Contacts of the strand formed by residues 272 - 277 (chain C) in PDB entry 2R2N


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 GLY 272 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  LEU*     5.3     0.2    -      -       -      +
    113C  VAL*     3.4     8.3    -      -       -      +
    114C  THR*     2.9    36.0    +      -       -      +
    116C  GLY      3.5     3.4    -      -       -      +
    117C  SER      3.8    10.3    -      -       -      -
    259C  ASP      3.5    11.4    -      -       -      -
    260C  SER*     4.4     4.0    -      -       -      -
    261C  PHE      4.6     0.2    -      -       -      -
    271C  ILE*     1.3    74.3    -      -       -      +
    273C  PHE*     1.3    71.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 273 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  LEU*     3.9    30.7    -      -       +      -
     90C  LEU*     4.5    10.5    -      -       +      -
     91C  GLN*     3.4    31.0    -      -       +      -
    111C  LEU*     3.8    28.3    -      -       +      -
    112C  CYS      3.3    12.6    -      -       -      +
    113C  VAL*     4.2     1.3    -      -       -      -
    114C  THR*     3.7     5.0    +      -       -      -
    117C  SER*     4.9     1.6    -      -       -      +
    235C  PHE*     5.2     5.2    -      +       -      -
    257C  ARG      4.0     0.3    -      -       -      +
    258C  ALA*     3.6     2.8    -      -       -      +
    259C  ASP*     2.8    67.7    +      -       +      +
    260C  SER      4.8     0.7    -      -       -      -
    261C  PHE*     3.8    34.3    -      +       -      -
    272C  GLY*     1.3    80.7    -      -       -      +
    274C  LEU*     1.3    60.3    +      -       -      +
    275C  THR*     4.2     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 274 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111C  LEU*     3.1     5.6    -      -       -      +
    112C  CYS*     2.9    39.6    +      -       -      +
    114C  THR*     4.3     7.4    -      -       +      +
    120C  GLY*     3.9    17.5    -      -       -      +
    121C  LEU      4.7     0.2    -      -       -      +
    124C  VAL*     3.6    27.6    -      -       +      -
    228C  ILE*     4.9     2.7    -      -       +      -
    256C  ILE*     3.6    18.8    -      -       +      -
    257C  ARG      3.4    14.1    -      -       -      +
    258C  ALA*     4.0    17.3    -      -       +      -
    273C  PHE*     1.3    74.0    -      -       -      +
    275C  THR*     1.3    61.3    +      -       -      +
    281C  ILE*     3.7    17.3    -      -       +      +
    284C  VAL*     3.7    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 275 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91C  GLN*     2.9    27.0    +      -       +      +
    109C  MET*     3.4    39.0    -      -       +      -
    110C  ASP      3.3     6.7    -      -       -      +
    111C  LEU*     3.5    12.8    -      -       +      +
    247C  LEU*     3.9    24.2    -      -       +      +
    255C  VAL      4.2     0.5    -      -       -      +
    256C  ILE*     3.5     2.8    -      -       -      +
    257C  ARG*     2.7    38.4    +      -       -      +
    259C  ASP*     4.5     0.7    +      -       -      -
    273C  PHE*     4.2     3.3    -      -       -      -
    274C  LEU*     1.3    76.7    -      -       -      +
    276C  GLY*     1.3    56.5    +      -       -      +
    281C  ILE*     3.9     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 276 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99C  THR*     6.0     1.8    -      -       -      -
    107C  GLY      4.9     0.2    -      -       -      -
    109C  MET*     3.8     4.8    -      -       -      -
    110C  ASP      2.9    30.9    +      -       -      +
    247C  LEU*     5.5     3.1    -      -       -      -
    255C  VAL      3.6     8.5    -      -       -      -
    256C  ILE*     4.3     3.8    -      -       -      -
    275C  THR*     1.3    76.1    -      -       -      +
    277C  PRO*     1.4    76.1    -      -       -      +
    281C  ILE*     3.5    11.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 277 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  TYR*     3.3    32.5    -      -       +      +
    107C  GLY*     3.5    16.6    -      -       -      +
    250C  ASP*     5.4     0.4    -      -       -      +
    253C  GLY*     3.2    30.3    -      -       -      +
    254C  ARG*     5.0     0.7    -      -       -      -
    255C  VAL      3.4    13.2    -      -       -      +
    256C  ILE*     4.2    12.1    -      -       +      -
    276C  GLY*     1.4    82.8    -      -       -      +
    278C  LYS*     1.3    67.5    +      -       -      +
    279C  PRO*     4.0     2.5    -      -       +      -
    280C  LEU*     3.0    23.3    +      -       +      -
    281C  ILE      3.1    10.4    +      -       -      -
----------------------------------------------------------
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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