Contacts of the strand formed by residues 154 - 158 (chain A) in PDB entry 1YXJ


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 ASN 154 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  TRP*     3.4     8.1    -      -       -      -
    151A  HIS*     3.0    27.6    +      -       -      -
    152A  GLY*     3.4     0.8    -      -       -      -
    153A  GLU*     1.3    88.4    -      -       -      +
    155A  CYS*     1.3    66.2    +      -       -      +
    156A  TYR*     3.3    33.3    +      -       +      +
    183A  ASN*     6.1     1.2    -      -       -      +
    187A  ASP*     5.6     2.2    +      -       -      -
    265A  GLN*     3.6    19.9    +      -       -      +
    266A  LYS      3.3     9.9    -      -       -      +
    267A  LYS*     3.1    40.2    +      -       -      +
    268A  ALA*     3.8     1.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  PRO      3.6     0.9    -      -       -      -
    144A  CYS*     2.0    52.9    -      -       +      -
    145A  PRO*     4.0     5.2    -      -       +      -
    148A  TRP*     3.6    19.3    -      -       +      -
    149A  ILE      3.3     5.2    -      -       -      -
    154A  ASN*     1.3    72.2    -      -       -      +
    156A  TYR*     1.3    62.9    +      -       -      +
    265A  GLN*     3.1     7.8    -      -       -      +
    266A  LYS*     2.7    35.0    +      -       +      +
    267A  LYS      4.2     3.1    -      -       -      -
    268A  ALA*     3.5    23.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ASP      4.3     0.2    -      -       -      +
    148A  TRP*     3.2     7.0    -      -       -      -
    149A  ILE*     2.7    54.8    +      -       +      +
    151A  HIS*     3.5    38.4    -      +       +      -
    154A  ASN*     3.3    39.1    +      -       +      -
    155A  CYS*     1.3    75.2    -      -       -      +
    157A  LEU*     1.3    59.9    +      -       -      +
    158A  PHE*     4.8     6.3    -      -       +      -
    180A  LEU*     3.6    21.8    -      -       +      -
    181A  LYS      5.1     0.5    +      -       -      -
    187A  ASP*     4.2    13.1    +      -       +      -
    190A  PHE*     3.6    29.2    -      +       +      -
    191A  ILE*     4.2     4.3    -      -       +      -
    263A  ILE*     4.2     7.9    -      -       +      -
    264A  CYS      3.3     5.6    -      -       -      +
    265A  GLN*     3.6    33.0    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ASP*     3.8    27.4    -      -       +      +
    148A  TRP*     3.6    38.4    -      -       +      +
    156A  TYR*     1.3    75.1    -      -       -      +
    158A  PHE*     1.3    78.5    +      -       -      +
    159A  SER*     3.6     6.1    +      -       -      -
    160A  SER      6.0     0.2    -      -       -      +
    175A  LEU*     3.6    31.0    -      -       +      -
    263A  ILE*     3.2     6.8    -      -       -      -
    264A  CYS*     2.8    41.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ASP      5.3     1.7    +      -       -      -
    149A  ILE*     4.4    22.7    -      -       +      -
    156A  TYR*     4.8     9.9    -      -       +      -
    157A  LEU*     1.3    85.3    -      -       -      +
    159A  SER*     1.3    68.3    +      -       -      +
    160A  SER*     3.7     1.0    +      -       -      -
    190A  PHE*     5.3     1.6    -      +       -      -
    191A  ILE*     4.6    10.8    -      -       +      -
    194A  ALA*     3.5    31.6    -      -       +      -
    195A  ILE*     3.7    20.6    -      -       +      -
    202A  PHE*     3.9    22.9    -      +       +      -
    262A  SER      3.7     3.1    -      -       -      -
    263A  ILE*     3.5    33.0    -      -       +      -
----------------------------------------------------------
 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