Contacts of the strand formed by residues 46 - 49 (chain A) in PDB entry 1PRH


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 46 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  CYS*     4.0     2.0    -      -       -      -
     44A  GLN      4.8     3.6    -      -       -      +
     45A  GLY*     1.3    75.1    -      -       -      -
     47A  CYS*     1.3    76.9    +      -       -      +
     48A  VAL*     3.2     9.9    +      -       +      +
     58A  ASP*     2.8    47.8    +      -       +      +
    130A  TYR*     3.7    31.6    -      -       +      +
    135A  ASP      5.0     7.4    -      -       -      +
    136A  TYR*     5.9     1.8    -      -       -      -
    137A  ILE*     6.0     5.4    -      -       +      -
    153A  PRO*     5.9     5.4    -      -       +      -
    546B  LYS*     4.7    13.9    -      -       +      +
    548B  SER*     3.7    29.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  CYS*     2.0    63.8    -      -       +      +
     40A  PRO*     4.0     9.9    -      -       +      -
     41A  CYS*     3.5    16.3    -      -       +      -
     45A  GLY      4.0     0.8    +      -       -      -
     46A  ILE*     1.3    81.8    -      -       +      +
     48A  VAL*     1.3    61.8    +      -       -      +
     49A  ARG*     3.7     0.9    +      -       -      +
     55A  TYR*     3.5    25.6    -      -       -      -
     56A  GLN      3.5     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  ILE*     3.2     8.8    +      -       +      +
     47A  CYS*     1.3    73.6    -      -       -      +
     49A  ARG*     1.3    67.4    +      -       -      +
     50A  PHE*     3.4    30.2    -      -       +      -
     55A  TYR*     3.4     1.6    -      -       -      +
     56A  GLN*     2.7    53.3    +      -       +      +
     57A  CYS      5.3     0.2    -      -       -      -
     58A  ASP*     5.0     4.0    -      -       +      +
    320B  HIS*     4.0     7.6    -      -       +      +
    323B  TRP*     3.7    26.2    -      -       +      -
    548B  SER*     4.7    23.6    -      -       -      +
    551B  GLY*     5.3     6.1    -      -       -      -
    552B  GLY*     5.7     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  VAL*     5.1     5.7    -      -       -      +
     34A  ASN*     2.8    54.2    -      -       -      +
     35A  PRO*     3.8    17.9    -      -       +      +
     36A  CYS*     4.2     8.5    -      -       -      -
     47A  CYS      3.7     3.8    +      -       -      -
     48A  VAL*     1.3    72.6    -      -       -      +
     50A  PHE*     1.3    78.3    +      -       -      +
     52A  LEU*     3.0    26.5    +      -       -      +
     54A  ARG      3.5     6.5    -      -       -      -
     55A  TYR*     4.1     4.5    -      -       -      +
    158A  ASP*     4.3     5.3    +      -       -      -
    320B  HIS*     3.1    20.4    -      -       -      +
    322B  THR*     3.5    34.2    +      -       -      +
    323B  TRP*     3.7    21.6    -      -       +      -
----------------------------------------------------------
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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