Contacts of the strand formed by residues 246 - 250 (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 246 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222J  GLY*     4.2     3.4    +      -       -      -
    223J  LEU*     3.6    27.5    -      -       +      +
    244J  ARG      3.7     1.6    +      -       -      -
    245J  SER*     1.3    69.6    -      -       -      +
    247J  ALA*     1.3    62.5    +      -       -      +
    248J  VAL*     5.5     6.3    -      -       +      -
    260J  VAL      4.0     0.5    -      -       -      +
    261J  VAL*     3.5     2.1    -      -       -      -
    262J  THR*     3.0    37.8    +      -       -      +
    263J  GLU*     2.9    52.6    +      -       +      +
    485J  ARG      5.3     2.6    +      -       -      -
    487J  GLU*     2.9    46.1    +      -       -      +
    250T  GLU*     4.9    14.3    +      -       -      -
    258T  ARG*     5.8     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 247 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245J  SER*     3.4     5.7    +      -       -      +
    246J  ARG*     1.3    74.9    -      -       -      +
    248J  VAL*     1.3    69.2    +      -       -      +
    259J  ILE*     4.3     3.1    -      -       +      -
    260J  VAL      3.2    10.1    -      -       -      +
    261J  VAL*     3.9    18.8    -      -       +      -
    318J  LEU*     3.9    25.5    -      -       +      +
    322J  TYR*     3.9    20.3    +      -       +      +
    327J  LEU*     5.3     0.2    -      -       +      -
    250T  GLU*     4.3    10.0    -      -       -      +
    251T  GLU*     4.9     3.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 248 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246J  ARG*     5.5     7.6    -      -       +      -
    247J  ALA*     1.3    79.8    -      -       -      +
    249J  ILE*     1.3    64.1    +      -       -      +
    250J  GLU*     4.1    11.6    +      -       -      +
    258J  ARG      3.9     0.3    -      -       -      +
    259J  ILE*     3.3     5.6    -      -       -      +
    260J  VAL*     2.8    44.6    +      -       +      +
    262J  THR*     6.2     1.8    -      -       +      -
    318J  LEU*     5.6     0.7    -      -       -      -
    248T  VAL*     4.0    30.5    -      -       +      -
    249T  ILE      3.4    10.1    -      -       -      +
    250T  GLU*     3.7    27.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 249 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248J  VAL*     1.3    74.6    -      -       -      +
    250J  GLU*     1.3    62.8    +      -       -      +
    257J  GLN*     4.0    24.2    -      -       +      +
    258J  ARG      3.4     9.2    -      -       -      +
    259J  ILE*     4.2    11.9    -      -       +      -
    314J  ALA*     3.6    27.1    -      -       +      +
    315J  SER*     3.4    41.5    -      -       -      +
    318J  LEU*     4.5    15.0    -      -       +      -
    248T  VAL*     3.4     5.1    -      -       -      -
    249T  ILE*     2.8    55.3    +      -       +      +
    250T  GLU*     6.0     0.4    -      -       -      -
    257T  GLN*     4.3     5.2    -      -       -      +
    315T  SER*     4.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 250 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248J  VAL*     4.1     6.3    -      -       +      +
    249J  ILE*     1.3    75.4    -      -       -      +
    251J  GLU*     1.3    64.5    +      -       +      +
    257J  GLN*     3.4     6.7    -      -       -      +
    258J  ARG*     2.2    78.8    +      -       +      +
    260J  VAL*     3.7    16.0    -      -       +      +
    303J  ARG*     3.6     8.0    +      -       -      -
    246T  ARG*     5.1    11.9    +      -       -      -
    247T  ALA      4.5     7.0    -      -       -      +
    248T  VAL*     3.8    25.7    -      -       +      +
    249T  ILE*     6.1     0.2    -      -       -      -
    318T  LEU*     6.6     0.2    -      -       -      -
----------------------------------------------------------
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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