Contacts of the strand formed by residues 193 - 197 (chain B) in PDB entry 5UNF


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 ASN 193 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  PHE*     6.0     4.0    -      -       -      -
    108B  TYR      4.0     1.3    -      -       -      -
    109B  ASP*     3.3    15.0    +      -       -      +
    110B  TRP*     2.8    40.4    +      -       -      +
    184B  VAL*     3.7    22.7    -      -       +      +
    185B  ARG      3.9     4.5    -      -       -      -
    186B  THR*     3.2    29.3    -      -       -      +
    191B  GLY      5.4     0.9    -      -       -      -
    192B  VAL*     1.3    72.5    -      -       -      +
    194B  ALA*     1.3    56.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  TYR*     3.6    12.1    -      -       -      +
    108B  TYR*     3.7    16.8    -      -       +      +
    110B  TRP*     4.6     0.9    -      -       -      -
    184B  VAL*     3.4     2.3    -      -       -      -
    185B  ARG      3.0    32.0    +      -       -      +
    187B  ILE*     3.8    17.5    -      -       +      -
    192B  VAL*     3.5     3.7    +      -       +      -
    193B  ASN*     1.3    72.5    -      -       -      +
    195B  CYS*     1.3    57.9    +      -       -      +
    196B  ILE*     3.1    24.2    +      -       +      +
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Residues in contact with CYS 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  TYR*     2.9    19.9    +      -       +      +
    110B  TRP*     3.6    32.5    -      -       +      +
    117B  CYS*     2.0    59.5    -      -       -      -
    182B  ARG*     2.7    25.4    +      -       -      -
    183B  ASP      3.8     1.3    -      -       -      -
    184B  VAL*     4.3     2.2    -      -       -      -
    194B  ALA*     1.3    66.2    -      -       -      +
    196B  ILE*     1.3    52.9    +      -       -      +
   1201B  8ES      3.8    25.4    -      -       -      +
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Residues in contact with ILE 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  TYR*     5.2     0.4    -      -       -      +
    182B  ARG*     3.3    15.2    -      -       -      +
    183B  ASP      3.0    40.3    +      -       -      +
    185B  ARG*     3.8    29.8    -      -       +      -
    187B  ILE*     4.0    18.8    -      -       +      -
    194B  ALA*     3.1    26.6    +      -       +      +
    195B  CYS*     1.3    72.0    -      -       -      +
    197B  MET*     1.3    59.1    +      -       -      +
    198B  ALA*     3.4    13.8    +      -       -      +
    204B  TYR*     4.5    14.8    -      -       +      +
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Residues in contact with MET 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  PRO*     3.5    28.0    -      -       +      +
    178B  THR*     3.8    12.1    -      -       -      -
    181B  PHE*     3.7    10.3    -      -       +      -
    182B  ARG*     3.6    40.6    -      -       -      +
    196B  ILE*     1.3    73.0    -      -       -      +
    198B  ALA*     1.3    52.9    +      -       -      +
    199B  PHE*     2.8    54.4    +      -       +      -
    204B  TYR*     3.1    22.3    +      -       -      +
    211B  ILE*     4.7     6.5    -      -       +      -
   1201B  8ES      4.0    21.3    -      -       +      +
----------------------------------------------------------
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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