Contacts of the strand formed by residues 235 - 241 (chain A) in PDB entry 4A3K


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 235 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  PRO*     5.4     2.6    -      -       -      +
     89A  PRO*     3.7    27.6    -      -       +      -
     90A  VAL      3.5    10.5    -      -       -      +
     91A  PHE*     4.0    20.6    -      -       +      -
     99A  ILE*     4.1     4.0    -      -       +      -
    204A  THR*     4.0     9.0    -      -       +      +
    207A  ILE*     3.8    19.7    -      -       +      -
    208A  LEU*     3.8    44.5    -      -       +      +
    211A  PHE*     4.1    15.3    -      -       +      -
    232A  GLU      3.5    18.3    +      -       -      +
    233A  TRP*     3.2     5.0    -      -       -      +
    234A  MET*     1.4    80.3    -      -       -      +
    236A  LEU*     1.3    64.4    +      -       -      +
    237A  THR*     3.8     8.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LEU*     3.6    17.3    -      -       +      +
     89A  PRO*     3.5     6.6    -      -       -      +
     90A  VAL*     2.7    37.0    +      -       +      +
     91A  PHE      4.1     2.5    -      -       -      +
     92A  HIS*     3.8    35.7    -      -       +      +
    233A  TRP      4.6     9.4    -      -       -      +
    234A  MET      4.5     1.6    -      -       -      +
    235A  ILE*     1.3    73.3    -      -       -      +
    237A  THR*     1.3    58.9    +      -       -      +
    238A  CYS      5.2     6.1    -      -       -      +
    239A  LEU*     4.8    11.2    -      -       +      -
    240A  PRO*     6.1     2.9    -      -       +      -
    300A  VAL*     3.7    19.3    -      -       +      -
    304A  MET*     3.7    30.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  PRO*     3.6    31.9    -      -       +      +
     85A  ASP*     4.2     3.1    -      -       -      +
     86A  LEU*     3.0    38.9    +      -       -      +
     88A  LYS      5.9     0.4    -      -       -      -
     89A  PRO*     5.1     6.1    -      -       +      -
    208A  LEU*     4.7    14.5    -      -       +      +
    232A  GLU      5.6     0.3    +      -       -      -
    235A  ILE      3.8     7.5    +      -       -      -
    236A  LEU*     1.3    75.2    -      -       -      +
    238A  CYS*     1.3    64.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  PRO*     4.0    29.2    -      -       +      +
     27A  VAL*     3.9    28.5    -      -       +      +
     28A  ARG*     4.2     8.1    -      -       -      -
     83A  HIS*     3.6    33.0    -      -       -      -
     84A  ILE      3.6     3.1    -      -       -      -
     85A  ASP*     3.6    15.7    -      -       -      +
     86A  LEU*     5.0     0.4    -      -       -      -
    236A  LEU*     5.2     4.2    -      -       -      +
    237A  THR*     1.3    82.1    +      -       +      +
    239A  LEU*     1.3    61.4    +      -       -      +
    240A  PRO*     3.6     8.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  VAL*     4.0     2.9    -      -       -      -
     83A  HIS*     3.4     1.7    -      -       -      -
     84A  ILE*     2.8    53.6    +      -       +      +
     86A  LEU*     4.4    11.4    -      -       +      +
    236A  LEU*     4.8    15.0    -      -       +      -
    237A  THR      4.0     1.0    -      -       -      -
    238A  CYS*     1.3    70.4    -      -       -      +
    240A  PRO*     1.4    85.1    -      -       +      +
    241A  VAL*     3.4     1.9    +      -       -      +
    266A  LEU*     4.7     7.2    -      -       +      -
    269A  ILE*     4.0    39.5    -      -       +      -
    300A  VAL*     4.4    23.3    -      -       +      -
    303A  TYR*     4.5    15.7    -      -       +      -
    304A  MET*     5.4     4.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  PHE*     4.8    18.2    -      -       +      -
     27A  VAL*     3.6    22.6    -      -       +      -
     30A  ILE*     5.8     1.8    -      -       +      -
     81A  PHE*     3.9    22.7    -      -       +      -
     82A  GLY      3.6     7.2    -      -       -      +
    236A  LEU*     6.1     3.8    -      -       +      -
    238A  CYS      3.6     9.2    -      -       -      +
    239A  LEU*     1.4   100.2    -      -       +      +
    241A  VAL*     1.3    61.1    -      -       -      +
    242A  PRO*     3.7    10.1    -      -       -      +
    266A  LEU*     5.2     0.7    -      -       -      +
    303A  TYR*     3.9     8.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ILE*     3.8    23.8    -      -       +      -
     53A  LEU*     5.6     2.9    -      -       +      -
     58A  LEU*     4.8     3.4    -      -       +      +
     80A  HIS      4.6     0.2    -      -       -      +
     81A  PHE*     3.3     7.3    -      -       -      -
     82A  GLY*     3.0    34.8    +      -       -      -
     83A  HIS      3.6    18.2    -      -       -      +
     84A  ILE*     3.3    33.4    -      -       +      -
    239A  LEU*     5.8     0.2    -      -       +      -
    240A  PRO*     1.3    72.1    -      -       -      +
    242A  PRO*     1.4    74.9    -      -       +      +
    243A  PRO      3.6     1.2    -      -       -      -
    247A  ARG*     4.0    13.7    -      -       -      +
    266A  LEU*     4.4    14.6    -      -       +      -
----------------------------------------------------------
 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