Contacts of the strand formed by residues 4 - 9 (chain F) in PDB entry 4Q44


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 4 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2F  ARG*     3.7    27.8    -      -       +      +
      3F  LYS*     1.3    76.1    -      -       -      +
      5F  ILE*     1.3    63.8    +      -       -      +
      6F  HIS      4.2     0.2    -      -       -      -
    106F  TYR*     4.0    26.9    -      -       +      -
    107F  LEU      3.5     6.1    -      -       -      +
    108F  ASP*     4.0    22.0    -      -       +      +
    141F  GLY      3.7     0.5    -      -       -      +
    142F  VAL*     3.4     6.4    -      -       -      +
    143F  ALA      2.8    39.3    +      -       -      +
    144F  PRO      3.3    23.8    -      -       -      +
    145F  VAL*     3.7    18.8    -      -       -      +
    146F  LYS*     4.2     9.4    -      -       +      +
    149F  ALA*     3.8     4.1    -      -       +      +
    234F  VAL*     4.5    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 5 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4F  ILE*     1.3    81.0    -      -       -      +
      6F  HIS*     1.3    62.8    +      -       -      +
      7F  VAL*     3.7    21.9    +      -       +      -
    105F  ALA      3.5     3.6    -      -       -      +
    106F  TYR*     3.6     0.5    -      -       -      -
    107F  LEU*     2.9    46.6    +      -       +      +
    109F  VAL*     3.6    30.3    -      -       +      -
    119F  ALA*     3.3    27.8    -      -       +      +
    122F  ILE*     3.9    18.6    -      -       +      -
    123F  ALA*     3.9    20.0    -      -       +      +
    126F  ILE*     5.2     2.5    -      -       +      -
    140F  ALA*     4.6     1.3    -      -       +      -
    141F  GLY      3.3     7.9    -      -       -      +
    142F  VAL*     4.0     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 6 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5F  ILE*     1.3    72.5    -      -       -      +
      7F  VAL*     1.3    61.3    +      -       -      +
      8F  ASP*     3.8    19.0    -      -       +      +
    100F  LEU*     4.0     5.1    -      -       +      +
    104F  GLU*     3.5    26.3    +      -       -      +
    105F  ALA      3.4    12.6    -      -       -      -
    106F  TYR*     3.5    31.4    -      +       +      -
    140F  ALA*     3.3     5.2    -      -       -      -
    141F  GLY      2.9    33.8    +      -       -      -
    149F  ALA*     3.6    28.0    -      -       +      +
    150F  LYS*     3.3    33.0    -      -       +      +
    153F  SER*     3.0    20.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 7 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5F  ILE*     3.8    20.0    -      -       +      -
      6F  HIS*     1.3    74.7    -      -       -      +
      8F  ASP*     1.3    64.8    +      -       -      +
      9F  MET*     5.2     1.1    -      -       -      +
     90F  PHE*     3.6    40.6    -      -       +      -
    103F  ASP      3.5     3.0    -      -       -      +
    104F  GLU*     3.2     6.9    -      -       -      +
    105F  ALA      2.9    31.6    +      -       -      +
    107F  LEU*     4.4    10.8    -      -       +      -
    123F  ALA*     5.9     0.7    -      -       +      -
    126F  ILE*     4.6    12.8    -      -       +      -
    127F  ARG*     5.4     2.5    -      -       +      -
    130F  ILE*     4.3    15.0    -      -       +      -
    138F  ALA*     4.3     9.0    -      -       +      -
    139F  SER      3.8     7.4    -      -       -      +
    140F  ALA*     4.6     6.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 8 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  HIS*     3.8    15.7    -      -       +      +
      7F  VAL*     1.3    76.7    -      -       -      +
      9F  MET*     1.3    61.0    +      -       -      +
    103F  ASP*     3.2     8.7    -      -       -      +
    104F  GLU*     3.3    14.1    -      -       -      +
    138F  ALA*     4.5     1.8    -      -       -      -
    139F  SER      2.9    37.3    +      -       -      +
    150F  LYS*     4.6     1.9    +      -       -      -
    153F  SER*     4.3     4.9    +      -       -      +
    154F  ASP*     3.7    11.8    -      -       -      +
    157F  LYS*     2.8    28.2    +      -       -      +
    401F  1FZ      3.5     7.8    +      -       -      -
    402F   MG      2.4    26.3    -      -       -      -
    403F   MG      3.2     6.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 9 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7F  VAL*     5.3     1.8    -      -       -      -
      8F  ASP*     1.3    75.1    +      -       -      +
     10F  ASP*     1.3    59.5    +      -       -      +
     12F  PHE*     3.8    22.6    +      -       +      -
     15F  ALA*     6.2     0.4    -      -       +      -
     86F  ILE*     3.9    27.4    -      -       +      -
    103F  ASP*     3.4    34.2    +      -       +      +
    130F  ILE*     3.8    21.1    -      -       +      -
    134F  LEU*     5.8     0.2    -      -       +      -
    136F  LEU*     3.6    29.4    -      -       +      -
    137F  THR      3.5    18.2    -      -       -      +
    138F  ALA*     3.8    17.7    -      -       -      +
    401F  1FZ      3.1     4.3    +      -       -      -
    402F   MG      2.0    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