Contacts of the strand formed by residues 218 - 223 (chain C) in PDB entry 1F1H


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 GLN 218 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131C  GLU*     4.8     3.6    -      -       +      -
    132C  PHE      3.2    16.8    -      -       -      +
    133C  PHE*     3.5    27.6    -      -       +      -
    211C  HIS*     2.9    12.2    +      -       -      -
    212C  GLU*     2.8    46.4    +      -       +      +
    213C  VAL      3.7     0.2    -      -       -      +
    214C  ALA*     3.4    27.3    +      -       +      +
    216C  ALA      3.8     0.2    -      -       -      -
    217C  GLY*     1.3    75.9    -      -       -      +
    219C  ASN*     1.3    62.5    +      -       -      +
    264C  ASN*     3.3    26.3    +      -       -      +
    265C  GLY      2.7    24.7    +      -       -      +
    266C  SER*     3.0    16.2    +      -       -      +
    474C   TL      4.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 219 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131C  GLU*     3.8     3.5    -      -       -      +
    132C  PHE*     2.8    53.3    +      -       +      +
    134C  LEU*     3.9    14.1    -      -       -      +
    188C  ALA*     3.8    11.2    -      -       -      +
    192C  ARG*     2.9    44.2    -      -       +      +
    210C  HIS      3.8     3.8    -      -       -      -
    211C  HIS*     3.5    16.7    +      -       -      +
    212C  GLU*     3.9     4.6    -      -       -      +
    217C  GLY*     2.9    25.8    -      -       -      +
    218C  GLN*     1.3    74.4    +      -       -      +
    220C  GLU*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 220 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129C  GLU*     3.6    16.7    -      -       -      +
    130C  PRO      3.7    15.5    -      -       -      +
    131C  GLU*     3.1     9.9    -      -       +      +
    132C  PHE*     4.0     5.4    -      -       -      -
    192C  ARG*     4.2     1.3    -      -       -      -
    209C  HIS*     3.4     4.7    -      -       -      +
    210C  HIS*     2.9    47.4    +      -       +      +
    212C  GLU*     3.0     8.0    -      -       +      +
    219C  ASN*     1.3    77.8    -      -       -      +
    221C  VAL*     1.3    71.7    +      -       -      +
    222C  ALA*     4.1     5.7    -      -       -      +
    469C   MN      2.2    34.2    +      -       -      -
   1473C  ADP      2.9    33.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 221 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130C  PRO*     4.5     4.2    -      -       -      +
    132C  PHE*     4.2    12.3    -      -       +      -
    192C  ARG*     4.5    11.9    -      -       +      +
    195C  MET*     4.6     6.7    -      -       +      -
    196C  CYS*     3.7    30.3    -      -       -      -
    199C  MET*     3.7    32.3    -      -       +      -
    206C  VAL*     4.2     9.0    -      -       +      -
    208C  ALA      3.6     4.7    -      -       -      +
    209C  HIS*     4.0     5.2    -      -       +      -
    220C  GLU*     1.3    80.2    -      -       -      +
    222C  ALA*     1.3    63.4    +      -       -      +
    223C  THR*     3.6     2.8    +      -       +      -
    238C  TYR*     2.9    44.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 222 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  PRO      5.9     1.6    -      -       -      -
    129C  GLU*     5.9     3.6    -      -       +      +
    206C  VAL*     3.6     4.5    -      -       -      +
    207C  GLU*     2.7    35.2    +      -       +      -
    208C  ALA*     2.7    30.1    +      -       +      +
    210C  HIS*     5.7     1.5    -      -       -      +
    220C  GLU*     4.1     6.5    -      -       -      +
    221C  VAL*     1.3    71.5    -      -       -      +
    223C  THR*     1.3    56.2    +      -       -      +
   1473C  ADP      4.2    39.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 223 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  PRO      4.7    10.7    +      -       -      +
    130C  PRO*     5.4     2.3    -      -       -      +
    199C  MET*     4.2    10.8    -      -       -      -
    204C  LEU*     3.9    26.5    -      -       +      +
    205C  VAL      3.2    12.8    -      -       -      +
    206C  VAL*     4.3     6.1    -      -       +      -
    207C  GLU*     3.9     3.6    -      -       -      -
    221C  VAL*     3.6     4.4    +      -       +      -
    222C  ALA*     1.3    77.9    -      -       -      +
    224C  ARG*     1.3    55.4    +      -       -      +
    231C  LYS*     3.1    25.4    +      -       -      -
    235C  ILE*     5.8     1.4    -      -       -      +
    238C  TYR*     4.0    22.8    -      -       +      -
   1473C  ADP      2.6    29.6    +      -       -      -
----------------------------------------------------------
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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