Contacts of the strand formed by residues 187 - 191 (chain 2) in PDB entry 1QJX


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 HIS 187 (chain 2).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     371  ALA      4.9     1.0    +      -       -      -
     401  GLY*     3.3    43.0    +      -       -      -
     322  VAL*     3.6     8.7    -      -       -      +
    1232  LEU*     4.3    10.8    -      -       +      -
    1242  VAL      3.1    16.2    -      -       -      +
    1252  VAL*     4.1    13.5    -      -       +      -
    1832  LEU*     3.1    52.5    +      -       +      +
    1852  PHE      2.9    20.3    +      -       -      +
    1862  PRO*     1.3    75.0    -      -       -      +
    1882  GLN*     1.3    79.0    +      -       -      +
    1892  PHE*     4.3    10.0    -      +       -      -
    2002  LEU*     3.8     7.0    -      -       -      +
     493  VAL*     5.4     2.7    -      -       +      -
     503  ASP      5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 188 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     381  GLU      3.4     7.4    -      -       -      +
     391  THR*     2.9    19.7    +      -       -      +
     401  GLY*     4.4     0.4    -      -       -      -
     292  ALA*     2.8    31.8    +      -       -      +
     302  ASN      3.5    13.3    +      -       -      +
     312  ALA      3.9     0.6    -      -       -      +
     322  VAL*     3.7    12.8    -      -       +      +
    1232  LEU*     3.8     3.5    -      -       -      +
    1242  VAL*     2.9    32.0    +      -       +      +
    1872  HIS*     1.3    88.2    -      -       -      +
    1892  PHE*     1.3    68.5    +      -       -      +
    1952  ASN*     5.4     0.2    +      -       -      -
    1972  SER      4.6     0.9    -      -       -      +
    1982  ALA*     3.3    19.1    -      -       +      -
    1992  THR      2.9    35.9    +      -       -      +
    2002  LEU*     4.6     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 189 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     371  ALA      3.6    23.1    -      -       -      -
     381  GLU*     2.9    29.1    +      -       +      +
    1212  THR*     3.7    16.4    -      -       +      -
    1222  LEU      3.2    16.6    -      -       -      -
    1232  LEU*     3.8    29.4    -      -       +      -
    1242  VAL*     4.7     0.4    -      -       -      +
    1832  LEU*     4.4    11.0    -      -       +      -
    1872  HIS*     4.3    15.7    -      +       -      -
    1882  GLN*     1.3    78.9    -      -       -      +
    1902  ILE*     1.3    63.9    +      -       -      +
    1912  ASN      3.6     0.4    -      -       -      -
    1952  ASN*     2.9    21.0    +      -       -      +
    1972  SER      4.8     0.2    -      -       -      +
    2262  VAL*     4.2     6.3    -      -       +      -
     523  LEU*     4.8     5.6    -      -       +      -
    1183  MET*     4.0     6.3    -      -       +      -
    2103  LEU*     4.1    20.4    -      -       +      -
    2123  PHE*     4.0    30.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 190 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     712  TRP*     5.2     0.2    -      -       -      -
    1102  VAL*     3.7    42.0    -      -       +      +
    1122  CYS*     4.2    27.4    -      -       +      +
    1202  GLY      3.8     0.5    -      -       -      +
    1212  THR*     3.4     4.1    -      -       -      -
    1222  LEU*     2.9    45.5    +      -       +      +
    1242  VAL*     4.3     5.8    -      -       +      -
    1892  PHE*     1.3    76.1    -      -       -      +
    1912  ASN*     1.3    56.1    +      -       -      +
    1922  LEU*     3.6    10.6    +      -       +      +
    1952  ASN*     3.7    21.8    -      -       -      +
    1972  SER*     3.8    16.4    -      -       -      +
    1982  ALA*     3.7    17.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 191 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     381  GLU*     3.0    34.3    +      -       +      +
    1202  GLY      3.3     5.9    -      -       -      +
    1212  THR*     2.8    29.1    +      -       +      +
    1892  PHE      3.6     0.8    -      -       -      -
    1902  ILE*     1.3    71.2    -      -       -      +
    1922  LEU*     1.3    55.0    +      -       -      +
    1932  ARG*     2.7    17.1    +      -       -      +
    1942  SER*     2.6    30.0    +      -       -      +
    1952  ASN*     3.0    15.9    +      -       -      -
    1183  MET*     3.9    10.4    -      -       -      +
    1193  PHE      2.9    27.1    +      -       -      -
    1203  CYS*     3.7    13.0    -      -       -      +
    1613  SER*     4.2     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