Contacts of the strand formed by residues 239 - 245 (chain A) in PDB entry 2FYU


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 SER 239 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  THR*     2.8    31.3    +      -       -      +
    159A  GLN*     3.3    20.6    -      -       -      -
    237A  THR      2.9    18.4    +      -       -      -
    238A  GLY*     1.3    74.3    -      -       -      -
    240A  GLN*     1.3    61.7    +      -       -      +
    420A  PRO      3.3     4.6    +      -       -      -
    421A  ALA*     3.4     2.6    -      -       -      +
    422A  VAL      2.9    23.9    +      -       -      -
    434A  TYR*     3.4    12.2    +      -       -      -
     17G  SER      3.3    14.4    -      -       -      -
     18G  LEU*     4.2     2.7    -      -       -      -
     19G  SER      4.2     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  THR*     4.0     6.1    +      -       -      -
    239A  SER*     1.3    74.2    -      -       -      +
    241A  ILE*     1.3    62.8    +      -       -      +
    242A  CYS*     3.3    30.4    -      -       -      -
    422A  VAL*     3.3    22.6    -      -       +      +
    431A  LEU*     4.4     2.4    -      -       -      +
    432A  PRO      3.9    15.2    +      -       -      -
    433A  ASP*     4.9     1.6    -      -       -      +
    434A  TYR*     3.3    35.7    -      -       +      +
    437A  ILE*     3.4    20.4    -      -       -      +
     15G  THR      4.3     1.1    -      -       -      -
     16G  TYR*     3.5     3.5    -      -       -      +
     17G  SER*     2.9    47.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  TYR*     3.6    59.7    -      -       +      +
    155A  ALA*     5.5     6.1    -      -       +      -
    156A  THR*     3.7    11.9    -      -       +      +
    240A  GLN*     1.3    73.8    -      -       -      +
    242A  CYS*     1.3    65.9    +      -       -      +
    243A  HIS      4.0     0.9    -      -       -      +
    422A  VAL      3.0    12.7    +      -       -      +
    423A  ALA*     3.5    13.3    -      -       +      -
    424A  GLY      2.9    26.5    +      -       -      +
     14G  ILE*     3.9    17.9    -      -       +      -
     15G  THR      3.4     3.1    -      -       -      -
     16G  TYR*     3.6    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  GLN*     3.3    39.7    -      -       -      -
    241A  ILE*     1.3    71.9    -      -       -      +
    243A  HIS*     1.3    61.0    +      -       -      +
    244A  ARG*     3.2     3.9    +      -       +      +
    424A  GLY      3.7     3.6    -      -       -      -
    428A  ILE*     3.7    10.3    -      -       +      -
    431A  LEU*     3.7    20.9    -      -       -      -
     13G  VAL      3.2     7.8    -      -       -      +
     14G  ILE*     4.3     1.6    -      -       -      -
     15G  THR*     2.8    46.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  TYR*     2.6    46.5    +      -       +      -
    241A  ILE*     4.0     1.4    -      -       +      +
    242A  CYS*     1.3    68.6    -      -       -      +
    244A  ARG*     1.3    75.6    +      -       -      +
    245A  GLU*     3.4     6.5    +      -       +      +
    424A  GLY      2.9    10.1    +      -       -      +
    425A  PHE*     3.3    31.6    -      +       +      -
    426A  GLY      3.0    25.1    +      -       -      -
    428A  ILE*     3.8     2.5    -      -       -      +
    238D  ARG*     5.3     8.1    +      -       +      -
     12G  HIS*     4.5    14.9    +      -       -      +
     13G  VAL      3.9     3.4    -      -       -      -
     14G  ILE*     3.6    31.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  CYS*     3.2     4.4    +      -       +      +
    243A  HIS*     1.3    72.5    -      -       -      +
    245A  GLU*     1.3    59.4    +      -       -      +
    246A  ASP*     2.8    46.4    +      -       -      -
    426A  GLY      3.6     8.7    -      -       -      -
    428A  ILE*     3.9    16.3    -      -       +      +
    429A  GLU*     3.4    46.3    +      -       -      +
    214C  ASP      5.1     3.0    +      -       -      -
    215C  VAL      4.6     8.5    +      -       -      -
      8G  THR      3.4    15.6    +      -       -      -
     10G  VAL*     3.4    45.2    -      -       +      +
     12G  HIS*     3.0    24.5    +      -       -      -
     13G  VAL*     3.1    21.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  HIS*     3.4     6.9    +      -       +      +
    244A  ARG*     1.3    73.2    -      -       -      +
    246A  ASP*     1.3    62.2    +      -       -      +
    247A  GLY*     2.9    15.8    +      -       -      -
    248A  LEU*     3.3    43.5    +      -       +      +
    425A  PHE*     4.2    14.6    -      -       +      -
    426A  GLY*     2.8    29.9    +      -       -      -
    427A  PRO      3.4     1.0    -      -       -      -
     10G  VAL      4.1     1.3    -      -       -      -
     11G  ARG*     2.7    48.8    +      -       -      +
     12G  HIS*     3.8    21.3    -      -       -      +
----------------------------------------------------------
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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