Contacts of the strand formed by residues 236 - 243 (chain G) 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 SER 236 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232G  CYS*     3.2     0.9    -      -       -      -
    233G  VAL      2.8    33.5    +      -       -      +
    234G  ASN      3.4     3.1    +      -       -      -
    235G  GLY*     1.3    77.7    -      -       -      +
    237G  CYS*     1.3    62.6    -      -       -      +
    238G  PHE*     3.2    23.6    -      -       -      -
    256G  LYS*     3.7    10.9    -      -       -      -
    257G  MET      3.4     5.6    -      -       -      -
    258G  GLU*     2.5    34.2    +      -       -      +
    308G  GLN*     5.1     4.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 237 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183G  CYS*     4.1     7.9    -      -       -      -
    185G  ASP*     3.6    19.3    -      -       -      -
    190G  LEU*     3.9    26.5    -      -       +      -
    207G  TYR*     6.4     0.7    -      -       -      -
    231G  ALA      3.4     4.0    -      -       -      +
    232G  CYS*     2.0    45.5    -      -       -      -
    235G  GLY      5.5     0.2    -      -       -      -
    236G  SER*     1.3    74.3    -      -       -      +
    238G  PHE*     1.3    65.0    +      -       -      +
    256G  LYS*     3.5     2.3    -      -       -      -
    257G  MET*     2.7    50.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 238 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226G  GLN*     4.2     0.3    +      -       -      -
    230G  CYS*     3.1    22.5    -      -       -      +
    231G  ALA*     2.9    23.5    +      -       -      +
    233G  VAL*     4.4     9.2    -      -       +      -
    236G  SER*     3.2    38.6    -      -       -      -
    237G  CYS*     1.3    73.0    -      -       -      +
    239G  THR*     1.3    62.4    +      -       -      +
    255G  PHE      3.2     7.9    -      -       -      +
    256G  LYS*     3.8    22.0    -      -       +      -
    257G  MET*     4.4     1.1    -      -       -      -
    280G  CYS*     5.7     2.1    -      -       -      +
    287G  ILE*     3.8    20.4    -      -       +      -
    305G  PHE*     3.7    28.3    -      +       +      -
    306G  ASN      4.3     0.7    -      -       -      -
    308G  GLN*     3.8    39.7    -      -       +      -
    310G  LEU*     3.7    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 239 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181G  SER*     3.9     3.5    +      -       -      -
    192G  ILE*     4.2     9.4    -      -       +      +
    225G  THR*     3.6    13.7    +      -       -      -
    226G  GLN*     2.8    21.8    +      -       -      +
    230G  CYS*     4.4     3.1    -      -       -      -
    238G  PHE*     1.3    77.5    -      -       -      +
    240G  VAL*     1.3    76.8    +      -       -      +
    241G  MET*     4.9     7.0    -      -       +      -
    254G  ILE*     3.6     6.6    -      -       -      +
    255G  PHE*     3.1    44.9    +      -       +      -
    257G  MET*     3.2    27.6    -      -       +      -
    280G  CYS*     5.5     2.0    -      -       -      -
    305G  PHE*     5.0     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 240 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225G  THR*     3.1    25.8    +      -       -      -
    226G  GLN*     3.9     7.4    +      -       +      +
    239G  THR*     1.3    85.2    +      -       -      +
    241G  MET*     1.3    72.8    +      -       -      +
    242G  THR*     5.2     4.9    -      -       -      +
    252G  TYR*     5.4     4.0    -      -       +      -
    253G  LYS      3.5    12.6    -      -       -      +
    254G  ILE*     5.1     5.6    -      -       +      -
    255G  PHE*     5.0     0.2    -      -       -      -
    268G  LEU*     5.7     5.4    -      -       +      -
    275G  TYR*     5.3     6.5    -      -       +      -
    278G  CYS*     3.9    28.9    -      -       +      -
    280G  CYS*     4.0     4.5    -      -       -      -
    289G  CYS*     3.8    29.4    -      -       -      -
    303G  VAL*     5.6     5.2    -      -       +      -
    305G  PHE*     4.9     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 241 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192G  ILE*     3.6    35.7    -      -       +      -
    194G  ILE*     4.4     1.8    -      -       +      -
    203G  ALA*     3.7    14.1    -      -       +      -
    205G  LEU*     4.9     0.2    -      -       +      -
    215G  ILE*     4.0    19.1    -      -       +      -
    218G  TRP*     3.9    11.2    -      -       +      -
    223G  LEU*     4.1    24.2    -      -       +      -
    224G  ARG      3.6     5.8    -      -       -      +
    225G  THR*     4.0    17.9    -      -       -      +
    239G  THR*     4.9     6.7    -      -       +      -
    240G  VAL*     1.3    82.8    -      -       -      +
    242G  THR*     1.3    61.8    +      -       -      +
    252G  TYR*     3.5     3.5    -      -       -      +
    253G  LYS      2.9    33.5    +      -       -      -
    255G  PHE*     3.6    30.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 242 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223G  LEU*     3.5     4.1    -      -       -      +
    224G  ARG*     3.0    62.8    +      -       -      +
    240G  VAL*     5.2     3.1    -      -       -      +
    241G  MET*     1.3    75.1    +      -       -      +
    243G  ASP*     1.3    66.3    +      -       -      +
    250G  ALA*     3.9    15.7    -      -       +      -
    251G  SER      3.4    11.0    -      -       -      +
    252G  TYR*     3.7     6.4    -      -       +      +
    275G  TYR*     2.6    33.2    +      -       -      +
    276G  GLU*     4.1    12.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 243 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217G  SER*     2.5    29.3    +      -       -      -
    218G  TRP*     2.7    39.4    +      -       +      -
    219G  ARG*     2.8    15.7    +      -       +      +
    221G  ASN      2.9    35.7    +      -       -      +
    223G  LEU*     3.9     8.5    +      -       +      -
    224G  ARG*     4.1     0.4    -      -       -      +
    242G  THR*     1.3    78.5    -      -       -      +
    244G  GLY*     1.3    58.9    +      -       -      +
    251G  SER*     3.1    32.0    +      -       -      -
----------------------------------------------------------
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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