Contacts of the strand formed by residues 218 - 223 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  GLU*     4.4     3.1    -      -       -      +
    132H  PHE      3.2    16.8    -      -       -      +
    133H  PHE*     3.5    27.9    -      -       +      -
    211H  HIS*     2.9    12.2    +      -       -      -
    212H  GLU*     2.8    47.2    +      -       +      +
    213H  VAL      3.7     0.4    -      -       -      +
    214H  ALA*     3.4    27.4    +      -       +      +
    216H  ALA      3.8     0.2    -      -       -      -
    217H  GLY*     1.3    74.7    -      -       -      +
    219H  ASN*     1.3    62.1    +      -       -      +
    264H  ASN*     3.3    25.7    +      -       -      +
    265H  GLY      2.7    24.3    +      -       -      +
    266H  SER*     3.0    16.9    +      -       -      +
    474H   TL      4.3     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 219 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  GLU*     3.8     3.5    -      -       -      +
    132H  PHE*     2.8    54.9    +      -       +      +
    134H  LEU*     3.9    14.0    -      -       -      +
    155H  GLU*     5.6     0.2    -      -       -      +
    188H  ALA*     3.8    10.6    -      -       -      +
    192H  ARG*     2.9    43.6    -      -       +      +
    210H  HIS      3.8     3.6    -      -       -      -
    211H  HIS*     3.5    15.4    +      -       -      +
    212H  GLU*     3.9     5.1    -      -       -      +
    217H  GLY*     2.9    26.4    -      -       -      +
    218H  GLN*     1.3    73.8    +      -       -      +
    220H  GLU*     1.3    64.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 220 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  GLU*     3.6    16.5    -      -       -      +
    130H  PRO      3.7    16.2    -      -       -      +
    131H  GLU*     3.1    10.1    -      -       +      +
    132H  PHE*     4.0     5.2    -      -       -      -
    192H  ARG*     4.2     1.6    -      -       -      -
    209H  HIS*     3.4     5.4    -      -       -      +
    210H  HIS*     2.9    46.9    +      -       +      +
    212H  GLU*     3.0     8.1    -      -       +      +
    219H  ASN*     1.3    79.0    -      -       -      +
    221H  VAL*     1.3    70.2    +      -       -      +
    222H  ALA*     4.1     6.0    -      -       -      +
    469H   MN      2.2    33.6    +      -       -      -
   1478H  ADP      2.9    33.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 221 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130H  PRO*     4.5     3.8    -      -       -      +
    132H  PHE*     4.2    11.8    -      -       +      -
    192H  ARG*     4.5    11.7    -      -       +      +
    195H  MET*     4.6     7.0    -      -       +      -
    196H  CYS*     3.7    30.5    -      -       -      -
    199H  MET*     3.7    32.5    -      -       +      -
    206H  VAL*     4.2     9.6    -      -       +      -
    208H  ALA      3.6     5.8    -      -       -      +
    209H  HIS*     4.0     4.9    -      -       +      -
    220H  GLU*     1.3    81.6    -      -       -      +
    222H  ALA*     1.3    61.7    +      -       -      +
    223H  THR*     3.6     1.9    +      -       +      -
    238H  TYR*     2.9    45.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 222 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  GLU*     5.9     5.4    -      -       +      +
    130H  PRO*     6.2     0.2    -      -       -      -
    206H  VAL*     3.6     4.5    -      -       -      +
    207H  GLU*     2.7    34.1    +      -       +      -
    208H  ALA*     2.7    30.4    +      -       +      +
    210H  HIS*     5.7     1.3    -      -       -      +
    220H  GLU*     4.1     6.5    +      -       +      +
    221H  VAL*     1.3    72.1    -      -       -      +
    223H  THR*     1.3    57.7    +      -       -      +
   1478H  ADP      4.2    39.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 223 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  PRO      4.7    10.5    +      -       -      +
    130H  PRO*     5.4     2.1    -      -       -      +
    199H  MET*     4.2    11.2    -      -       -      -
    204H  LEU*     3.9    26.2    -      -       +      +
    205H  VAL      3.2    11.7    -      -       -      +
    206H  VAL*     4.3     6.5    -      -       +      -
    207H  GLU*     3.9     3.8    -      -       -      -
    221H  VAL*     3.6     4.2    +      -       +      -
    222H  ALA*     1.3    77.4    -      -       -      +
    224H  ARG*     1.3    55.7    +      -       -      +
    231H  LYS*     3.1    26.4    +      -       -      -
    235H  ILE*     5.8     1.2    -      -       -      +
    238H  TYR*     4.0    22.8    -      -       +      -
   1478H  ADP      2.6    30.1    +      -       -      -
----------------------------------------------------------
 Back to top of page


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