Contacts of the strand formed by residues 238 - 244 (chain j) in PDB entry 6QX2


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 ARG 238 (chain j).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232j  ARG*     3.1    16.3    -      -       -      +
    233j  ALA*     3.7     4.5    -      -       -      -
    236j  THR*     2.8    24.0    +      -       -      +
    237j  GLY*     1.3    84.5    -      -       -      +
    239j  GLY*     1.3    57.8    +      -       -      +
    333j  VAL      3.3     7.9    -      -       -      +
    334j  ASN*     3.8    21.7    +      -       -      +
    345j  LEU*     3.9    23.3    -      -       +      +
   2019o    T      3.7    26.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 239 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229j  GLY      4.1     8.3    -      -       -      -
    232j  ARG*     4.6    10.3    -      -       -      -
    233j  ALA*     4.0    14.7    -      -       -      +
    238j  ARG*     1.3    74.4    -      -       -      +
    240j  SER*     1.3    60.7    +      -       -      -
    332j  GLY*     3.8     0.9    -      -       -      -
    333j  VAL*     2.9    35.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 240 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229j  GLY*     3.1    23.0    -      -       -      -
    232j  ARG*     4.9     6.7    +      -       -      +
    239j  GLY*     1.3    71.3    -      -       -      -
    241j  ILE*     1.3    57.5    +      -       -      +
    242j  GLN*     3.5    15.9    +      -       -      +
    330j  SER*     2.6    25.5    +      -       -      -
    331j  PHE      3.9     3.6    -      -       -      -
    332j  GLY*     4.7     2.5    -      -       -      -
   2019o    T      4.6     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 241 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184j  PRO*     4.9     0.4    -      -       +      -
    216j  PRO*     3.7    25.4    -      -       +      -
    218j  PHE*     4.9     1.6    -      -       +      -
    224j  ILE*     3.8    39.3    -      -       +      -
    229j  GLY*     4.0     3.1    -      -       -      -
    230j  ILE*     3.9    32.5    -      -       +      +
    233j  ALA*     4.6     2.2    -      -       +      -
    234j  TYR*     6.0     1.6    -      -       +      -
    239j  GLY      4.8     0.2    -      -       -      +
    240j  SER*     1.3    75.9    +      -       -      +
    242j  GLN*     1.3    65.0    +      -       -      +
    243j  MET*     3.6     6.8    +      -       +      -
    330j  SER*     3.4     1.4    -      -       -      -
    331j  PHE*     2.7    46.1    +      -       +      +
    333j  VAL*     3.5    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 242 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224j  ILE*     3.4     5.9    -      -       -      +
    225j  LEU*     3.0    48.8    +      -       +      +
    240j  SER*     3.5    14.6    +      -       -      +
    241j  ILE*     1.3    69.4    -      -       -      +
    243j  MET*     1.3    61.1    +      -       -      +
    328j  GLN*     3.2    35.3    +      -       -      +
    329j  THR      4.0     5.5    -      -       -      +
    330j  SER*     3.4    26.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 243 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218j  PHE*     3.5    42.4    -      -       +      -
    223j  LEU      3.3     8.1    -      -       -      +
    224j  ILE*     4.7     1.1    -      -       +      +
    241j  ILE*     4.3     9.0    -      -       +      +
    242j  GLN*     1.3    73.1    -      -       -      +
    244j  ARG*     1.3    60.1    +      -       -      +
    265j  PRO*     3.9    15.7    -      -       +      -
    266j  PHE*     3.7    37.0    -      -       +      +
    328j  GLN*     3.4     9.2    -      -       -      +
    329j  THR*     2.8    58.9    +      -       +      +
    330j  SER      4.0     0.7    -      -       -      +
    331j  PHE*     4.0    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 244 (chain j). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222j  GLY*     3.8     2.8    -      -       -      -
    223j  LEU*     2.7    50.6    +      -       +      +
    225j  LEU*     3.7    38.8    -      -       +      +
    243j  MET*     1.3    74.5    -      -       -      +
    245j  SER*     1.3    64.9    -      -       -      +
    246j  ARG      3.7     0.2    +      -       -      -
    265j  PRO*     4.4     5.1    -      -       -      +
    319j  ASN*     5.6     4.0    +      -       -      -
    322j  TYR*     3.4    56.2    -      -       +      +
    327j  LEU      3.8     3.1    -      -       -      -
    328j  GLN*     3.0    29.3    +      -       +      +
    251t  GLU*     4.5    16.1    -      -       -      +
----------------------------------------------------------
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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