Contacts of the strand formed by residues 131 - 134 (chain A) in PDB entry 1UFU


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 PHE 131 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  PRO*     4.6     0.9    -      -       +      -
    122A  CYS*     3.2    38.1    -      -       +      -
    124A  SER*     3.8    31.0    -      -       -      -
    128A  PHE*     3.4    33.4    -      +       +      -
    129A  ASP      5.2     0.2    -      -       -      -
    130A  GLY*     1.3    77.8    -      -       -      -
    132A  ILE*     1.3    66.8    +      -       -      +
    146A  ASN*     3.7     1.3    +      -       -      +
    147A  SER*     3.0    33.1    +      -       -      -
    154A  SER      4.2     2.0    -      -       -      -
    155A  SER*     3.9    12.6    -      -       -      -
    156A  ARG*     4.1    15.7    -      -       -      -
    157A  ALA*     3.6    30.1    -      -       +      -
    159A  PHE*     3.5     6.9    -      -       +      -
    175A  TYR      3.3    11.7    -      -       -      +
    176A  ALA*     3.9    11.4    -      -       +      -
    177A  TYR*     3.9     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  PHE*     1.3    73.2    -      -       -      +
    133A  LEU*     1.3    62.3    +      -       -      +
    134A  CYS*     4.0     6.3    -      -       -      -
    144A  CYS*     3.5    27.6    -      -       +      -
    145A  LEU*     3.6     1.8    -      -       -      +
    146A  ASN*     3.2    52.3    -      -       -      +
    159A  PHE*     4.3     1.1    -      -       -      -
    174A  CYS*     2.9     8.4    -      -       -      +
    175A  TYR*     2.7    43.4    +      -       +      -
    177A  TYR*     3.6    20.2    -      -       +      -
    185A  TRP*     3.8    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  LEU*     4.3    14.1    -      -       +      -
    120A  LEU*     3.6    21.8    -      -       +      -
    132A  ILE*     1.3    74.7    -      -       -      +
    134A  CYS*     1.3    57.9    +      -       -      +
    135A  LYS*     3.9     0.4    +      -       +      -
    144A  CYS*     3.0    21.4    -      -       -      -
    145A  LEU*     3.0    26.8    +      -       +      +
    159A  PHE*     3.2    52.7    -      -       +      -
    160A  SER      5.2     1.8    -      -       -      +
    161A  VAL*     5.7     0.9    -      -       +      -
    172A  TYR*     3.5    39.9    -      -       +      -
    173A  ARG      3.5     8.1    -      -       -      +
    174A  CYS*     4.1     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  VAL*     5.1     4.0    -      -       -      -
    132A  ILE*     4.0    10.5    -      -       -      -
    133A  LEU*     1.3    71.0    -      -       -      +
    135A  LYS*     1.3    60.3    +      -       -      +
    136A  GLU*     2.9    21.5    +      -       -      +
    144A  CYS*     2.0    47.8    -      -       -      -
    172A  TYR*     3.6     2.2    -      -       -      -
    173A  ARG      2.6    34.1    +      -       -      +
    175A  TYR*     4.0    20.0    -      -       +      -
    185A  TRP*     4.1     7.2    -      -       -      -
----------------------------------------------------------
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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