Contacts of the strand formed by residues 103 - 108 (chain F) in PDB entry 3UF2


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 103 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36F  GLU*     4.3    11.0    -      -       +      +
     37F  PHE      3.5    10.3    -      -       -      +
     39F  ASP*     4.3     2.2    -      -       -      +
     42F  GLN*     4.4     5.5    +      -       -      +
     52F  LYS*     4.0     6.5    -      -       +      +
     56F  LEU*     3.6    32.1    -      -       +      -
    100F  LYS*     3.5    48.1    +      -       +      +
    101F  ALA      3.3    15.9    -      -       -      +
    102F  CYS*     1.3    80.7    -      -       -      +
    104F  ARG*     1.3    63.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 104 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70D  ASN*     3.4    39.2    +      -       +      +
     36F  GLU*     3.7     8.3    -      -       -      +
     37F  PHE      3.1    27.3    +      -       -      +
     39F  ASP*     3.8    34.3    +      -       +      +
    103F  VAL*     1.3    75.1    -      -       -      +
    105F  THR*     1.3    83.6    +      -       -      +
    106F  PHE*     3.3    53.3    -      -       +      +
    107F  TYR      4.9     1.6    -      -       -      +
    108F  GLU*     5.3     0.4    +      -       -      -
      3I  VAL      5.6     2.6    +      -       -      -
      4I  SER*     4.7    17.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 105 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70D  ASN*     3.9    17.7    +      -       -      +
     72D  PRO*     3.9    29.5    -      -       +      +
     75D  ILE*     3.5    29.0    -      -       +      +
     34F  THR*     4.8     6.5    -      -       +      -
     35F  PHE      3.6    15.0    -      -       -      +
     36F  GLU*     4.0    16.3    +      -       +      +
    104F  ARG*     1.3    93.4    +      -       -      +
    106F  PHE*     1.3    68.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 106 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75D  ILE*     4.3     2.2    -      -       -      -
     33F  ILE      3.6     0.2    -      -       -      +
     34F  THR*     3.3     6.9    -      -       -      -
     35F  PHE*     2.9    53.7    +      +       +      -
     37F  PHE*     3.5    36.1    -      -       +      -
     38F  VAL      3.3    20.0    -      -       -      -
     39F  ASP*     4.8     0.9    -      -       -      -
     40F  GLN      5.4     1.6    -      -       -      -
    104F  ARG*     3.3    59.9    -      -       +      +
    105F  THR*     1.3    79.5    -      -       -      +
    107F  TYR*     1.3    62.2    +      -       -      +
    108F  GLU*     3.2    25.8    -      -       +      +
    116F  LYS*     4.2    14.1    -      -       -      -
      4I  SER*     5.6     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 107 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75D  ILE*     3.8    26.0    -      -       +      +
     78D  VAL*     4.1    15.0    -      -       +      -
     79D  GLN*     3.8    26.0    -      -       +      +
     82D  GLU*     2.7    38.3    +      -       -      -
     32F  GLN*     2.9    62.2    +      -       +      +
     33F  ILE      3.3    14.1    -      -       -      -
     34F  THR*     3.7    13.5    -      -       +      -
    104F  ARG*     4.9     2.4    -      -       -      +
    105F  THR      4.4     0.2    +      -       -      -
    106F  PHE*     1.3    74.6    -      -       -      +
    108F  GLU*     1.3    64.0    +      -       -      +
     86I  ARG*     5.3     1.6    -      -       +      -
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Residues in contact with GLU 108 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32F  GLN*     3.8    11.4    -      -       -      +
     33F  ILE*     2.8    31.2    +      -       -      +
     35F  PHE*     3.7    18.1    -      -       +      -
    104F  ARG*     5.3     0.6    +      -       -      +
    106F  PHE*     3.2    27.8    -      -       +      -
    107F  TYR*     1.3    85.2    -      -       -      +
    109F  THR*     1.3    66.0    +      -       -      +
    112F  GLN*     3.1    42.3    +      -       +      +
    116F  LYS*     3.4    24.3    +      -       -      +
      4I  SER*     4.5    10.9    +      -       -      -
      6I  TYR*     5.1     2.7    -      -       +      +
----------------------------------------------------------
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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