Contacts of the strand formed by residues 158 - 163 (chain A) in PDB entry 5IH2


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 ILE 158 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  TYR*     4.0    26.5    -      -       +      -
    137A  VAL      3.3     7.9    -      -       -      +
    138A  ARG*     3.6    23.1    -      -       +      +
    156A  GLY      3.7    12.1    -      -       -      +
    157A  ASP*     1.3    72.0    -      -       -      +
    159A  LEU*     1.3    67.5    +      -       -      +
    174A  ASP*     4.3     2.8    -      -       -      +
    175A  SER*     4.4     3.5    +      -       -      -
    190A  TYR*     3.6    39.5    -      -       +      -
    201A  PEG      3.5    28.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  TYR*     3.3     7.3    -      -       -      -
    137A  VAL*     2.8    47.0    +      -       +      +
    139A  ALA*     5.2     0.7    -      -       +      -
    151A  LEU*     4.2     8.1    -      -       +      -
    153A  PHE*     3.8    35.4    -      -       +      -
    157A  ASP*     4.3    21.1    -      -       +      +
    158A  ILE*     1.3    80.1    -      -       -      +
    160A  ARG*     1.3    60.2    +      -       -      +
    172A  ALA*     4.2     8.3    -      -       +      -
    173A  GLU      3.3     4.5    -      -       -      +
    174A  ASP*     3.6    31.2    -      -       +      -
    182A  ILE*     4.0    25.1    -      -       +      -
    187A  VAL*     4.6     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  ALA*     3.9    15.5    -      -       +      +
    135A  GLU      3.6     8.5    -      -       -      +
    136A  TYR*     3.6    38.5    -      -       +      -
    159A  LEU*     1.3    72.1    -      -       -      +
    161A  ILE*     1.3    79.6    +      -       -      +
    162A  ARG*     3.5    11.3    +      -       -      +
    172A  ALA*     3.2     3.3    -      -       -      -
    173A  GLU*     2.8    64.1    +      -       +      +
    201A  PEG      3.8    20.9    -      -       -      -
    155B  LYS      4.2     4.2    +      -       -      -
    156B  GLY*     3.6    29.6    +      -       -      -
    157B  ASP*     2.9    35.2    +      -       -      +
    158B  ILE*     4.6     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  GLU*     2.8    44.4    +      -       +      +
    137A  VAL*     3.8    37.7    -      -       +      -
    160A  ARG*     1.3    84.4    +      -       -      +
    162A  ARG*     1.3    62.7    +      -       -      +
    163A  ASP      4.0    14.6    -      -       -      +
    164A  LYS*     4.1    14.8    -      -       +      -
    170A  TRP*     3.8    34.3    -      -       +      -
    171A  ASN      3.8     6.5    -      -       -      +
    172A  ALA*     4.0     6.3    -      -       +      -
    182A  ILE*     4.0    15.3    -      -       +      -
    155B  LYS      5.1     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  ARG*     3.9    24.9    -      -       -      +
    161A  ILE*     1.3    78.1    -      -       -      +
    163A  ASP*     1.3    59.9    +      -       -      +
    171A  ASN*     2.8    48.8    +      -       +      +
    173A  GLU*     3.6    24.7    -      -       +      -
    179A  ARG*     3.3    31.3    -      -       -      +
    142B  ASP*     5.0     1.4    -      -       -      +
    152B  PRO      5.2     0.4    +      -       -      -
    153B  PHE*     4.2     4.0    -      -       -      +
    154B  LYS*     3.4    45.8    -      -       +      +
    155B  LYS      4.5     5.4    +      -       -      +
    157B  ASP*     2.7    38.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  ILE*     3.8     2.1    -      -       -      +
    162A  ARG*     1.3    81.1    -      -       -      +
    164A  LYS*     1.3    69.9    +      -       -      +
    165A  PRO*     3.4    23.0    -      -       +      +
    170A  TRP*     3.5     8.0    -      -       -      +
    171A  ASN*     2.9    36.5    +      -       +      +
    142B  ASP*     4.8     5.7    -      -       -      +
    154B  LYS*     3.9    32.8    +      -       +      +
----------------------------------------------------------
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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