Contacts of the strand formed by residues 200 - 203 (chain F) in PDB entry 5U07


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 GLU 200 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  ARG*     4.8     7.2    +      -       -      +
    175B  HIS*     4.4    12.1    -      -       +      -
     27E  THR      4.3    14.1    -      -       -      +
     28E  VAL*     3.5    15.2    -      -       -      +
     29E  VAL*     4.7    11.8    +      -       +      +
     37E  ARG*     5.2     2.0    -      -       -      +
     14F  TYR*     3.0    41.5    +      -       +      +
    198F  THR      3.2    19.6    -      -       -      +
    199F  VAL*     1.3    70.1    -      -       -      +
    201F  VAL*     1.3    65.1    +      -       -      +
    202F  ASP      3.6     1.2    +      -       -      -
    226F  PHE*     2.9    36.8    +      -       -      +
    227F  SER*     4.0    10.2    -      -       -      -
    228F  ALA*     4.1     5.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 201 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159B  GLN*     4.9     6.1    -      -       +      +
    163B  LEU*     3.4    44.9    -      -       +      +
    166B  ARG*     4.1     7.2    -      -       -      +
    175B  HIS*     5.0     2.8    -      -       -      -
    178B  ARG*     4.3    16.8    +      -       -      -
     20E  ASP*     5.7     0.9    -      -       -      +
     37E  ARG*     5.0     2.4    +      -       -      -
    199F  VAL*     3.7     4.6    +      -       +      +
    200F  GLU*     1.3    72.8    -      -       -      +
    202F  ASP*     1.3    60.8    +      -       -      +
    203F  PHE*     4.0     9.0    +      -       +      -
    223F  ALA*     3.5    31.4    -      -       +      +
    224F  GLY      3.6     9.2    -      -       -      +
    225F  GLN*     3.5    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 202 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20E  ASP*     5.7     1.8    -      -       -      -
     26E  LYS*     5.2     3.8    -      -       +      +
     37E  ARG*     3.1    18.9    +      -       -      +
     39E  SER*     5.2     0.7    -      -       -      +
     41E  GLN*     5.4     6.8    +      -       -      +
    190E  HIS*     4.6     2.4    -      -       -      -
     14F  TYR*     2.6    30.3    +      -       -      +
    200F  GLU      3.6     0.6    +      -       -      -
    201F  VAL*     1.3    70.7    -      -       -      +
    203F  PHE*     1.3    67.8    +      -       -      +
    204F  PHE*     3.5     8.2    +      -       -      -
    223F  ALA*     4.2     0.7    -      -       -      -
    224F  GLY*     2.7    44.4    +      -       -      +
    226F  PHE*     2.9    30.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 203 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  SER*     3.2    44.2    -      -       -      -
    159B  GLN*     4.3     3.4    -      -       +      -
    160B  ARG*     3.2    50.7    -      -       +      -
    178B  ARG*     4.1    16.6    -      -       -      -
     20E  ASP*     4.8    10.4    +      -       +      -
     21E  ASP*     4.4    17.0    -      -       +      +
     26E  LYS*     3.1    27.2    +      -       -      +
    201F  VAL*     4.3    16.4    -      -       +      -
    202F  ASP*     1.3    74.1    -      -       -      +
    204F  PHE*     1.3    58.0    +      -       -      +
    221F  MET      5.0     6.5    -      -       -      +
    222F  ASN      5.1     0.4    -      -       -      +
    223F  ALA*     3.2    29.8    -      -       +      +
     33K    G      4.8     2.5    -      -       +      +
----------------------------------------------------------
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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