Contacts of the strand formed by residues 218 - 223 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  GLU*     4.4     3.3    -      -       -      +
    132A  PHE      3.2    16.4    -      -       -      +
    133A  PHE*     3.5    28.8    -      -       +      -
    211A  HIS*     2.9    12.9    +      -       -      -
    212A  GLU*     2.8    47.1    +      -       +      +
    213A  VAL      3.7     0.2    -      -       -      +
    214A  ALA*     3.4    28.2    +      -       +      +
    217A  GLY*     1.3    75.5    -      -       -      +
    219A  ASN*     1.3    62.8    +      -       -      +
    264A  ASN*     3.3    25.5    +      -       -      +
    265A  GLY      2.7    24.5    +      -       -      +
    266A  SER*     3.0    16.4    +      -       -      +
    474A   TL      4.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  GLU*     3.8     3.3    -      -       -      +
    132A  PHE*     2.8    54.4    +      -       +      +
    134A  LEU*     3.9    13.6    -      -       -      +
    155A  GLU*     5.6     0.2    -      -       -      +
    188A  ALA*     3.8    11.5    -      -       -      +
    192A  ARG*     2.9    43.4    -      -       +      +
    210A  HIS      3.8     3.8    -      -       -      -
    211A  HIS*     3.5    15.4    +      -       -      +
    212A  GLU*     3.9     5.0    -      -       -      +
    217A  GLY*     2.9    26.5    -      -       -      +
    218A  GLN*     1.3    74.7    +      -       -      +
    220A  GLU*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  GLU*     3.6    16.1    -      -       -      +
    130A  PRO      3.7    15.5    -      -       -      +
    131A  GLU*     3.1    10.3    -      -       +      +
    132A  PHE*     4.0     4.5    -      -       -      -
    192A  ARG*     4.2     1.0    -      -       -      -
    209A  HIS*     3.4     4.9    -      -       -      +
    210A  HIS*     2.9    47.9    +      -       +      +
    212A  GLU*     3.0     7.8    -      -       +      +
    219A  ASN*     1.3    78.1    -      -       -      +
    221A  VAL*     1.3    72.5    +      -       -      +
    222A  ALA*     4.1     5.9    -      -       -      +
    469A   MN      2.2    33.5    +      -       -      -
   1471A  ADP      2.9    33.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  PRO*     4.5     4.0    -      -       -      +
    132A  PHE*     4.2    11.9    -      -       +      -
    192A  ARG*     4.5    11.4    -      -       +      +
    195A  MET*     4.6     7.0    -      -       +      -
    196A  CYS*     3.7    30.7    -      -       -      -
    199A  MET*     3.7    32.3    -      -       +      -
    206A  VAL*     4.2    10.3    -      -       +      -
    208A  ALA      3.6     5.6    -      -       -      +
    209A  HIS*     4.0     4.9    -      -       +      -
    220A  GLU*     1.3    80.5    -      -       -      +
    222A  ALA*     1.3    63.3    +      -       -      +
    223A  THR*     3.6     2.0    +      -       +      -
    238A  TYR*     2.9    44.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  GLU*     5.9     5.4    -      -       +      +
    206A  VAL*     3.6     4.3    -      -       -      +
    207A  GLU*     2.7    35.2    +      -       +      -
    208A  ALA*     2.7    31.9    +      -       +      +
    210A  HIS*     5.7     1.1    -      -       -      +
    220A  GLU*     4.1     6.1    -      -       -      +
    221A  VAL*     1.3    71.4    -      -       -      +
    223A  THR*     1.3    56.3    +      -       -      +
   1471A  ADP      4.2    39.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PRO      4.7     9.9    +      -       -      +
    130A  PRO*     5.4     2.5    -      -       -      +
    199A  MET*     4.2    11.7    -      -       -      -
    204A  LEU*     3.9    27.0    -      -       +      +
    205A  VAL      3.2    12.8    -      -       -      +
    206A  VAL*     4.3     6.3    -      -       +      -
    207A  GLU*     3.7     4.0    -      -       -      +
    221A  VAL*     3.6     4.4    +      -       +      -
    222A  ALA*     1.3    78.6    -      -       -      +
    224A  ARG*     1.3    54.9    +      -       -      +
    231A  LYS*     3.1    25.2    +      -       -      -
    235A  ILE*     5.8     1.7    -      -       -      +
    238A  TYR*     4.0    21.5    -      -       +      -
   1471A  ADP      2.6    29.8    +      -       -      -
----------------------------------------------------------
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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