Contacts of the strand formed by residues 44 - 48 (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 THR 44 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     4.0     3.4    -      -       -      -
     21A  ALA*     3.4    10.4    -      -       -      +
     23A  VAL*     4.1     8.3    -      -       +      -
     34A  ALA*     3.8    16.4    -      -       -      +
     37A  LEU*     3.3    35.4    -      -       +      +
     38A  SER*     3.7    15.1    +      -       -      -
     42A  PHE*     2.8    19.8    +      -       -      +
     43A  ASN*     1.3    76.4    +      -       -      +
     45A  ALA*     1.3    71.8    +      -       -      +
    169A  ASP*     4.8     1.8    +      -       -      +
    170A  THR*     3.5     7.4    -      -       +      +
    171A  SER*     3.0    27.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     3.7    34.9    -      -       +      -
     21A  ALA      3.0     9.8    +      -       -      +
     22A  VAL*     3.3     7.7    -      -       +      -
     23A  VAL*     2.7    35.5    +      -       -      +
     44A  THR*     1.3    77.3    -      -       -      +
     46A  CYS*     1.3    54.8    +      -       -      +
     47A  VAL*     4.1     1.6    -      -       +      -
    171A  SER      3.3     4.9    -      -       -      -
    173A  PHE*     3.9    15.7    -      -       +      -
    204A  PHE*     4.4     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  VAL*     3.3     4.9    -      -       -      +
     25A  GLY      3.3    27.6    -      -       -      -
     26A  ALA*     4.0    13.2    -      -       -      -
     30A  GLY      4.9     0.4    -      -       -      -
     31A  LEU*     5.0     1.1    -      -       -      -
     34A  ALA*     4.0    20.6    -      -       +      -
     45A  ALA*     1.3    72.7    -      -       -      +
     47A  VAL*     1.3    64.1    +      -       -      +
     48A  THR*     4.0     2.1    +      -       -      +
    170A  THR*     4.2     2.2    -      -       +      +
    171A  SER      2.9     8.9    +      -       -      -
    172A  TYR*     3.4    39.3    -      -       +      -
    173A  PHE*     2.9    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  VAL*     4.1    18.2    -      -       +      -
     23A  VAL      2.8    11.4    +      -       -      +
     24A  VAL*     3.5    12.0    -      -       +      +
     25A  GLY      3.0    23.0    +      -       -      -
     45A  ALA*     4.8     0.7    -      -       +      -
     46A  CYS*     1.3    74.1    -      -       -      +
     48A  THR*     1.3    60.4    +      -       -      +
    173A  PHE*     3.7     8.1    -      -       +      -
    176A  TYR*     3.6    32.8    -      -       +      +
    178A  ALA*     5.0    10.3    -      -       +      +
    191A  VAL*     5.1     1.8    -      -       +      -
    193A  ALA*     4.4    14.8    -      -       +      -
    204A  PHE*     3.8    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  GLY*     4.7     2.4    -      -       -      +
     26A  ALA*     3.5    38.1    +      -       +      +
     46A  CYS*     4.5     7.4    -      -       -      +
     47A  VAL*     1.3    75.9    -      -       -      +
     49A  LYS*     1.3    61.2    +      -       -      +
     50A  LEU*     2.7    31.4    +      -       -      +
     52A  PRO*     4.6     3.9    -      -       +      +
     55A  SER*     5.1     2.3    +      -       -      -
    172A  TYR*     5.1     1.6    -      -       +      -
    173A  PHE      3.2    11.0    +      -       -      +
    174A  VAL*     4.1    16.2    -      -       +      -
    175A  GLU      2.7    26.5    +      -       -      -
    176A  TYR      3.0     8.4    +      -       -      -
----------------------------------------------------------
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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