Contacts of the strand formed by residues 278 - 283 (chain E) 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 LYS 278 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230E  PHE*     3.5    10.5    -      -       +      -
    265E  PHE*     3.0    36.6    -      -       +      +
    266E  THR      5.1     3.8    -      -       -      -
    267E  GLY*     5.5     0.6    -      -       -      +
    273E  LEU*     3.2    40.7    +      -       +      -
    274E  ALA*     4.4     2.2    -      -       -      +
    275E  GLY      4.1     4.4    -      -       -      +
    276E  LYS      2.7    30.3    +      -       -      +
    277E  PRO*     1.3    73.6    -      -       -      +
    279E  VAL*     1.3    60.4    +      -       -      +
    280E  PHE*     4.0     8.9    -      -       +      -
    323F  ASP      5.6     0.9    -      -       -      -
    325F  ALA      3.7    10.0    +      -       -      -
    326F  ASP*     3.0    17.2    +      -       -      +
    327F  PHE*     3.5    35.8    -      -       +      -
    328F  LEU*     3.1    22.6    +      -       -      +
    394F  LEU*     5.2     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 279 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229E  CYS*     4.4     8.1    -      -       -      -
    230E  PHE      2.9    15.5    +      -       -      +
    231E  ILE*     3.3    14.3    -      -       +      +
    232E  CYS      2.9    25.5    +      -       -      -
    277E  PRO*     4.7     0.4    -      -       +      -
    278E  LYS*     1.3    75.1    -      -       -      +
    280E  PHE*     1.3    69.2    +      -       -      +
    281E  PHE*     3.5    40.8    -      -       +      -
    328F  LEU*     3.4    22.2    -      -       +      +
    398F  LEU*     3.7    29.8    -      -       +      -
    400F  PHE*     4.6     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 280 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215E  LEU*     5.2     1.1    -      -       +      -
    230E  PHE*     4.4     8.5    -      +       -      -
    232E  CYS*     3.2    32.1    -      -       +      +
    234E  ILE*     5.4     4.5    -      -       +      -
    261E  LEU*     4.2    11.0    -      -       +      -
    262E  THR*     3.7    37.2    -      -       +      -
    265E  PHE*     3.6    31.2    -      +       -      -
    278E  LYS*     4.0    15.7    -      -       +      -
    279E  VAL*     1.3    80.6    -      -       -      +
    281E  PHE*     1.3    58.3    +      -       -      +
    282E  ILE*     4.0     7.9    -      -       +      -
    327F  PHE*     3.9    24.5    -      +       -      -
    328F  LEU      2.7    12.5    +      -       -      +
    329F  LEU*     3.3    15.7    -      -       +      +
    330F  GLY*     2.7    32.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 281 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193E  PHE*     3.7    25.4    -      +       -      -
    231E  ILE*     4.2     5.4    -      -       +      -
    232E  CYS      3.0     6.7    +      -       -      +
    233E  CYS*     3.3    27.1    -      -       +      +
    234E  ILE      2.9    26.3    +      -       -      +
    235E  LEU*     5.4     0.9    -      -       -      +
    279E  VAL*     3.5    28.9    -      -       +      -
    280E  PHE*     1.3    76.7    -      -       -      +
    282E  ILE*     1.3    62.2    +      -       -      +
    283E  GLN*     4.0     0.6    +      -       -      -
    328F  LEU*     5.4     0.7    -      -       +      -
    330F  GLY*     3.5     6.5    -      -       -      +
    349F  TYR*     3.8    19.5    -      -       +      -
    350F  ILE*     4.9     6.7    -      -       +      -
    353F  LEU*     3.4    44.6    -      -       +      -
    357F  LEU*     5.2     1.1    -      -       +      -
    366F  ILE*     4.4    16.4    -      -       +      -
    370F  LEU*     4.4    13.0    -      -       +      -
    400F  PHE*     5.8     2.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 282 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234E  ILE*     3.6    23.3    -      -       +      +
    243E  ILE*     3.4    29.4    -      -       +      -
    258E  ILE*     3.3    49.6    -      -       +      -
    261E  LEU*     5.2     2.5    -      -       +      -
    262E  THR*     5.7     0.9    -      -       +      -
    280E  PHE*     3.9     8.0    +      -       +      -
    281E  PHE*     1.3    78.8    -      -       -      +
    283E  GLN*     1.3    65.2    +      -       -      +
    284E  ALA*     3.9     3.8    +      -       +      +
    286E  GLN*     5.4     0.7    -      -       -      +
    329F  LEU*     4.2    13.0    -      -       +      -
    330F  GLY      3.0     8.6    +      -       -      +
    331F  MET*     3.8    14.2    -      -       +      +
    332F  ALA*     3.2    25.8    +      -       -      +
    349F  TYR*     4.3     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 283 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179E  ARG*     4.0     7.1    +      -       -      +
    185E  ASP*     4.3     1.8    -      -       -      +
    234E  ILE      2.8    13.1    +      -       -      +
    235E  LEU*     4.0     4.9    -      -       +      -
    236E  SER      3.0    24.9    +      -       -      +
    281E  PHE      4.0     1.0    +      -       -      -
    282E  ILE*     1.3    70.9    -      -       -      +
    284E  ALA*     1.3    62.1    +      -       -      +
    332F  ALA*     3.3     7.9    -      -       +      +
    339F  SER*     3.2    22.9    +      -       -      -
    340F  TYR      4.5     1.6    +      -       -      +
    347F  THR*     3.3    35.5    -      -       +      +
    349F  TYR*     3.2    28.5    +      -       +      +
    350F  ILE*     3.7    24.0    -      -       +      -
    385F  GLN*     4.7     0.5    +      -       -      -
   4304S  ASA      2.9    26.7    +      -       -      -
----------------------------------------------------------
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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