Contacts of the strand formed by residues 19 - 24 (chain J) in PDB entry 6H25


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 ILE 19 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  ASN*     5.6     0.2    -      -       -      +
      5J  LYS      5.6     0.2    -      -       -      +
      6J  THR*     3.4     4.9    -      -       -      +
      7J  PHE*     2.8    50.8    +      -       +      +
      9J  LYS*     4.1    35.4    -      -       +      +
     17J  MET*     3.5    23.3    -      -       +      +
     18J  LYS*     1.3    83.0    -      -       -      +
     20J  VAL*     1.3    67.6    +      -       -      +
     21J  ARG*     3.8    45.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 20 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  ASN*     4.4    15.0    -      -       -      +
    129B  GLN*     5.4     4.0    +      -       -      +
    131B  ASP*     4.3    12.5    -      -       -      +
     43E  SER*     3.3    38.8    -      -       -      +
     44E  ASN*     5.5     5.6    -      -       -      +
      4J  SER*     3.3    26.2    -      -       -      +
      5J  LYS      3.4     2.7    -      -       -      +
      6J  THR*     3.9    18.8    -      -       +      +
     18J  LYS*     4.4    12.3    -      -       +      -
     19J  ILE*     1.3    79.9    -      -       -      +
     21J  ARG*     1.3    64.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 21 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  VAL*     5.4    11.2    -      -       -      +
     15B  ASP*     5.7     2.2    -      -       -      +
     45B  ASN*     4.1     2.9    -      -       -      -
    131B  ASP*     5.4     2.0    -      -       -      -
    176B  VAL*     3.3    33.5    -      -       +      +
      4J  SER*     3.5     6.3    +      -       -      -
      5J  LYS*     2.9    44.8    +      -       +      +
      7J  PHE*     4.0    27.2    -      -       +      -
      9J  LYS*     5.1    12.1    -      -       -      +
     19J  ILE*     3.8    32.0    -      -       +      +
     20J  VAL*     1.3    79.0    -      -       -      +
     22J  GLU*     1.3    67.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 22 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  VAL      5.5     0.2    -      -       -      +
     15B  ASP*     3.1    44.4    -      -       +      +
     17B  ARG*     4.7     0.2    -      -       -      -
     23B  ARG*     3.7    22.1    -      -       -      +
     44B  GLY*     3.6    19.5    -      -       -      -
     45B  ASN*     3.5    21.4    +      -       -      +
    131B  ASP*     5.3     2.8    +      -       -      +
    174B  SER*     5.2     3.1    -      -       -      -
      2J  LEU*     4.1    13.4    -      -       +      +
      3J  LYS      3.9     4.5    -      -       -      -
      4J  SER*     4.7     2.0    -      -       -      +
      5J  LYS*     5.5     0.2    -      -       -      +
     21J  ARG*     1.3    81.6    -      -       -      +
     23J  HIS*     1.3    66.1    +      -       -      +
     24J  TYR*     3.3    28.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 23 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  VAL      4.8     5.3    +      -       -      -
     15B  ASP      4.1     4.9    +      -       -      -
      1J  MET      4.1     0.2    -      -       -      +
      2J  LEU*     3.9     1.4    -      -       -      +
      3J  LYS*     2.9    44.9    +      -       +      +
      4J  SER      5.2     0.2    -      -       -      -
      5J  LYS*     4.9    19.9    -      -       +      +
     22J  GLU*     1.3    79.3    +      -       -      +
     24J  TYR*     1.3    69.2    +      -       -      +
     25J  LEU*     4.2     5.0    -      -       +      +
    126J  GLU*     2.9    30.0    +      -       +      +
    127J  HIS*     3.3    31.6    +      +       -      -
    132J  TYR*     3.5    32.6    -      +       -      +
----------------------------------------------------------
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Residues in contact with TYR 24 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ASP*     3.2    12.9    +      -       +      +
     16B  GLY      3.6    23.1    -      -       -      +
     17B  ARG*     4.2    27.8    -      -       +      -
     21B  GLU*     6.3     0.7    -      -       -      -
     22B  LEU      4.3     9.2    -      -       -      -
     23B  ARG*     3.3     5.5    -      -       -      +
     24B  LYS*     2.8    36.1    +      -       +      +
     44B  GLY*     4.8     0.7    -      -       -      -
      1J  MET      4.0     2.5    -      -       -      -
      2J  LEU*     3.5    39.9    -      -       +      +
     22J  GLU*     3.3    26.2    +      -       -      -
     23J  HIS*     1.3    76.5    -      -       -      +
     25J  LEU*     1.3    72.5    +      -       -      +
     26J  ARG*     4.1     2.5    -      -       +      -
    127J  HIS*     3.5    19.8    -      -       -      +
----------------------------------------------------------
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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