Contacts of the strand formed by residues 324 - 329 (chain A) in PDB entry 5FN2


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 ASN 324 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  MET*     3.6     8.7    -      -       -      +
    260A  LEU*     3.4     3.3    -      -       -      +
    261A  LYS*     3.0    56.3    +      -       +      +
    263A  ILE*     3.2    32.3    -      -       -      +
    273A  ASP*     5.9     1.6    -      -       -      +
    274A  ARG      3.4     5.7    +      -       -      -
    275A  VAL*     2.9    23.1    -      -       +      +
    276A  VAL*     2.6    31.2    +      -       -      -
    322A  PRO      4.1     1.0    +      -       -      +
    323A  ARG*     1.3    74.3    -      -       -      +
    325A  VAL*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  MET*     3.1    11.2    -      -       -      +
    260A  LEU*     2.8    58.0    +      -       +      -
    276A  VAL*     3.2    23.1    -      -       +      +
    278A  ALA*     4.8     0.4    -      -       +      -
    312A  LEU*     4.2     9.9    -      -       +      -
    324A  ASN*     1.3    83.6    +      -       -      +
    326A  MET*     1.3    64.8    -      -       -      +
    327A  PHE*     3.9    21.5    -      -       +      -
    498A  LEU*     3.9    27.4    -      -       +      +
    502A  ALA*     4.3    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  TRP*     4.2    15.3    -      -       -      +
    258A  SER      3.6    16.6    -      -       -      +
    259A  MET*     3.7    14.4    -      -       +      -
    275A  VAL*     5.1     7.6    -      -       +      -
    276A  VAL      2.8    17.2    +      -       -      +
    277A  VAL*     3.8    23.1    -      -       +      -
    278A  ALA*     2.8    29.5    +      -       -      +
    325A  VAL*     1.3    73.2    -      -       -      +
    327A  PHE*     1.3    60.8    +      -       -      +
    328A  VAL*     3.4    32.7    +      -       +      -
    330A  PHE*     4.9     1.3    -      -       +      -
    343A  MET*     3.5    29.8    -      -       +      -
    347A  MET*     5.5     4.3    -      -       -      -
    352A  PHE*     5.1     2.0    -      -       +      -
    354A  VAL*     5.6     9.2    -      -       +      -
    430A  PHE*     5.7     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  TRP      3.6     1.0    -      -       -      -
    258A  SER*     2.8    44.9    +      -       -      -
    259A  MET      5.0     8.7    -      -       -      -
    260A  LEU*     5.2     2.7    -      -       +      -
    278A  ALA*     3.6    13.2    -      -       +      -
    305A  GLN*     3.7    18.8    -      -       +      +
    308A  ALA*     4.1     1.8    -      -       +      -
    309A  ALA*     3.2    49.8    -      -       +      -
    312A  LEU*     3.5    26.5    -      -       +      -
    313A  GLN*     5.3     2.9    -      -       -      -
    325A  VAL*     3.9    17.7    -      -       +      -
    326A  MET*     1.3    69.1    -      -       -      +
    328A  VAL*     1.3    59.5    -      -       -      +
    329A  PHE*     3.8    12.6    -      -       +      -
    498A  LEU*     3.4    33.2    -      -       +      -
    571A  LEU*     5.0     0.9    -      -       +      -
    575A  THR*     5.5     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  ASN*     4.8     3.4    -      -       +      -
    256A  VAL      3.5    12.1    -      -       -      +
    257A  TRP*     4.4     3.6    -      -       +      +
    277A  VAL*     4.0     8.7    -      -       +      -
    278A  ALA      2.8    20.1    +      -       -      +
    279A  ALA*     4.0     3.6    -      -       -      -
    280A  THR*     3.2    14.8    +      -       -      -
    305A  GLN*     2.8    17.2    +      -       -      -
    326A  MET*     3.4    33.7    -      -       +      +
    327A  PHE*     1.3    72.1    -      -       -      +
    329A  PHE*     1.3    68.7    +      -       -      +
    330A  PHE*     3.3    50.3    -      -       +      -
    343A  MET*     4.6     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  ASN*     3.4     3.5    -      -       -      +
    256A  VAL*     2.8    47.5    +      -       +      +
    280A  THR*     3.7    10.3    -      -       -      -
    282A  LEU*     3.5    40.2    -      -       +      +
    302A  PHE*     3.6    25.4    -      +       +      -
    305A  GLN*     3.5    19.7    -      -       +      -
    306A  LEU*     3.3    36.3    -      -       +      -
    327A  PHE*     3.8    15.5    -      +       +      -
    328A  VAL*     1.3    80.1    -      -       -      +
    330A  PHE*     1.3    63.5    +      -       -      +
    331A  GLN      3.8     0.5    +      -       -      -
    567A  VAL*     4.4     3.1    -      -       +      -
    571A  LEU*     3.4    25.4    -      -       +      -
----------------------------------------------------------
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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