Contacts of the strand formed by residues 447 - 449 (chain D) in PDB entry 6JBQ


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 447 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353D  SER*     3.7    33.6    -      -       -      +
    354D  VAL      3.1     8.0    +      -       -      +
    355D  ILE*     3.4     7.8    -      -       +      +
    356D  THR*     2.8    26.5    +      -       -      -
    366D  CYS*     4.9     1.1    -      -       -      -
    367D  GLY      3.4    21.3    -      -       -      +
    368D  LEU*     4.8     2.9    -      -       +      -
    369D  PRO*     4.1     7.2    -      -       +      -
    372D  MET*     3.8    18.8    -      -       +      -
    423D  LEU*     4.7    17.7    -      -       +      -
    446D  ALA*     1.3    73.5    -      -       -      +
    448D  GLN*     1.3    67.9    +      -       -      +
    449D  LEU*     5.5     1.6    -      -       +      -
    466D  MET*     4.7    14.6    -      -       +      +
    468D  VAL*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 448 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    810C  TYR*     5.6     2.0    -      -       -      -
   1077C  SER      5.2     2.8    +      -       -      -
   1078C  LYS*     5.3    10.9    -      -       -      +
    356D  THR*     3.3    26.4    -      -       +      +
    357D  VAL      4.0    11.5    +      -       -      -
    358D  GLY*     3.9     6.7    -      -       -      -
    359D  PRO*     5.3     0.8    -      -       -      +
    360D  TYR*     3.3    39.6    +      -       -      -
    361D  LEU*     3.6    14.5    -      -       +      +
    366D  CYS*     3.4     7.3    -      -       -      +
    367D  GLY*     2.9    27.8    +      -       -      -
    442D  ILE*     3.7    29.7    -      -       +      +
    446D  ALA      3.8     2.2    +      -       -      +
    447D  ILE*     1.3    79.6    -      -       -      +
    449D  LEU*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 449 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355D  ILE*     4.5     9.2    -      -       +      -
    356D  THR      2.9    11.9    +      -       -      +
    357D  VAL*     3.9     2.3    -      -       -      -
    358D  GLY      2.9    23.7    +      -       -      +
    361D  LEU*     4.1     5.8    -      -       -      -
    366D  CYS*     4.0    15.7    -      -       +      -
    423D  LEU*     3.8    24.7    -      -       +      -
    437D  PHE*     4.6     8.7    -      -       +      -
    447D  ILE*     5.0     3.4    -      -       +      +
    448D  GLN*     1.3    75.7    -      -       -      +
    450D  HIS*     1.3    70.2    +      -       -      +
    451D  PRO      3.7     0.3    -      -       -      -
    453D  VAL*     4.0    14.8    -      -       +      -
    454D  CYS*     3.9    20.6    -      -       -      -
    457D  TYR*     4.4    12.6    -      -       +      -
    461D  PHE*     4.7     4.8    -      -       +      -
    466D  MET*     3.8    31.2    -      -       +      -
----------------------------------------------------------
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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