Contacts of the strand formed by residues 154 - 158 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  TRP*     3.6     9.2    -      -       -      -
    151B  HIS      3.0    27.9    +      -       -      +
    153B  GLU*     1.3    88.0    +      -       -      +
    155B  CYS*     1.3    66.1    +      -       -      +
    156B  TYR*     3.5    33.5    +      -       +      +
    265B  GLN*     3.7    16.9    +      -       -      +
    266B  LYS*     3.4    12.2    +      -       -      +
    267B  LYS*     3.1    45.0    +      -       -      +
    268B  ALA*     4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  PRO      3.6     0.4    -      -       -      -
    144B  CYS*     2.0    51.8    -      -       +      -
    145B  PRO*     4.2     4.9    -      -       +      -
    148B  TRP*     3.5    19.5    -      -       +      -
    149B  ILE      3.4     5.2    -      -       -      -
    154B  ASN*     1.3    72.2    -      -       -      +
    156B  TYR*     1.3    64.0    +      -       -      +
    265B  GLN*     3.1     8.1    -      -       -      +
    266B  LYS*     2.8    33.1    +      -       +      +
    267B  LYS      4.1     3.8    -      -       -      -
    268B  ALA*     3.4    25.6    -      -       -      -
    269B  ASN*     5.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 156 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  ASP      4.5     0.2    -      -       -      +
    148B  TRP*     3.3     6.0    -      -       -      -
    149B  ILE*     2.6    52.1    +      -       +      +
    151B  HIS*     3.7    27.9    +      -       +      -
    154B  ASN*     3.5    37.8    +      -       +      +
    155B  CYS*     1.3    75.0    -      -       -      +
    157B  LEU*     1.3    60.8    +      -       -      +
    158B  PHE*     4.2    17.9    -      -       +      -
    180B  LEU*     3.8    19.7    -      -       +      -
    181B  LYS      5.4     0.5    +      -       -      -
    187B  ASP*     4.6    14.1    +      -       -      -
    190B  PHE*     3.5    28.3    -      +       +      -
    191B  ILE*     4.3     0.9    -      -       +      -
    263B  ILE*     4.2     6.1    -      -       +      -
    264B  CYS      3.3     5.8    -      -       -      +
    265B  GLN*     3.6    34.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  ASP*     3.8    27.8    -      -       +      +
    148B  TRP*     3.7    36.8    -      -       +      +
    156B  TYR*     1.3    74.8    -      -       -      +
    158B  PHE*     1.3    75.2    +      -       -      +
    159B  SER*     3.5    11.2    +      -       -      +
    175B  LEU*     3.6    31.2    -      -       +      -
    263B  ILE*     3.1     8.6    -      -       -      -
    264B  CYS*     2.8    47.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  MSE      4.0    23.6    -      -       +      -
    147B  ASP      5.3     1.0    +      -       -      -
    149B  ILE*     4.1    24.2    -      -       +      -
    156B  TYR*     4.2    15.0    -      -       +      -
    157B  LEU*     1.3    81.8    -      -       -      +
    159B  SER*     1.3    67.7    +      -       -      +
    160B  SER*     3.8     0.5    +      -       -      -
    190B  PHE*     4.9     2.2    -      +       -      -
    191B  ILE*     4.3    16.4    -      -       +      -
    194B  ALA*     3.4    26.2    -      -       +      -
    195B  ILE*     3.7    31.0    -      -       +      -
    202B  PHE*     4.2    14.6    -      +       +      -
    262B  SER      3.7     3.8    -      -       -      -
    263B  ILE*     3.6    32.1    -      -       +      -
----------------------------------------------------------
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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