Contacts of the strand formed by residues 172 - 176 (chain E) 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 ARG 172 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  GLU*     4.3     5.7    +      -       -      -
    130E  ARG*     3.3    49.6    -      -       -      +
    132E  PHE*     5.3     1.0    -      -       -      -
    159E  MET*     3.2     7.8    -      -       -      +
    160E  SER*     2.6    38.3    +      -       -      +
    170E  ASN      4.0     1.4    +      -       -      -
    171E  SER*     1.3    72.7    -      -       -      +
    173E  PHE*     1.3    67.6    +      -       -      +
    174E  GLU*     2.7    32.4    +      -       -      +
    189E  TRP*     3.9    24.2    -      -       -      +
    165H  GLU*     3.9     7.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 173 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157E  THR*     3.7    13.2    -      -       +      -
    159E  MET*     3.6    25.3    -      -       +      +
    171E  SER      3.9     0.4    +      -       -      -
    172E  ARG*     1.3    84.3    -      -       -      +
    174E  GLU*     1.3    66.0    +      -       -      +
    175E  SER*     3.3    39.7    -      -       -      -
    176E  VAL*     3.8     2.0    -      -       +      -
    206E  LYS*     4.3     2.2    -      -       -      -
    100H  TYR      3.3    20.2    -      -       -      -
    101H  SER*     3.6    24.0    -      -       -      -
    102H  LYS      3.5    19.7    -      -       -      -
    163H  VAL*     3.5    27.2    -      -       +      +
    164H  GLY*     3.6    23.1    -      -       -      -
    165H  GLU*     4.3     6.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 174 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132E  PHE*     4.0    19.5    -      -       +      -
    158E  LEU*     2.9    38.8    +      -       +      +
    159E  MET*     3.9    18.2    -      -       -      -
    160E  SER*     3.0    12.7    +      -       -      +
    172E  ARG*     2.7    41.8    +      -       -      +
    173E  PHE*     1.3    82.1    -      -       -      +
    175E  SER*     1.3    62.3    +      -       -      +
    189E  TRP*     5.9     1.1    -      -       -      +
    191E  THR*     3.5    20.4    +      -       +      +
    206E  LYS*     3.1    23.4    +      -       -      +
    209E  GLY*     6.0     2.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 175 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157E  THR*     3.4     3.6    -      -       -      -
    158E  LEU*     2.7    45.5    +      -       -      +
    173E  PHE*     3.3    20.2    -      -       -      -
    174E  GLU*     1.3    82.0    +      -       -      +
    176E  VAL*     1.3    66.8    +      -       -      +
    191E  THR*     4.9     3.6    -      -       -      -
    193E  GLY*     4.4    17.2    +      -       -      -
    204E  VAL*     4.5    11.3    +      -       -      +
    206E  LYS*     3.7    20.6    -      -       -      +
     99H  VAL      4.8     2.3    +      -       -      -
    100H  TYR      4.7     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 176 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154E  PRO      4.1     6.3    -      -       -      +
    156E  ARG      3.7    13.7    -      -       -      +
    157E  THR*     4.3     3.8    -      -       +      -
    173E  PHE*     4.1     0.7    -      -       +      -
    175E  SER*     1.3    78.1    +      -       -      +
    177E  ALA*     1.3    68.7    +      -       -      +
    193E  GLY      4.0     6.1    -      -       -      +
    195E  SER*     3.6    25.8    -      -       -      +
    204E  VAL*     5.7     2.1    -      -       -      +
     99H  VAL*     3.6    31.8    +      -       +      +
    100H  TYR      4.3     1.7    +      -       -      +
    101H  SER*     3.7    33.0    -      -       -      +
    102H  LYS*     3.9    10.1    -      -       +      +
    458H  TRP*     3.9    21.1    -      -       +      +
----------------------------------------------------------
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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