Contacts of the strand formed by residues 14 - 24 (chain A) in PDB entry 2FBW


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 VAL 14 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR      5.8     3.4    -      -       -      +
     12A  TYR*     3.7    14.6    -      -       +      +
     13A  PRO*     1.3    74.2    -      -       -      +
     15A  VAL*     1.3    66.2    +      -       -      +
     16A  ASP*     3.8    20.9    -      -       -      +
    192A  ILE*     6.0     0.2    -      -       +      -
    201A  ILE*     3.3    20.0    -      -       +      +
    203A  ARG*     4.0    26.0    -      -       +      +
    450A  VAL*     6.0     3.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  PRO*     4.9     3.8    -      -       +      +
     14A  VAL*     1.3    78.9    -      -       -      +
     16A  ASP*     1.3    63.0    +      -       -      +
     17A  HIS*     3.6    25.2    -      -       +      +
    200A  THR*     4.9    10.1    -      -       +      -
    201A  ILE      2.7    11.0    +      -       -      +
    202A  HIS*     3.1    31.5    -      -       +      +
    203A  ARG      2.8    30.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  VAL*     3.8     5.6    -      -       -      +
     15A  VAL*     1.3    79.8    -      -       -      +
     17A  HIS*     1.3    65.6    +      -       -      +
     18A  GLU*     5.8     1.1    -      -       +      -
    203A  ARG*     2.8    58.8    +      -       -      +
    205A  ARG*     4.9    16.0    +      -       -      +
    441A  ILE*     5.1     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  VAL*     3.6    23.2    -      -       +      +
     16A  ASP*     1.3    75.9    +      -       -      +
     18A  GLU*     1.3    64.3    +      -       -      +
     19A  PHE*     3.4    22.4    -      -       +      -
    173A  PHE*     3.7    28.2    -      +       -      -
    202A  HIS*     2.9    35.7    +      +       +      +
    203A  ARG      2.8    18.6    +      -       -      +
    204A  PHE*     3.7    20.4    -      +       +      -
    205A  ARG*     2.9    31.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ASP*     5.8     1.3    -      -       +      -
     17A  HIS*     1.3    75.8    -      -       -      +
     19A  PHE*     1.3    69.1    +      -       -      +
     43A  ASN*     3.9    10.0    +      -       -      -
    205A  ARG*     2.7    37.8    +      -       -      +
    438A  VAL*     3.9    24.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  HIS*     3.4    29.6    -      -       +      -
     18A  GLU*     1.3    78.9    -      -       -      +
     20A  ASP*     1.3    64.6    +      -       -      +
     21A  ALA      3.5    17.9    -      -       -      +
     22A  VAL*     5.4     1.3    -      -       +      -
     43A  ASN*     3.5    33.0    -      -       -      +
     44A  THR      4.4     0.2    -      -       -      -
     45A  ALA*     3.7    24.7    -      -       +      -
    171A  SER*     3.7    25.4    -      -       -      -
    173A  PHE*     3.7    24.0    -      +       -      -
    204A  PHE*     4.0    12.6    -      +       +      -
    205A  ARG      2.9    20.4    +      -       -      +
    206A  ALA*     3.3     8.3    -      -       +      -
    207A  LYS      4.1     0.9    +      -       -      -
    438A  VAL*     4.3     8.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     1.3    72.6    -      -       -      +
     21A  ALA*     1.3    59.9    +      -       -      +
     42A  PHE*     3.8    17.0    -      -       +      -
     43A  ASN*     2.8    44.6    +      -       -      +
    206A  ALA*     3.7     0.9    -      -       -      -
    207A  LYS*     3.3    27.3    +      -       -      +
    208A  ASN*     3.5     8.7    +      -       -      +
    428A  ILE*     6.1     0.2    -      -       -      +
    433A  LYS      4.8     0.6    -      -       -      +
    434A  PRO*     3.7    12.9    -      -       -      +
    435A  GLY*     2.9    35.3    +      -       -      -
    436A  GLU      4.3     6.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     3.4     6.9    -      -       -      +
     20A  ASP*     1.3    81.7    -      -       +      +
     22A  VAL*     1.3    61.5    +      -       -      +
     37A  LEU*     3.8    34.5    -      -       +      -
     42A  PHE*     5.1     3.8    -      -       +      -
     43A  ASN      3.3     1.8    +      -       -      -
     44A  THR*     3.4    11.2    -      -       +      +
     45A  ALA      3.0    23.3    +      -       -      -
    206A  ALA*     3.7     4.0    -      -       -      -
    208A  ASN*     3.2    18.6    -      -       +      +
    210A  VAL*     5.7     0.9    -      -       +      -
    428A  ILE*     5.3     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     5.5     1.3    -      -       +      -
     21A  ALA*     1.3    75.1    -      -       -      +
     23A  VAL*     1.3    68.7    +      -       -      +
     24A  VAL*     4.3    10.3    -      -       +      -
     45A  ALA*     3.3    13.2    -      -       +      +
     47A  VAL*     4.1    22.4    -      -       +      -
    190A  GLY*     4.5     5.4    -      -       -      -
    191A  VAL*     4.4    14.1    -      -       +      -
    204A  PHE*     4.4    15.0    -      -       +      +
    206A  ALA*     3.8    12.8    -      -       +      -
    208A  ASN      3.1     4.8    +      -       -      +
    209A  THR*     3.2    28.0    -      -       +      +
    210A  VAL*     2.9    24.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  VAL*     1.3    76.7    -      -       -      +
     24A  VAL*     1.3    64.4    +      -       -      +
     25A  GLY      3.6    13.4    +      -       -      +
     30A  GLY*     3.6    27.1    -      -       -      +
     33A  ALA*     4.4     4.5    -      -       +      -
     34A  ALA*     3.9    22.2    -      -       +      +
     37A  LEU*     3.9    27.6    -      -       +      -
     44A  THR*     4.1     2.9    -      -       +      -
     45A  ALA      2.7    15.0    +      -       -      +
     46A  CYS*     3.3     2.5    -      -       -      -
     47A  VAL*     2.8    28.2    +      -       -      +
    210A  VAL*     3.5    22.0    -      -       +      +
    212A  ALA*     4.6     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  VAL*     4.3     8.3    -      -       +      -
     23A  VAL*     1.3    73.2    -      -       -      +
     25A  GLY*     1.3    58.3    +      -       -      +
     47A  VAL*     3.5    13.2    -      -       +      +
    178A  ALA*     3.7    25.8    -      -       +      -
    191A  VAL*     3.9    33.7    -      -       +      -
    209A  THR*     4.7     0.9    -      -       +      -
    210A  VAL      2.8    15.8    +      -       -      +
    211A  ILE*     4.2    13.0    -      -       +      -
    212A  ALA*     2.7    34.1    +      -       -      +
    213A  THR*     3.6    21.9    +      -       +      -
    236A  MET*     4.4     3.8    -      -       +      -
----------------------------------------------------------
 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