Contacts of the strand formed by residues 321 - 326 (chain E) in PDB entry 1FZB


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 321 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313E  GLU*     3.6    35.2    +      -       +      +
    314E  MET      3.0    21.3    -      -       -      +
    315E  GLU*     3.7    18.3    -      -       +      +
    319E  GLY      3.6     2.8    +      -       -      +
    320E  ASP*     1.3    76.2    -      -       -      +
    322E  VAL*     1.3    72.6    +      -       -      +
    348E  THR*     5.0     0.2    +      -       -      -
    440E  TRP*     4.5     0.2    -      -       -      -
    449E  LYS*     4.3    28.3    -      -       -      +
    451E  SER*     5.0     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 322 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313E  GLU*     3.6     2.8    -      -       -      +
    314E  MET*     3.1    48.5    +      -       +      +
    321E  LYS*     1.3    83.8    -      -       -      +
    323E  LYS*     1.3    67.1    +      -       -      +
    348E  THR*     3.3    26.7    -      -       -      +
    349E  ALA*     3.6    18.8    -      -       +      +
    440E  TRP*     3.7    38.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 323 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245E  GLU*     3.5    33.7    +      -       -      +
    311E  LEU*     4.1    18.6    -      -       +      -
    312E  ILE      3.4    10.1    -      -       -      +
    313E  GLU*     4.2     8.5    -      -       +      +
    314E  MET*     5.6     0.2    -      -       -      -
    322E  VAL*     1.3    80.2    -      -       -      +
    324E  ALA*     1.3    61.1    +      -       -      +
    325E  HIS*     4.3     4.0    -      -       +      -
    346E  ARG*     5.6     7.8    -      -       -      +
    347E  GLY*     4.5     7.4    -      -       -      -
    348E  THR*     3.0    25.4    +      -       -      +
    349E  ALA*     2.8    27.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 324 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310E  LEU      4.2     0.2    -      -       -      +
    311E  LEU*     3.7     2.0    -      -       -      +
    312E  ILE*     2.8    43.5    +      -       +      +
    314E  MET*     5.1     0.2    -      -       +      -
    323E  LYS*     1.3    75.3    -      -       -      +
    325E  HIS*     1.3    59.2    +      -       -      +
    326E  TYR*     4.1    11.2    -      -       +      -
    345E  TYR*     3.7    23.1    -      -       +      -
    346E  ARG      4.2     0.7    -      -       -      -
    349E  ALA*     3.9    12.1    -      -       +      -
    437E  TRP*     4.0    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 325 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245E  GLU*     5.5     6.2    +      -       +      +
    249E  TRP*     4.2    20.3    -      +       -      -
    309E  GLU*     2.9    29.4    +      -       -      +
    310E  LEU      3.5     7.3    +      -       -      -
    311E  LEU*     4.5    13.6    -      -       +      +
    323E  LYS*     5.8     4.9    -      -       +      -
    324E  ALA*     1.3    73.6    -      -       -      +
    326E  TYR*     1.3    95.8    +      -       -      +
    327E  GLY*     3.8     3.2    +      -       -      -
    345E  TYR*     3.0     5.5    -      -       -      -
    346E  ARG*     2.7    82.0    +      -       +      +
    455E  ARG*     5.2     3.1    -      -       -      -
    457E  PHE*     5.8     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 326 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309E  GLU*     3.4     3.5    -      -       -      +
    310E  LEU*     2.8    42.6    +      -       +      +
    312E  ILE*     4.4     8.5    -      -       +      -
    324E  ALA*     4.1    16.6    -      -       +      -
    325E  HIS*     1.3    79.2    -      -       -      +
    327E  GLY*     1.3    66.7    +      -       -      +
    328E  GLY      3.2    11.4    +      -       -      +
    342E  VAL*     3.7    22.2    -      -       +      -
    343E  ASN      3.5    15.9    -      -       -      +
    344E  LYS      3.4     4.3    -      -       -      -
    345E  TYR*     3.3    37.9    -      +       +      -
    350E  GLY      4.6     1.0    +      -       -      -
    351E  ASN*     3.0    33.6    +      -       -      -
    352E  ALA      4.1     0.5    +      -       -      -
    353E  LEU*     3.5    30.0    +      -       +      +
    354E  MET*     3.7    14.1    -      -       +      -
    437E  TRP*     4.6     2.0    -      +       -      -
----------------------------------------------------------
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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