Contacts of the strand formed by residues 27 - 30 (chain I) in PDB entry 5U0A


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 THR 27 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ARG*     5.7     3.4    -      -       -      +
    200E  GLU*     3.5    28.9    +      -       -      +
     25I  PRO*     3.3    19.9    +      -       +      +
     26I  LYS*     1.3    76.6    -      -       -      +
     28I  VAL*     1.3    63.5    +      -       -      +
     29I  VAL*     5.6     2.0    -      -       -      +
     34I  GLU*     3.2    39.3    +      -       +      +
     35I  ARG      3.5     4.9    -      -       -      -
     36I  THR*     4.0    14.1    -      -       -      +
     37I  ARG*     3.9     8.4    +      -       -      +
    197I  THR      5.7     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 28 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14E  TYR*     3.2    40.2    -      -       +      +
    200E  GLU*     4.9     0.2    -      -       -      -
    228E  ALA*     4.5     7.0    -      -       +      -
     27I  THR*     1.3    71.9    -      -       -      +
     29I  VAL*     1.3    65.3    +      -       -      +
     30I  TYR*     3.2    28.1    +      -       +      +
     34I  GLU*     4.3     0.7    -      -       -      -
     35I  ARG*     2.7    37.3    +      -       +      +
     37I  ARG*     3.3    37.7    -      -       +      -
    190I  HIS*     5.8     0.9    -      -       +      -
    192I  PHE*     4.7    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 29 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195E  HIS*     5.9     0.5    +      -       -      -
    198E  THR*     5.7     9.4    -      -       +      -
    200E  GLU*     4.0    19.8    +      -       -      +
    228E  ALA*     5.0     8.7    -      -       -      +
     27I  THR*     4.4     2.2    +      -       -      +
     28I  VAL*     1.3    74.6    -      -       -      +
     30I  TYR*     1.3    57.2    +      -       -      +
     31I  GLY      4.1     1.2    +      -       -      -
     32I  GLY*     4.2    26.1    +      -       -      +
     33I  LYS      3.8     6.7    -      -       -      -
     34I  GLU*     4.1    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 30 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  THR*     4.2     8.1    +      -       -      -
     12E  LEU      4.3     5.4    -      -       -      -
     13E  PRO*     3.9    26.6    -      -       +      +
    228E  ALA*     4.0    18.8    -      -       +      -
    229E  GLY*     5.1     4.9    -      -       -      -
     28I  VAL*     3.2    20.3    +      -       +      -
     29I  VAL*     1.3    72.7    -      -       -      +
     31I  GLY*     1.3    69.7    +      -       -      +
     32I  GLY      3.1     0.2    -      -       -      -
     33I  LYS      2.9    20.9    +      -       -      +
     35I  ARG*     3.1    43.5    +      -       -      -
    192I  PHE*     3.7    28.3    -      +       +      -
    297I  ALA      2.9    25.7    +      -       -      -
    298I  PRO*     3.5     4.0    -      -       -      +
    300I  PHE      3.8     0.7    -      -       -      -
    301I  GLU*     3.3    37.0    -      -       +      +
----------------------------------------------------------
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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