       -      +
    120F  PRO*     4.4    15.7    -      -       +      -
    131F  THR*     6.3     0.7    -      -       +      -
    133F  PHE*     3.7    38.4    -      -       +      -
    134F  LEU      3.4    12.6    -      -       -      +
    135F  THR*     4.1     2.7    -      -       -      +
    136F  GLN*     4.9     1.8    -      -       -      -
    156F  ARG*     4.6     1.3    -      -       -      -
    167F  PRO*     4.1    18.4    -      -       +      -
    439F  THR      4.0     1.4    -      -       -      +
    440F  SER*     3.0    27.5    +      -       -      +
    441F  GLY      3.4    25.7    +      -       -      +
    442F  SER*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 118 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117F  ILE*     1.3    85.5    -      -       -      +
    119F  GLU*     1.3   108.3    +      -       -      +
    120F  PRO*     3.4     6.3    -      -       -      +
    134F  LEU      3.2    17.3    +      -       -      +
    136F  GLN*     5.3     0.4    -      -       -      +
    148F  THR      5.3     4.0    -      -       -      +
    151F  ASP*     5.5     1.4    +      -       -      -
    156F  ARG*     3.3    12.3    -      -       -      +
    371F  ARG*     4.8     0.6    -      -       -      +
    406F  TYR*     3.6    23.8    -      -       -      -
    425F  GLU*     2.5    34.0    +      -       -      -
    427F  ILE*     4.0    22.2    -      -       -      +
    439F  THR*     4.3    32.4    -      -       +      +
    440F  SER      4.5     6.5    -      -       -      -
    441F  GLY*     5.1     0.9    -      -       -      +
    805F  G39      3.4    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 119 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118F  ARG*     1.3   114.9    +      -       -      +
    120F  PRO*     1.3    66.1    -      -       -      +
    121F  PHE*     3.9    13.0    -      -       -      -
    133F  PHE*     3.9     7.4    -      -       -      -
    134F  LEU*     3.7    27.2    +      -       +      +
    151F  ASP*     4.8     0.3    -      -       -      +
    156F  ARG*     3.0    15.2    +      -       -      -
    227F  GLU*     4.1    25.4    -      -       +      +
    406F  TYR*     4.4    20.6    -      -       +      -
    425F  GLU*     2.9    15.1    +      -       -      -
    805F  G39      3.0    30.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 120 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117F  ILE*     4.4    20.4    -      -       +      -
    118F  ARG*     3.4     4.9    -      -       -      -
    119F  GLU*     1.3    90.7    -      -       -      +
    121F  PHE*     1.3    66.4    +      -       -      +
    131F  THR*     4.8     6.7    -      -       +      -
    132F  PHE      3.4    10.3    -      -       -      +
    133F  PHE*     4.2     3.1    -      -       +      -
    227F  GLU      4.2     0.3    -      -       -      +
    423F  TRP*     3.2    27.0    -      -       +      -
    425F  GLU*     3.1    41.5    -      -       +      +
    441F  GLY*     5.8     1.1    -      -       -      -
    442F  SER      4.6     6.5    -      -       -      +
    443F  SER*     4.7    14.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 121 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119F  GLU      3.9    11.9    -      -       -      -
    120F  PRO*     1.3    76.3    -      -       -      +
    122F  ILE*     1.3    66.3    +      -       -      +
    131F  THR*     3.5     2.9    -      -       -      +
    132F  PHE*     2.7    79.9    +      +       +      +
    133F  PHE      4.8     0.2    -      -       -      -
    134F  LEU*     6.2     1.3    -      -       +      -
    158F  LEU*     4.4    12.8    -      -       +      -
    180F  ALA*     4.7     3.4    -      -       +      -
    181F  SER*     4.1    11.2    -      -       -      -
    182F  ALA*     3.8    28.3    -      -       +      -
    227F  GLU*     3.8    16.2    -      -       -      +
    228F  SER*     3.4    17.7    -      -       -      -
    229F  GLU*     3.4    25.1    -      -       +      -
    423F  TRP*     3.4    22.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 122 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  SER*     4.3     3.8    -      -       -      +
    121F  PHE*     1.3    78.1    -      -       -      +
    123F  SER*     1.3    70.7    +      -       -      +
    129F  CYS*     4.5     3.8    -      -       +      -
    130F  ARG      3.4    10.3    -      -       -      +
    131F  THR*     3.6    21.5    -      -       +      +
    163F  VAL*     3.5    22.4    -      -       +      -
    229F  GLU*     3.9     7.3    +      -       -      +
    410F  PHE*     3.2    54.1    -      -       +      +
    423F  TRP*     3.4    17.3    +      -       +      -
    443F  SER*     5.7     6.7    -      -       -      +
    444F  ILE      5.5     0.7    -      -       -      -
    445F  SER*     3.4    36.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 123 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121F  PHE*     4.2     1.5    +      -       -      -
    122F  ILE*     1.3    77.0    -      -       -      +
    124F  CYS*     1.3    65.3    +      -       -      +
    130F  ARG*     3.0    26.7    +      -       -      +
    132F  PHE*     4.0    17.4    -      -       -      -
    182F  ALA      4.1     2.7    -      -       -      -
    183F  CYS*     3.7    11.8    -      -       -      +
    189F  TRP*     3.3    24.1    -      -       -      -
    229F  GLU*     2.9    34.6    +      -       -      -
    410F  PHE*     4.8     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 124 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85F  LEU*     5.1     4.3    -      -       -      +
    122F  ILE*     4.6     0.4    -      -       -      -
    123F  SER*     1.3    79.9    +      -       -      +
    125F  SER*     1.3    67.1    +      -       -      +
    128F  GLU      3.3     6.1    -      -       -      +
    129F  CYS*     2.1    48.2    -      -       -      -
    184F  HIS*     3.6    16.1    +      -       -      +
    189F  TRP*     3.8     5.4    -      -       -      -
    229F  GLU*     3.9     4.1    +      -       -      +
    410F  PHE*     4.1    15.7    -      -       -      -
    411F  VAL      4.0    20.4    +      -       -      +
    412F  HIS*     4.0    13.2    -      -       -      +
----------------------------------------------------------
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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