Contacts of the strand formed by residues 295 - 301 (chain A) in PDB entry 3KHR


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 295 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  VAL*     3.5    26.2    -      -       +      -
    288A  ALA      3.6     3.6    -      -       -      +
    289A  VAL*     4.4    15.3    -      -       +      -
    293A  LEU      4.1     8.7    -      -       -      +
    294A  ASP*     1.3    89.8    +      -       -      +
    296A  VAL*     1.3    69.5    +      -       -      +
    297A  SER*     5.6     0.7    -      -       -      -
    810D    G      4.1    15.8    +      -       -      +
    811D    T      5.6    12.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  VAL*     3.2     6.1    -      -       -      +
    288A  ALA*     2.8    38.0    +      -       +      +
    290A  THR*     4.3    17.7    -      -       +      -
    294A  ASP*     4.9     0.4    -      -       -      +
    295A  ILE*     1.3    79.6    -      -       -      +
    297A  SER*     1.3    64.1    +      -       -      +
    298A  ARG*     3.5    27.6    -      -       -      +
    322A  ILE*     3.9    29.1    -      -       +      +
    326A  ASP*     3.7    26.9    -      -       +      +
    328A  ARG*     4.3     5.2    -      -       -      +
    810D    G      3.6     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  HIS*     4.8     9.9    +      -       -      +
    286A  VAL      3.2    14.1    -      -       -      -
    287A  VAL*     4.1    13.5    -      -       -      -
    295A  ILE*     5.6     1.1    -      -       -      -
    296A  VAL*     1.3    76.0    -      -       -      +
    298A  ARG*     1.3    86.7    +      -       -      +
    322A  ILE*     4.6     0.7    -      -       -      -
    809D    G      3.5    30.0    +      -       -      +
    810D    G      2.9    12.3    +      -       -      -
    926E   AF      4.9     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  HIS*     3.6     3.3    -      -       -      -
    286A  VAL*     2.9    30.5    +      -       -      +
    296A  VAL*     3.5    27.9    -      -       -      +
    297A  SER*     1.3    97.5    +      -       -      +
    299A  GLY*     1.3    58.9    +      -       -      +
    318A  LEU*     3.6    31.4    -      -       +      +
    321A  LYS*     3.6    20.3    -      -       +      +
    322A  ILE*     3.6    19.7    -      -       +      +
    325A  GLU*     2.9    43.0    +      -       -      +
    809D    G      3.2    36.4    +      -       -      +
    810D    G      3.6    14.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  ILE      3.2    11.4    -      -       -      -
    285A  HIS*     3.4    17.2    +      -       -      -
    298A  ARG*     1.3    74.3    -      -       -      +
    300A  ARG*     1.3    63.9    +      -       -      +
    318A  LEU*     3.7     9.9    -      -       -      +
    321A  LYS*     5.4     3.8    +      -       -      -
    808D    T      4.5    10.9    +      -       -      +
    809D    G      2.8    21.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  LYS      4.3     0.5    -      -       -      +
    283A  ALA*     3.5     2.0    -      -       -      +
    284A  ILE*     2.9    35.5    +      -       +      +
    285A  HIS*     4.8     1.5    -      -       -      -
    299A  GLY*     1.3    75.0    -      -       -      +
    301A  THR*     1.3    70.0    +      -       -      +
    302A  PHE*     3.5    34.9    -      -       +      -
    314A  GLU*     2.5    51.0    +      -       -      +
    317A  LYS*     3.6    15.4    -      -       -      +
    318A  LEU*     4.3     5.1    -      -       +      +
    808D    T      3.8     9.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  LYS*     3.6     7.6    -      -       +      +
    283A  ALA*     3.8     3.6    -      -       -      +
    285A  HIS*     5.0     0.7    +      -       -      -
    300A  ARG*     1.3    80.9    +      -       -      +
    302A  PHE*     1.3    74.0    +      -       -      +
    303A  PRO*     4.6     1.4    -      -       -      +
    339A  LYS*     2.6    50.4    +      -       +      +
    807D    A      4.0    27.1    -      -       -      +
    808D    T      2.8    20.2    +      -       -      -
----------------------------------------------------------
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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