Contacts of the strand formed by residues 39 - 44 (chain A) in PDB entry 3RJD


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 VAL 39 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  LEU*     3.8    26.7    -      -       +      -
     28A  PRO*     4.1    19.7    -      -       +      +
     30A  TRP      4.4     7.0    -      -       -      +
     33A  VAL*     4.5    23.6    -      -       +      -
     37A  GLU      5.0     0.9    -      -       -      +
     38A  THR*     1.3    74.9    -      -       -      +
     40A  THR*     1.3    64.9    +      -       -      +
     41A  LEU*     4.8     1.1    -      -       +      -
     70A  TYR      3.8     2.3    -      -       -      +
     72A  ILE*     2.9    47.8    +      -       +      +
     75A  ALA*     5.2     1.8    -      -       +      -
     98A  LEU*     4.0    30.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  LEU*     3.3     9.2    -      -       -      +
     27A  GLN*     3.0    35.3    +      -       -      +
     28A  PRO*     3.9     5.8    -      -       -      +
     38A  THR*     4.6     4.5    -      -       -      +
     39A  VAL*     1.3    75.3    -      -       -      +
     41A  LEU*     1.3    62.2    +      -       -      +
     42A  HIS*     3.6    28.9    -      -       +      +
     69A  SER*     3.9    16.8    -      -       -      -
     70A  TYR      3.5     7.4    -      -       -      +
     71A  ARG*     3.6    29.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ILE*     3.9     7.6    -      -       +      -
     25A  THR      3.5     4.5    -      -       -      -
     26A  LEU*     3.6    16.2    -      -       +      -
     39A  VAL*     4.5     3.4    -      -       +      +
     40A  THR*     1.3    73.9    -      -       -      +
     42A  HIS*     1.3    61.8    +      -       -      +
     56A  TRP*     3.3    20.8    -      -       +      -
     69A  SER*     3.3     0.9    -      -       -      -
     70A  TYR*     2.6    65.7    +      -       +      +
     72A  ILE*     3.8    17.9    -      -       +      -
     83A  TYR*     3.7    41.1    -      -       +      -
     96A  ILE*     3.9    17.5    -      -       +      -
     98A  LEU*     4.6     6.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  VAL      3.6     1.9    -      -       -      +
     24A  ILE*     3.6     4.9    -      -       -      -
     25A  THR*     2.8    60.1    +      -       +      +
     26A  LEU      4.1     0.4    -      -       -      -
     27A  GLN*     3.3    47.1    -      -       +      +
     40A  THR*     3.6    22.4    -      -       +      +
     41A  LEU*     1.3    72.8    -      -       -      +
     43A  CYS*     1.3    61.6    +      -       -      +
     44A  GLU*     3.8     7.0    -      -       -      +
     56A  TRP*     3.9     3.1    -      -       -      -
     68A  PRO      3.5     6.7    -      -       -      +
     69A  SER*     3.1    24.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ALA*     3.8    17.3    -      -       -      -
     23A  VAL      3.9     0.7    -      -       -      -
     42A  HIS*     1.3    69.2    -      -       -      +
     44A  GLU*     1.3    61.1    +      -       -      +
     54A  THR*     4.6     3.4    -      -       +      -
     56A  TRP*     3.5    15.8    -      -       +      -
     68A  PRO*     3.0    16.8    +      -       -      +
     85A  CYS*     2.0    50.9    -      -       +      -
     86A  GLN      3.8     6.3    -      -       -      -
     87A  ARG*     3.2    41.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ALA      4.2     0.2    -      -       -      -
     23A  VAL*     3.3    45.4    +      -       +      +
     25A  THR*     3.6    31.5    -      -       +      +
     42A  HIS*     4.6     6.1    -      -       +      +
     43A  CYS*     1.3    75.2    -      -       -      +
     45A  VAL*     1.3    63.9    +      -       -      +
     46A  LEU*     4.3     9.3    +      -       +      +
     87A  ARG*     4.2    10.5    -      -       -      +
----------------------------------------------------------
 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