Contacts of the strand formed by residues 206 - 211 (chain E) 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 VAL 206 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196E  CYS*     3.7    44.4    -      -       +      +
    199E  MET*     4.3    10.1    -      -       +      -
    200E  GLU*     3.0    30.6    +      -       +      +
    205E  VAL*     1.3    74.5    -      -       -      +
    207E  GLU*     1.3    63.4    -      -       -      +
    208E  ALA      3.6    13.7    -      -       -      +
    221E  VAL*     4.2     9.9    -      -       +      -
    222E  ALA      3.6    11.2    -      -       -      +
    223E  THR*     4.3     4.7    -      -       +      +
     34F  PRO*     3.2    26.6    -      -       +      +
     36F  HIS*     3.2    16.8    -      -       -      -
     37F  GLN*     4.2     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 207 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205E  VAL*     3.8     1.9    +      -       +      -
    206E  VAL*     1.3    74.3    -      -       -      +
    208E  ALA*     1.3    61.9    +      -       +      +
    222E  ALA*     2.7    20.3    +      -       +      +
    223E  THR      3.7     1.8    -      -       -      +
    224E  ARG*     3.5    39.4    -      -       +      +
    225E  PHE*     5.2     0.5    -      -       -      -
   1475E  ADP      3.2    43.0    +      -       -      +
     33F  ILE*     3.2    12.1    -      -       -      +
     34F  PRO*     3.2    16.0    -      -       -      +
     37F  GLN*     3.5    28.0    +      -       -      +
     47F  LYS*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 208 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206E  VAL*     3.6     7.3    -      -       -      +
    207E  GLU*     1.3    82.4    -      -       +      +
    209E  HIS*     1.3    62.1    +      -       -      +
    210E  HIS*     5.0     4.9    -      -       +      -
    221E  VAL*     3.6     1.4    -      -       -      -
    222E  ALA*     2.7    44.3    +      -       +      +
   1475E  ADP      5.6     2.5    -      -       -      +
     31F  VAL*     4.8     7.9    -      -       +      -
     32F  THR      3.2     6.7    -      -       -      +
     33F  ILE*     3.3    20.4    -      -       +      -
     34F  PRO*     4.1     4.5    -      -       -      -
     47F  LYS*     4.9     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 209 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189E  GLN*     3.2    32.6    +      -       -      -
    192E  ARG*     2.8    37.0    +      -       +      -
    193E  SER*     2.8    32.2    +      -       -      -
    196E  CYS*     3.7    28.3    -      -       -      -
    208E  ALA*     1.3    76.4    -      -       -      +
    210E  HIS*     1.3    64.4    +      -       -      +
    220E  GLU      3.4    12.3    -      -       -      +
    221E  VAL*     4.0     6.3    -      -       +      -
     16F  PHE*     4.3     5.2    -      +       -      -
     31F  VAL*     3.9     0.3    -      -       -      +
     32F  THR*     2.8    53.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 210 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179E  TYR*     3.5    11.2    -      -       -      -
    180E  PHE*     3.5    24.3    -      +       +      -
    192E  ARG*     3.4    16.4    -      -       -      +
    208E  ALA*     5.0     5.8    -      -       +      -
    209E  HIS*     1.3    86.3    +      -       -      +
    211E  HIS*     1.3    78.7    +      -       -      +
    212E  GLU*     3.3    26.2    -      -       -      -
    220E  GLU*     2.9    53.3    +      -       +      +
    222E  ALA*     5.8     1.3    -      -       +      -
    469E   MN      4.4     0.2    -      -       -      -
   1475E  ADP      2.8    25.6    +      -       -      -
     30F  HIS*     4.8     1.1    -      -       -      +
     31F  VAL*     4.0    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 211 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155E  GLU*     2.7    35.8    +      -       -      -
    173E  PRO*     4.5     6.4    -      -       +      +
    178E  GLY*     2.9    20.9    +      -       -      +
    179E  TYR*     3.0    12.2    -      -       -      -
    180E  PHE*     3.4    10.8    -      -       +      +
    186E  ASP*     3.5    31.1    +      -       +      +
    192E  ARG*     3.6    11.3    -      -       -      +
    210E  HIS*     1.3    90.5    +      -       -      +
    212E  GLU*     1.3    91.9    +      -       -      +
    214E  ALA      3.4    17.0    +      -       -      -
    217E  GLY*     4.2     5.2    -      -       -      -
    218E  GLN      2.9    14.4    +      -       -      -
    219E  ASN*     3.5    14.6    +      -       -      +
     30F  HIS*     5.7     1.4    +      -       +      -
----------------------------------------------------------
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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