Contacts of the strand formed by residues 201 - 204 (chain R) in PDB entry 5IYB


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 201 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52Q  LEU      3.7     8.5    -      -       -      +
     53Q  LYS*     3.5    31.0    -      -       +      +
    164R  GLY      5.6     1.8    -      -       -      +
    165R  GLY      3.4    15.5    -      -       -      +
    166R  ILE*     4.1    21.1    -      -       +      -
    190R  LEU      3.7     0.2    -      -       -      +
    191R  PHE*     3.5     4.7    -      -       -      -
    192R  VAL*     3.1    41.2    +      -       +      +
    194R  ARG*     2.9    41.3    -      -       +      -
    195R  PRO*     5.3     4.3    -      -       +      -
    199R  LYS*     6.1     0.9    -      -       +      -
    200R  ILE*     1.3    80.3    -      -       -      +
    202R  PHE*     1.3    65.2    +      -       -      +
    203R  PHE*     3.9    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 202 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155R  LEU*     5.0    14.2    -      -       +      +
    161R  ARG      5.4     0.9    -      -       -      +
    164R  GLY*     3.8     1.6    -      -       -      -
    165R  GLY*     3.3    32.9    +      -       -      +
    166R  ILE      5.6     1.1    -      -       -      -
    167R  LEU*     4.5    12.3    -      -       +      -
    170R  ASP*     5.5     2.9    -      -       +      -
    177R  ASN*     3.2    34.8    -      -       -      -
    180R  LYS*     6.4     2.0    -      -       -      -
    181R  ALA*     3.7    26.2    -      -       +      -
    184R  ALA*     5.8     2.9    -      -       +      -
    185R  LEU*     6.1     2.0    -      -       +      -
    189R  ILE*     3.6    23.3    -      -       +      -
    190R  LEU      3.4     3.8    -      -       -      -
    191R  PHE*     3.7    17.9    -      -       +      -
    200R  ILE*     3.6    22.0    -      -       +      -
    201R  LEU*     1.3    79.4    -      -       -      +
    203R  PHE*     1.3    73.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 203 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28Q  ILE*     5.5     6.3    -      -       +      -
     29Q  GLU*     6.0     0.9    -      -       +      -
     32Q  LEU*     3.4    40.4    -      -       +      -
     51Q  LEU      6.0     0.2    -      -       -      -
     52Q  LEU*     3.9    12.1    -      -       -      -
     54Q  PHE*     4.0     9.9    -      +       -      -
    161R  ARG      5.3     3.1    -      -       -      -
    163R  LEU      3.4    26.2    -      -       -      -
    164R  GLY*     3.7     9.6    -      -       -      -
    189R  ILE*     3.3     8.8    -      -       -      +
    190R  LEU*     2.8    37.7    +      -       +      +
    192R  VAL*     3.6    36.1    -      -       +      -
    201R  LEU*     3.9    27.8    -      -       +      -
    202R  PHE*     1.3    87.8    -      -       -      +
    204R  ASN*     1.3    66.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 204 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155R  LEU*     3.0    23.7    +      -       -      +
    156R  ASP      3.9     2.6    +      -       -      -
    161R  ARG*     3.3    59.5    +      -       +      +
    188R  GLN*     2.8    43.3    +      -       -      +
    189R  ILE*     3.3    13.6    -      -       -      +
    190R  LEU*     5.2     0.2    -      -       -      -
    203R  PHE*     1.3    75.9    -      -       -      +
    205R  ASP*     1.3    62.2    +      -       -      +
    206R  LYS*     4.0    10.8    +      -       -      +
----------------------------------------------------------
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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