Contacts of the strand formed by residues 296 - 301 (chain C) in PDB entry 1FBA


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 ALA 296 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  VAL*     3.8    42.2    -      -       +      +
    265C  THR      3.9     6.7    +      -       -      +
    267C  VAL*     3.0    30.0    +      -       -      +
    295C  TRP*     1.3    75.4    -      -       -      +
    297C  LEU*     1.3    60.8    +      -       -      +
    298C  THR*     3.9     4.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 297 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253C  VAL*     4.7     2.7    -      -       +      -
    256C  LEU*     3.8    22.4    -      -       +      -
    267C  VAL*     3.6    14.8    -      -       +      -
    269C  PHE*     3.8    25.4    -      -       +      -
    283C  LEU*     3.5     4.7    -      -       -      +
    286C  ILE*     3.9    16.4    -      -       +      +
    287C  ASN*     2.8    47.6    +      -       -      +
    293C  ARG*     3.7    41.5    -      -       +      +
    295C  TRP*     3.4    21.1    +      -       +      +
    296C  ALA*     1.3    70.8    -      -       -      +
    298C  THR*     1.3    61.8    +      -       -      +
    338C  ALA*     3.8     7.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 298 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  ILE      5.2     0.4    -      -       -      +
     23C  VAL*     4.0    19.3    -      -       +      -
     27C  LYS      2.6    28.5    +      -       -      +
     28C  GLY*     3.5     2.2    -      -       -      -
    267C  VAL      2.9    11.2    +      -       -      +
    268C  THR*     3.8    25.1    -      -       +      -
    269C  PHE*     3.0    32.1    +      -       -      +
    283C  LEU*     3.9     8.7    -      -       -      +
    296C  ALA*     5.2     2.5    -      -       +      -
    297C  LEU*     1.3    75.2    -      -       -      +
    299C  PHE*     1.3    80.5    +      -       -      +
    338C  ALA*     3.5    12.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 299 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  LYS      4.1     0.4    -      -       -      -
     28C  GLY*     3.4    36.9    -      -       -      -
     29C  ILE*     2.8    41.2    +      -       -      +
     72C  ASN      3.5    10.5    -      -       -      -
     73C  ILE*     3.9    14.8    -      -       +      -
    268C  THR*     3.9     8.2    -      -       -      -
    269C  PHE      3.8     4.5    -      -       -      -
    283C  LEU*     3.9     7.0    -      -       +      -
    298C  THR*     1.3    92.1    +      -       -      +
    300C  SER*     1.3    59.0    +      -       -      +
    301C  TYR*     3.6    32.5    -      +       +      -
    305C  LEU*     3.9    13.2    -      -       +      -
    331C  ALA      4.4     3.4    -      -       -      -
    334C  ASN*     3.4    49.4    -      -       +      -
    335C  GLY*     3.8     6.7    -      -       -      -
    338C  ALA*     4.5     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 300 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  ILE*     3.4    30.3    -      -       -      +
     31C  ALA*     4.4     1.6    -      -       -      +
     77C  ILE*     3.8     5.2    -      -       -      +
    185C  ILE*     5.2     0.3    -      -       -      +
    229C  LYS*     3.0    44.9    +      -       -      +
    268C  THR*     3.7    23.8    -      -       -      -
    269C  PHE      2.9    14.0    +      -       -      +
    270C  LEU*     4.0     3.5    -      -       -      -
    271C  SER      4.9     0.2    +      -       -      -
    299C  PHE*     1.3    74.4    -      -       -      +
    301C  TYR*     1.3    62.6    +      -       -      +
    302C  GLY      4.1     0.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 301 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  ILE      3.2     8.5    +      -       -      +
     30C  LEU*     3.8     4.0    -      -       -      +
     31C  ALA*     2.9    23.9    +      -       -      +
    232C  MET*     3.3    17.3    -      -       -      +
    269C  PHE*     3.0    30.3    -      -       -      +
    270C  LEU      4.0     1.3    -      -       -      -
    271C  SER*     3.9    21.1    -      -       -      +
    279C  ALA*     2.9    37.0    +      -       +      +
    283C  LEU*     3.9     7.7    -      -       +      +
    299C  PHE*     3.6    20.3    -      +       +      +
    300C  SER*     1.3    76.7    -      -       -      +
    302C  GLY*     1.3    62.1    +      -       -      +
    304C  ALA*     3.8    22.7    -      -       +      -
    305C  LEU*     3.9    21.4    -      -       +      +
    334C  ASN*     3.5    36.3    -      -       -      -
----------------------------------------------------------
 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