Contacts of the strand formed by residues 327 - 331 (chain H) in PDB entry 1F9E


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 PHE 327 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262G  THR*     3.2    37.7    -      -       +      -
    263G  SER*     5.2     0.2    -      -       -      -
    265G  PHE*     3.6    22.0    -      -       +      -
    266G  THR*     4.1    12.1    -      -       +      -
    278G  LYS*     3.4    31.0    -      -       +      -
    280G  PHE*     3.9    22.0    -      +       -      -
    323H  ASP      4.7     0.2    -      -       -      -
    324H  GLU*     3.4    22.0    -      -       +      +
    325H  ALA      3.1    21.1    -      -       -      -
    326H  ASP*     1.3    74.6    -      -       -      +
    328H  LEU*     1.3    62.4    +      -       -      +
    329H  LEU*     4.2     2.0    -      -       +      +
    392H  PHE*     3.4     2.3    -      -       -      -
    393H  THR*     2.8    41.1    +      -       +      +
    394H  LEU*     3.3    10.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 328 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278G  LYS      3.0     7.1    +      -       -      +
    279G  VAL*     4.1    24.2    -      -       +      -
    280G  PHE*     2.8    29.1    +      -       -      +
    281G  PHE*     5.3     0.9    -      -       +      -
    327H  PHE*     1.3    77.5    -      -       -      +
    329H  LEU*     1.3    72.5    +      -       -      +
    330H  GLY      4.9     0.7    -      -       -      +
    366H  ILE*     3.3    48.5    -      -       +      -
    367H  LEU*     4.9     3.8    -      -       +      -
    370H  LEU*     4.0    16.6    -      -       +      -
    389H  PRO*     4.6     3.6    -      -       +      -
    390H  THR      3.6    12.3    -      -       -      +
    392H  PHE*     4.0     8.5    -      -       +      -
    394H  LEU*     3.8    16.6    -      -       +      -
    398H  LEU*     4.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 329 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258G  ILE*     4.1    20.9    -      -       +      -
    262G  THR*     4.9     9.2    -      -       +      -
    280G  PHE*     3.3    24.2    -      -       +      +
    282G  ILE*     4.1    11.2    -      -       +      -
    327H  PHE*     4.2     2.6    -      -       +      +
    328H  LEU*     1.3    75.3    -      -       -      +
    330H  GLY*     1.3    70.0    +      -       -      +
    331H  MET*     3.8    32.7    +      -       +      -
    388H  GLN      4.3     0.2    -      -       -      +
    389H  PRO*     3.3     3.6    -      -       -      +
    390H  THR*     2.9    45.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 330 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280G  PHE      2.7    14.8    +      -       -      -
    281G  PHE*     3.5    10.9    -      -       -      -
    282G  ILE      3.0    24.8    +      -       -      -
    328H  LEU*     4.0     3.4    +      -       -      +
    329H  LEU*     1.3    75.6    -      -       -      +
    331H  MET*     1.3    60.6    +      -       -      -
    349H  TYR*     3.4    23.0    +      -       -      -
    370H  LEU*     5.2     0.9    -      -       -      -
    389H  PRO*     4.4     9.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 331 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258G  ILE*     3.5    19.5    -      -       +      -
    282G  ILE*     3.8    25.4    -      -       +      +
    284G  ALA      6.0     0.2    -      -       -      +
    286G  GLN*     3.5    42.0    -      -       +      +
    329H  LEU*     3.9    25.8    -      -       +      -
    330H  GLY*     1.3    75.0    -      -       -      -
    332H  ALA*     1.3    61.2    +      -       -      +
    333H  THR*     3.3    14.1    -      -       +      +
    349H  TYR*     3.7     9.8    +      -       -      -
    387H  PRO*     3.7     1.9    -      -       -      +
    388H  GLN*     3.2    46.0    +      -       +      +
    389H  PRO*     4.7     0.5    -      -       -      +
    390H  THR*     5.6     1.1    -      -       -      +
----------------------------------------------------------
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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