Contacts of the strand formed by residues 173 - 177 (chain A) in PDB entry 3F9C


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 173 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  LEU*     3.6    29.8    -      -       +      -
     84A  TYR      3.4     6.7    -      -       -      +
     85A  TYR*     4.0    15.5    -      -       +      -
     86A  PRO*     4.2     0.7    -      -       +      -
    138A  LEU*     4.2    11.4    -      -       +      -
    144A  TYR*     3.6    33.4    -      -       +      +
    145A  PRO      3.2     8.6    +      -       -      +
    146A  LEU*     3.4    19.8    -      -       +      +
    147A  VAL      2.9    25.1    +      -       -      -
    172A  PHE*     1.3    74.9    -      -       -      +
    174A  VAL*     1.3    64.6    +      -       -      +
    236A  ILE*     5.8     1.3    -      -       +      -
    258A  LEU*     4.3     8.3    -      -       +      -
    261A  SER*     4.0    10.8    -      -       -      +
    262A  ILE*     3.9    24.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ARG      3.5     1.4    -      -       -      +
     83A  LEU*     3.1    11.6    -      -       -      +
     84A  TYR*     2.8    59.4    +      -       +      +
    147A  VAL*     3.5    16.4    -      -       +      +
    149A  PHE*     4.2    24.2    -      -       +      -
    164A  GLY*     3.8    17.5    -      -       -      +
    167A  LEU*     3.7    36.8    -      -       +      -
    168A  ALA      4.4     1.8    -      -       -      +
    172A  PHE*     4.3     6.3    -      -       +      -
    173A  ILE*     1.3    77.9    -      -       -      +
    175A  ALA*     1.3    63.1    +      -       -      +
    176A  ALA*     4.4     0.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  LEU*     3.9    15.0    -      -       +      -
     82A  ARG      3.7     4.0    -      -       -      -
     83A  LEU*     4.1     8.5    -      -       +      -
    146A  LEU*     4.5     4.0    -      -       +      +
    147A  VAL      2.9    12.1    +      -       -      +
    148A  VAL*     3.5    14.2    -      -       +      +
    149A  PHE      2.8    24.0    +      -       -      -
    173A  ILE      4.2     0.4    -      -       -      -
    174A  VAL*     1.3    72.4    -      -       -      +
    176A  ALA*     1.3    62.8    +      -       -      +
    177A  VAL*     3.5     3.6    +      -       +      +
    232A  ALA*     5.4     0.2    -      -       +      -
    236A  ILE*     3.8    29.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  LEU*     3.1     2.3    -      -       -      -
     82A  ARG*     2.8    42.8    +      -       +      +
     84A  TYR*     4.1    15.5    -      -       +      -
    149A  PHE*     3.6    25.4    -      -       +      +
    157A  ARG*     3.4    27.7    -      -       +      +
    160A  TYR*     6.1     2.5    -      -       +      -
    174A  VAL*     3.8     2.3    -      -       +      -
    175A  ALA*     1.3    69.4    -      -       -      +
    177A  VAL*     1.3    64.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  THR*     5.6     1.3    -      -       +      -
     80A  PHE      3.5    10.5    -      -       -      +
     81A  LEU*     4.2     4.9    -      -       +      -
    148A  VAL*     4.0    21.8    -      -       +      -
    149A  PHE      3.0    15.5    +      -       -      +
    151A  HIS*     3.1    20.6    +      -       -      +
    157A  ARG*     3.7     6.4    -      -       -      +
    175A  ALA*     4.1     3.4    -      -       +      +
    176A  ALA*     1.3    74.7    -      -       -      +
    178A  GLU*     1.3    73.6    +      -       -      +
    179A  HIS*     3.9    24.2    -      -       +      +
    228A  GLU*     4.3    16.4    -      -       +      +
    229A  CYS*     4.7     2.2    -      -       -      -
    232A  ALA*     3.6    29.2    -      -       +      -
----------------------------------------------------------
 Back to top of page


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