Contacts of the strand formed by residues 28 - 32 (chain C) 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 LEU 28 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  TRP*     1.3   116.9    -      -       +      +
     29C  ILE*     1.3    63.5    +      -       -      +
     30C  ALA      3.4     1.0    +      -       -      -
     41C  MET*     3.2     1.1    -      -       -      -
     42C  LEU*     2.8    41.4    +      -       +      +
     43C  GLY      4.1     0.9    -      -       -      +
     44C  LEU*     3.9    17.3    -      -       +      -
     47C  VAL*     3.5    31.9    -      -       +      -
     57C  VAL*     3.6    26.5    -      -       +      -
     58C  GLU      4.9     0.9    -      -       -      -
     59C  ILE*     4.5     8.1    -      -       +      -
     68C  LEU*     4.5    11.7    -      -       +      -
     72C  LEU*     5.4     7.2    -      -       +      -
    183C  TRP*     5.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 29 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  TRP      3.2    10.6    +      -       -      +
     28C  LEU*     1.3    71.1    -      -       -      +
     30C  ALA*     1.3    62.8    +      -       -      +
     31C  ARG*     4.8     8.7    -      -       +      +
     39C  PRO*     3.8    30.1    -      -       +      +
     40C  GLU      3.9     4.7    -      -       -      +
     41C  MET*     3.7    32.3    -      -       +      -
     57C  VAL*     3.2     9.2    -      -       -      +
     58C  GLU*     3.0    55.7    +      -       +      +
     60C  PRO*     4.0    24.0    -      -       +      -
    183C  TRP*     4.4     6.5    -      -       +      +
    215N  SER*     6.2     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 30 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  ILE*     1.3    77.7    -      -       -      +
     31C  ARG*     1.3    62.8    +      -       -      +
     32C  SER      4.3     0.7    +      -       -      -
     39C  PRO*     3.1     6.7    -      -       -      +
     40C  GLU*     2.9    37.4    +      -       +      +
     42C  LEU*     3.7    18.4    -      -       +      -
     54C  LEU*     3.7    31.2    -      -       +      +
     56C  ASP      3.8     4.0    -      -       -      -
     57C  VAL*     3.9     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 31 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  ILE*     4.8     5.0    -      -       +      +
     30C  ALA*     1.3    77.4    -      -       -      +
     32C  SER*     1.3    62.4    +      -       -      +
     36C  LEU*     5.4    14.3    +      -       +      +
     37C  ALA*     6.0     0.2    -      -       -      +
     38C  ALA      5.4     0.4    -      -       -      +
     39C  PRO*     3.1    43.6    -      -       +      +
     54C  LEU*     3.1    11.1    -      -       -      +
     55C  SER*     2.8    25.9    +      -       -      +
     56C  ASP*     3.0    21.9    +      -       +      +
     58C  GLU*     3.1    27.2    +      -       +      +
    215N  SER*     5.1     4.8    -      -       -      -
    216N  THR*     2.7    42.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 32 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30C  ALA      4.2     0.8    +      -       -      -
     31C  ARG*     1.3    77.7    -      -       -      +
     33C  ARG*     1.3    64.6    +      -       -      +
     34C  ASP*     2.7    40.7    +      -       -      +
     35C  VAL*     4.9     0.9    -      -       -      +
     36C  LEU*     4.2    13.9    +      -       -      +
     37C  ALA      5.2     4.0    +      -       -      -
     39C  PRO*     5.8     0.6    -      -       -      +
     53C  GLU      4.4     1.8    -      -       -      -
     54C  LEU*     3.7    17.8    -      -       -      +
     55C  SER*     3.8    10.0    +      -       -      -
----------------------------------------------------------
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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