Contacts of the strand formed by residues 27 - 29 (chain H) in PDB entry 4R2G


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 HIS 27 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25H  GLN*     4.4     7.3    +      -       -      +
     26H  PHE*     1.3    95.9    +      -       -      +
     28H  TRP*     1.3    65.1    +      -       -      +
     29H  LYS*     3.8     3.5    +      -       +      +
     35H  LYS*     4.6    17.6    -      -       +      +
     37H  LEU      3.6    17.7    -      -       -      -
     38H  GLY*     4.1     5.7    -      -       -      -
     39H  ASN      3.5    21.3    -      -       -      -
     40H  GLN*     4.0    12.0    +      -       -      -
     45H  THR*     4.3     8.0    +      -       -      -
     83H  ILE      3.5     2.1    -      -       -      +
     84H  CYS*     4.7     0.2    -      -       -      -
     85H  GLU*     3.1    49.3    +      -       +      +
    281K  ALA*     3.9    34.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 28 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14H  LEU*     3.7    38.6    -      -       +      -
     15H  THR      3.7    13.5    -      -       -      -
     16H  CYS*     3.4    21.3    -      -       +      -
     26H  PHE*     3.9    19.9    -      +       -      -
     27H  HIS*     1.3    73.9    -      -       -      +
     29H  LYS*     1.3    63.9    +      -       -      +
     35H  LYS*     3.9     1.4    -      -       -      +
     36H  ILE*     2.9    36.8    +      -       +      -
     37H  LEU*     3.2    23.0    +      -       +      +
     67H  PHE      3.0    20.4    +      -       -      -
     69H  LEU*     3.5    32.4    -      -       +      +
     82H  TYR*     3.9    24.7    -      -       +      -
     83H  ILE      3.2    19.5    -      -       -      -
     84H  CYS*     3.9    17.7    -      -       +      -
     91H  GLU      5.5     0.4    -      -       -      -
     93H  VAL*     4.8     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 29 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27H  HIS*     3.8     5.6    +      -       +      +
     28H  TRP*     1.3    79.6    -      -       -      +
     30H  ASN*     1.3    65.6    +      -       -      +
     33H  GLN*     3.8    35.7    -      -       -      +
     34H  ILE      3.2    15.0    -      -       -      +
     35H  LYS*     4.4     7.9    -      -       +      -
     36H  ILE*     4.0     6.3    -      -       -      -
     82H  TYR*     3.2     8.8    -      -       -      +
     83H  ILE*     2.8    37.2    +      -       +      +
     85H  GLU*     3.1    34.4    +      -       +      +
    279K  ASP*     2.9    24.4    +      -       -      -
    280K  ASN*     3.0    18.2    +      -       -      +
    281K  ALA*     3.7     9.0    -      -       -      -
    511K  NAG      3.3    11.5    -      -       -      +
----------------------------------------------------------
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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