Contacts of the strand formed by residues 220 - 223 (chain C) in PDB entry 1F4J


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 220 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143C  TRP*     6.1     1.1    -      -       -      -
    145C  LEU*     4.4    13.7    -      -       +      -
    216C  GLY*     3.9    15.9    -      -       -      -
    218C  HIS*     3.3    38.8    -      +       +      -
    219C  THR*     1.3    73.8    -      -       -      +
    221C  LYS*     1.3    64.2    +      -       -      +
    231C  TYR*     3.2    10.1    -      -       -      -
    232C  CYS*     2.8    35.7    +      -       -      -
    234C  PHE*     3.7    39.3    -      +       +      -
    336C  PRO*     5.3     5.6    -      -       +      -
    339C  MET*     4.1    19.5    -      -       +      -
    343C  ILE*     5.0     3.6    -      -       +      -
    344C  GLU      3.4    13.0    -      -       -      +
    346C  SER*     4.3     3.1    -      -       -      +
    351C  LEU*     3.8    29.8    -      -       +      -
    354C  ARG*     5.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 221 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  GLN*     5.8     4.0    -      -       -      +
    220C  PHE*     1.3    74.7    -      -       -      +
    222C  LEU*     1.3    72.8    +      -       -      +
    223C  VAL*     4.4     1.3    -      -       +      -
    229C  ALA*     3.8    17.7    -      -       +      -
    230C  VAL      3.2    11.7    -      -       -      +
    231C  TYR*     4.1    14.3    -      -       +      -
    286C  PHE*     4.1    13.9    -      -       +      -
    342C  GLY      3.6     0.2    -      -       -      +
    343C  ILE*     3.5     4.9    -      -       -      +
    344C  GLU*     2.7    70.3    +      -       -      +
    345C  ALA      4.0    14.9    +      -       -      +
    421C  HIS*     3.3    35.1    +      -       -      +
    423C  ILE*     3.5    15.2    -      -       -      +
    425C  TYR*     5.0     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 222 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91C  ILE*     5.5     3.1    -      -       +      -
     94C  TYR*     3.4    31.0    -      -       +      +
     95C  SER*     3.8    13.7    -      -       -      +
    100C  PHE*     4.9     4.0    -      -       +      -
    221C  LYS*     1.3    76.4    -      -       -      +
    223C  VAL*     1.3    61.2    +      -       -      +
    229C  ALA*     3.1     5.4    -      -       -      +
    230C  VAL*     2.7    42.8    +      -       +      +
    232C  CYS*     3.7    37.7    -      -       +      -
    234C  PHE*     4.3    11.2    -      -       +      -
    281C  ILE*     4.2    19.7    -      -       +      -
    283C  VAL*     4.9     0.9    -      -       +      -
    342C  GLY      3.2    11.0    -      -       -      +
    343C  ILE*     4.3    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 223 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94C  TYR      3.2     5.2    +      -       -      -
     95C  SER*     3.0     1.2    -      -       -      -
     96C  LYS*     2.7    45.4    +      -       -      +
    221C  LYS*     4.4     4.7    -      -       +      -
    222C  LEU*     1.3    80.1    -      -       -      +
    224C  ASN*     1.3    65.3    +      -       -      +
    227C  GLY*     4.2    14.4    -      -       -      +
    228C  GLU      3.3     8.3    -      -       -      +
    229C  ALA*     3.9     8.3    -      -       +      -
    342C  GLY*     2.8    20.1    +      -       -      +
    344C  GLU*     3.9    19.5    -      -       +      +
    421C  HIS*     3.8    28.5    -      -       +      +
----------------------------------------------------------
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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