Contacts of the strand formed by residues 29 - 35 (chain A) in PDB entry 4FQX


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 ASP 29 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ASP*     3.2     3.1    -      -       -      -
     26A  PHE*     2.7    38.9    +      -       -      +
     27A  ASP*     4.1     3.3    -      -       -      +
     28A  GLY*     1.3    79.6    -      -       -      +
     30A  GLU*     1.3    63.4    +      -       -      +
     31A  ILE      3.4     0.3    +      -       -      -
    138A  LEU*     5.8     0.4    -      -       -      -
    146A  ARG*     5.3     0.2    +      -       -      -
    123B  TYR*     3.8    24.1    +      -       -      -
    149B  GLN*     3.3    30.7    +      -       -      +
    151B  GLY*     4.2    13.4    +      -       -      +
    153B  TRP*     3.4    48.2    +      -       +      +
    155B  PHE*     4.6     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  MET*     3.8    19.5    -      -       +      -
     24A  PHE      3.6     5.8    -      -       -      -
     25A  ASP*     4.0     1.6    +      -       -      -
     28A  GLY      4.1     1.0    +      -       -      -
     29A  ASP*     1.3    71.1    -      -       -      +
     31A  ILE*     1.3    61.3    +      -       -      +
     32A  PHE*     3.6    14.0    -      -       -      +
     33A  HIS*     2.4    46.4    +      -       -      +
     42A  VAL      4.3     1.3    -      -       -      +
     44A  ARG*     3.1    38.3    -      -       +      +
     48A  PHE*     4.3     0.2    -      -       -      -
    135A  THR*     3.7    14.6    +      -       -      -
    136A  VAL*     4.3     5.2    +      -       -      +
    138A  LEU*     3.8    22.3    -      -       +      +
    151B  GLY      5.4     3.4    +      -       -      +
    153B  TRP*     3.0    22.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ILE*     4.9     3.6    -      -       +      -
     24A  PHE*     3.0    24.7    +      -       +      +
     25A  ASP      3.7    20.9    -      -       -      +
     26A  PHE*     3.9    19.1    -      -       +      +
     29A  ASP      3.4     0.6    +      -       -      -
     30A  GLU*     1.3    73.7    -      -       -      +
     32A  PHE*     1.3    63.2    +      -       +      +
     43A  TRP*     3.8     1.2    -      -       -      -
     44A  ARG      3.0    20.6    +      -       -      -
     48A  PHE*     3.5    29.7    -      -       +      +
     51A  PHE*     3.6    30.3    -      -       +      -
     89B  PHE*     4.2    30.3    -      -       +      -
    153B  TRP*     4.1    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  PHE*     3.9    21.8    -      +       -      -
     23A  MET*     3.3     4.9    -      -       -      +
     24A  PHE*     3.1    54.6    +      +       +      +
     30A  GLU*     3.6     9.3    -      -       -      +
     31A  ILE*     1.3    83.5    -      -       +      +
     33A  HIS*     1.3    74.1    +      -       -      +
     41A  THR*     4.3     1.8    -      -       +      -
     42A  VAL      3.3    15.3    -      -       -      +
     43A  TRP*     3.7     1.8    -      -       -      +
     51A  PHE*     3.5    34.3    -      +       -      -
     52A  ALA*     3.6    27.4    -      -       +      -
     55A  GLU*     3.9    20.0    -      -       +      -
     56A  ALA*     3.5    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  GLU*     5.0     1.6    -      -       -      +
     22A  PHE      3.3     5.8    -      -       -      +
     23A  MET*     3.8    13.7    -      -       +      -
     30A  GLU*     2.4    31.5    +      -       -      +
     32A  PHE*     1.3    77.8    -      -       -      +
     34A  VAL*     1.3    76.1    +      -       -      +
     35A  ASP*     4.0     9.5    -      -       +      +
     40A  GLU      4.7     0.2    -      -       -      -
     41A  THR*     3.4     4.7    -      -       -      -
     42A  VAL*     2.9    72.6    +      -       +      +
    134A  GLU      6.1     1.1    -      -       -      -
    135A  THR*     6.2     0.2    -      -       -      -
    136A  VAL*     3.4    42.2    -      -       +      +
    100C  PHE*     5.4     3.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  GLU*     3.3     9.7    -      -       -      +
     22A  PHE*     2.7    39.5    +      -       +      +
     33A  HIS*     1.3    83.7    -      -       -      +
     35A  ASP*     1.3    72.7    +      -       -      +
     39A  LYS*     4.9     0.2    -      -       -      -
     40A  GLU      3.4     4.9    -      -       -      +
     41A  THR*     3.6    22.9    -      -       -      +
     56A  ALA*     3.9    10.8    -      -       +      -
     59A  ALA*     3.7    28.0    -      -       +      -
     60A  LEU*     4.0    16.2    -      -       +      -
     63A  ILE*     4.4     5.1    -      -       +      +
     95C  PRO*     3.9    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLY      3.8     3.0    -      -       -      +
     21A  GLU*     3.6    23.6    -      -       -      +
     33A  HIS*     4.0     8.4    -      -       +      +
     34A  VAL*     1.3    81.3    -      -       -      +
     36A  MET*     1.3    63.4    +      -       -      +
     37A  ALA*     3.2    27.0    -      -       -      +
     38A  LYS*     3.8    19.4    +      -       +      +
     39A  LYS*     3.1    27.4    +      -       -      +
     40A  GLU      3.6     6.1    +      -       -      +
     63A  ILE*     5.0     0.7    -      -       -      -
    136A  VAL*     4.2    15.7    -      -       -      +
    137A  PHE*     5.9     0.3    -      -       -      -
----------------------------------------------------------
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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