Contacts of the strand formed by residues 240 - 244 (chain A) in PDB entry 4X2Q


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 LYS 240 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  ILE*     3.8    29.4    -      -       +      -
    161A  VAL      3.3     3.0    +      -       -      -
    162A  CYS*     3.5    10.0    -      -       +      -
    163A  GLY      2.6    33.8    +      -       -      +
    238A  ILE*     3.2     8.3    -      -       -      +
    239A  ASP*     1.3    81.5    -      -       -      +
    241A  ILE*     1.3    73.0    +      -       -      +
    242A  ALA*     3.4    11.5    -      -       +      +
    263A  LYS*     3.9     2.7    -      -       -      +
    264A  ARG*     3.4    24.7    -      -       +      +
    266A  THR*     3.0    26.5    +      -       -      +
    484A  GLU*     3.2    36.5    +      -       -      +
    485A  TYR*     4.3    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  GLY*     3.3    10.5    -      -       -      +
    165A  ILE*     4.0    21.8    -      -       +      -
    232A  ILE*     4.0     5.8    -      -       +      -
    233A  ALA*     3.7    38.1    -      -       +      +
    240A  LYS*     1.3    88.6    +      -       -      +
    242A  ALA*     1.3    69.5    +      -       -      +
    243A  PHE*     4.1     1.1    -      -       +      +
    253A  ILE*     3.9    17.9    -      -       +      -
    257A  ALA*     4.8     2.9    -      -       -      +
    263A  LYS*     3.8    18.8    -      -       +      +
    264A  ARG      2.9    16.6    +      -       -      +
    265A  VAL*     4.0    23.8    -      -       +      -
    266A  THR      3.1    17.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  GLY      2.8    13.6    +      -       -      +
    164A  GLN*     3.5     2.7    -      -       +      -
    165A  ILE      3.1    23.7    +      -       -      +
    178A  LYS*     3.5    20.8    -      -       -      -
    240A  LYS*     3.4    18.2    -      -       +      +
    241A  ILE*     1.3    72.9    -      -       -      +
    243A  PHE*     1.3    61.2    +      -       -      +
    266A  THR*     3.4    11.2    -      -       +      +
    484A  GLU*     4.5     2.0    -      -       -      +
    485A  TYR*     3.5    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  ILE*     3.6    31.6    -      -       +      -
    178A  LYS*     4.6     0.9    +      -       -      -
    241A  ILE*     4.1     2.8    -      -       +      -
    242A  ALA*     1.3    73.9    -      -       -      +
    244A  THR*     1.3    78.2    +      -       -      +
    245A  GLY*     3.6    19.3    -      -       -      -
    246A  SER      3.4    22.2    -      -       -      -
    249A  VAL*     3.6    29.8    -      -       +      -
    250A  GLY*     3.6    20.2    -      -       -      -
    253A  ILE*     4.1    23.3    -      -       +      -
    266A  THR      2.9     8.7    +      -       -      +
    267A  LEU*     4.0    17.5    -      -       +      -
    268A  GLU*     2.8    30.0    +      -       -      +
    269A  LEU*     3.8     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  ILE      3.0    10.6    +      -       -      +
    166A  ILE      4.0     1.4    -      -       -      -
    167A  PRO*     3.3    34.1    -      -       +      +
    174A  MET*     3.7    18.4    -      -       +      -
    178A  LYS*     2.6    31.3    +      -       -      -
    243A  PHE*     1.3    87.9    +      -       -      +
    245A  GLY*     1.3    60.2    +      -       -      +
    268A  GLU*     2.9    34.7    +      -       +      +
    302A  CYS*     4.9    12.3    -      -       -      -
----------------------------------------------------------
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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