Contacts of the strand formed by residues 46 - 51 (chain H) in PDB entry 2R4S


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 GLU 46 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  VAL*     3.8     2.9    -      -       -      +
     38H  ARG*     2.8    82.1    +      -       +      +
     40H  ARG*     3.2    22.1    +      -       -      +
     44H  GLY      5.7     0.4    -      -       -      +
     45H  PHE*     1.3    76.9    -      -       -      +
     47H  TRP*     1.3    63.0    +      -       -      +
     48H  ILE*     3.4     1.4    +      -       -      +
     63H  ARG*     4.6    20.9    +      -       -      +
     64H  PHE*     3.2    21.6    -      -       +      -
     98L  PHE*     4.8     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 47 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  ASN*     3.1    30.9    +      -       +      -
     37H  VAL*     4.0    13.0    -      -       +      -
     46H  GLU*     1.3    72.2    -      -       -      +
     48H  ILE*     1.3    60.0    +      -       -      +
     49H  GLY*     3.2    23.9    +      -       -      -
     50H  GLU*     3.5     5.2    -      -       +      -
     59H  ASP      3.4    27.8    -      -       -      -
     60H  TYR      4.1     2.9    -      -       -      -
     61H  ASN*     3.3    59.8    +      -       +      +
     63H  ARG*     5.8     0.2    -      -       -      +
     64H  PHE*     3.9     4.5    -      -       -      -
    100H  PHE*     3.8     8.1    -      +       -      -
     94L  PHE*     3.5    26.5    -      +       +      -
     95L  PRO*     3.4    23.3    -      -       +      -
     96L  TYR*     3.2    49.9    +      +       +      +
     98L  PHE*     4.0    15.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  TRP*     2.8    27.3    +      -       +      +
     37H  VAL      4.1     0.9    -      -       -      -
     38H  ARG*     3.5    23.1    -      -       +      +
     46H  GLU      3.8     2.0    -      -       -      +
     47H  TRP*     1.3    73.9    -      -       -      +
     49H  GLY*     1.3    57.6    +      -       -      +
     60H  TYR*     4.3     7.1    -      -       -      -
     61H  ASN*     3.7    15.5    +      -       -      +
     64H  PHE*     3.4    42.2    -      -       +      +
     68H  ALA*     4.0    17.5    -      -       +      -
     70H  LEU*     5.3     2.9    -      -       +      +
     81H  MET*     3.9    13.5    -      -       +      -
     83H  LEU*     5.3     0.2    -      -       +      -
     94H  TYR*     3.3    42.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  ASN*     3.2     2.6    -      -       -      -
     36H  TRP      2.9    25.8    +      -       -      -
     47H  TRP*     3.2    28.4    +      -       -      -
     48H  ILE*     1.3    82.2    -      -       -      +
     50H  GLU*     1.3    57.6    +      -       -      -
     59H  ASP      3.4     7.6    -      -       -      -
     60H  TYR*     4.2     3.8    -      -       -      -
     70H  LEU*     3.8    12.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 50 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  ARG*     2.7    41.1    +      -       -      -
     33H  TYR*     3.7    28.5    -      -       +      -
     35H  ASN*     3.0    38.6    +      -       -      +
     47H  TRP*     3.8     9.0    -      -       +      +
     49H  GLY*     1.3    74.3    -      -       -      -
     51H  ILE*     1.3    62.9    +      -       -      +
     57H  ASN      3.9     1.0    -      -       -      +
     58H  ILE*     3.3     1.9    -      -       -      +
     59H  ASP*     2.9    35.1    +      -       +      +
     70H  LEU*     3.7     3.7    -      -       -      +
     99H  GLY*     4.7     1.0    -      -       -      -
    100H  PHE*     4.9     1.2    -      -       -      -
     94L  PHE*     3.9    11.0    -      -       +      -
     96L  TYR*     2.9    16.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  TYR*     3.3     3.3    -      -       -      +
     34H  ILE*     3.1    45.6    +      -       +      +
     36H  TRP*     4.7     4.5    -      -       +      +
     50H  GLU*     1.3    74.8    -      -       -      +
     52H  TYR*     1.3    66.8    +      -       -      +
     53H  PRO*     3.1    20.1    -      -       +      +
     56H  GLY*     4.5     4.9    -      -       -      +
     57H  ASN      3.4     3.6    -      -       -      +
     58H  ILE*     3.3    29.8    -      -       +      -
     70H  LEU*     3.6    28.5    -      -       +      -
     71H  THR*     4.6     6.5    -      -       -      +
     72H  ALA*     3.6    26.5    -      -       +      +
     79H  ALA*     5.3     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page


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