Contacts of the strand formed by residues 50 - 57 (chain A) in PDB entry 1X8E


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 50 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  VAL*     3.8    24.9    -      -       +      -
     25A  ARG      4.1     2.7    -      -       -      +
     26A  ARG*     3.2    33.5    -      -       +      +
     49A  PRO*     1.3    75.0    -      -       -      +
     51A  VAL*     1.3    62.1    +      -       -      +
     52A  TYR      3.8     9.9    -      -       -      +
     53A  GLU*     4.5     6.1    -      -       -      +
     74A  TYR*     3.6    50.0    -      -       +      +
     83A  PHE*     4.1     7.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ARG      3.0    11.6    +      -       -      +
     27A  LEU*     3.6    44.9    -      -       +      +
     30A  MET*     3.8    13.7    -      -       -      -
     34A  PHE*     5.1     1.1    -      -       +      -
     49A  PRO      3.6     1.3    +      -       -      +
     50A  VAL*     1.3    76.2    -      -       -      +
     52A  TYR*     1.3    68.6    +      -       +      +
     73A  LEU*     3.2    13.5    -      -       +      +
     74A  TYR*     2.9    25.4    +      -       -      +
     83A  PHE*     4.0    24.9    -      -       +      -
     84A  PHE      3.5    29.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  SER      4.1     0.2    -      -       -      +
     24A  VAL*     3.8     2.1    -      -       -      +
     25A  ARG*     3.0    54.7    +      -       +      +
     30A  MET*     3.9    15.3    -      -       -      -
     50A  VAL*     3.8     9.8    -      -       -      -
     51A  VAL*     1.3    93.7    -      -       +      +
     53A  GLU*     1.3    58.5    +      -       -      +
     54A  VAL*     3.7    26.6    -      -       +      +
     71A  THR*     3.9     5.6    -      -       +      -
     72A  VAL      3.1    14.1    -      -       -      +
     73A  LEU*     3.8    10.5    -      -       +      -
     74A  TYR*     4.3     0.2    -      -       -      -
     84A  PHE      4.0     4.0    -      -       -      -
     85A  THR*     3.7    30.5    -      -       +      -
     86A  LYS*     3.2    41.4    +      -       -      +
     88A  HIS*     6.3     1.8    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  LYS*     5.0     6.5    -      -       +      -
     23A  SER      3.4     4.9    -      -       -      +
     24A  VAL*     4.2    27.2    -      -       +      +
     50A  VAL*     4.5     7.1    -      -       -      +
     52A  TYR*     1.3    73.7    -      -       -      +
     54A  VAL*     1.3    63.9    +      -       -      +
     55A  TYR*     3.8    28.5    +      -       +      +
     70A  THR      3.8     0.2    -      -       -      +
     71A  THR*     3.1     8.3    -      -       -      +
     72A  VAL*     2.9    45.0    +      -       +      +
     74A  TYR*     2.9    33.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  LYS      3.7     1.1    -      -       -      +
     22A  LYS*     3.5     6.8    -      -       -      +
     23A  SER*     2.9    42.4    +      -       -      +
     25A  ARG*     6.0     0.9    -      -       +      -
     52A  TYR*     3.7    29.2    -      -       +      +
     53A  GLU*     1.3    79.7    -      -       -      +
     55A  TYR*     1.3    69.6    +      -       -      +
     56A  ALA*     3.9     8.1    -      -       +      +
     69A  ALA*     4.3    17.9    -      -       +      -
     70A  THR      3.4     9.2    -      -       -      +
     71A  THR*     3.8    12.1    -      -       -      +
    152A  TYR*     5.7     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  GLY      3.2    25.8    -      -       -      -
     16A  ILE*     3.3    39.0    -      -       +      +
     17A  ILE*     3.7    32.8    -      -       +      +
     20A  ALA*     3.9    10.5    -      -       +      -
     21A  LYS      4.0     2.7    -      -       -      -
     22A  LYS*     3.7    32.8    -      -       +      +
     53A  GLU*     3.8    23.9    +      -       +      +
     54A  VAL*     1.3    78.2    -      -       -      +
     56A  ALA*     1.3    61.1    +      -       -      +
     69A  ALA*     3.6     3.1    -      -       -      -
     70A  THR*     2.9    40.4    +      -       -      +
     72A  VAL*     4.2    17.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ALA*     3.5     1.0    -      -       -      +
     21A  LYS*     3.2    39.1    +      -       +      +
     54A  VAL*     3.9     6.9    -      -       +      -
     55A  TYR*     1.3    73.2    -      -       -      +
     57A  VAL*     1.3    64.4    +      -       -      +
     58A  GLU*     3.6    30.9    +      -       +      +
     68A  PHE      3.6     7.4    -      -       -      +
     69A  ALA*     4.3     4.0    -      -       +      +
    152A  TYR*     4.3     9.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  PHE*     3.9    26.5    -      -       +      -
      8A  VAL*     5.1     3.4    -      -       +      -
     17A  ILE*     4.2    13.9    -      -       +      -
     20A  ALA*     4.1    17.5    -      -       +      -
     56A  ALA*     1.3    77.7    -      -       -      +
     58A  GLU*     1.3    60.5    +      -       -      +
     59A  GLN*     4.2     6.8    +      -       -      +
     66A  LEU      4.8     0.3    -      -       -      +
     67A  ASN*     3.6     2.9    -      -       -      -
     68A  PHE*     2.8    74.7    +      -       +      +
----------------------------------------------------------
 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