Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 4RRO


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 SER 230 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ARG*     6.2     2.0    -      -       -      -
     69A  GLY      3.4     8.1    +      -       -      -
     70A  LYS*     3.8    19.2    +      -       -      +
    217A  GLY      5.0     4.5    -      -       -      -
    228A  LEU      3.5     2.0    +      -       -      -
    229A  ALA*     1.3    77.1    -      -       -      +
    231A  VAL*     1.3    67.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ARG*     3.5    10.6    -      -       -      -
     69A  GLY*     2.8    51.4    +      -       -      +
     70A  LYS      4.1     5.4    -      -       -      +
     71A  SER*     4.0    25.8    -      -       -      +
     74A  GLY      4.8     0.7    -      -       -      +
     75A  TYR*     3.6    31.4    -      -       +      +
    216A  CYS      3.7     9.6    -      -       -      +
    217A  GLY*     4.0    20.0    -      -       -      -
    229A  ALA*     4.3     2.0    -      -       +      +
    230A  SER*     1.3    81.9    -      -       -      +
    232A  GLY*     1.3    58.3    +      -       -      +
    368A  ARG*     5.7     2.0    -      -       -      +
    400A  GLU*     5.3     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ASP*     5.0     1.6    -      -       -      -
     67A  LEU      3.3    12.6    -      -       -      -
     68A  ARG*     3.9     9.9    -      -       -      -
     75A  TYR*     3.4     8.4    -      -       -      -
    216A  CYS*     2.9    37.0    +      -       -      +
    217A  GLY      5.4     0.2    -      -       -      -
    231A  VAL*     1.3    76.8    -      -       -      +
    233A  GLY*     1.3    58.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ASP*     3.1    18.0    +      -       -      -
     67A  LEU*     2.9    35.9    +      -       -      +
     68A  ARG*     4.2     2.0    -      -       -      +
    214A  GLN*     3.1    14.4    -      -       -      -
    215A  LEU*     4.6     0.7    -      -       -      -
    216A  CYS*     4.3     8.7    -      -       -      -
    232A  GLY*     1.3    75.0    -      -       -      -
    234A  SER*     1.3    62.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  MET      4.1     0.4    -      -       -      -
     64A  VAL*     3.6     8.7    -      -       -      +
     65A  ASP*     2.9    24.7    +      -       -      +
     66A  ASN*     3.4     4.9    -      -       -      -
     67A  LEU*     3.6     7.7    -      -       -      +
    212A  SER      3.7     0.5    -      -       -      +
    213A  LEU*     3.4     4.5    -      -       -      -
    214A  GLN*     2.8    47.9    +      -       -      +
    233A  GLY*     1.3    72.4    -      -       -      -
    235A  MET*     1.3    58.5    +      -       -      +
    236A  ILE*     4.0    10.5    -      -       -      +
    244A  LEU*     3.9    23.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  MET*     3.9     5.7    -      -       -      +
     66A  ASN*     2.7    28.4    +      -       -      +
     67A  LEU*     3.7    11.8    -      -       +      +
     77A  VAL*     3.8    37.7    -      -       +      -
     92A  VAL*     4.0    24.9    -      -       +      -
    148A  ILE*     4.7     2.9    -      -       +      -
    180A  LEU*     4.5     9.6    -      -       +      -
    182A  LEU*     4.1    15.7    -      -       -      -
    211A  PHE*     4.8     6.7    -      -       +      -
    212A  SER      3.3     5.8    -      -       -      +
    213A  LEU*     3.6    16.8    -      -       +      -
    234A  SER*     1.3    71.9    -      -       -      +
    236A  ILE*     1.3    63.3    +      -       -      +
    237A  ILE*     3.7    37.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  PHE*     3.5    42.8    -      -       +      +
     63A  MET*     3.7    33.2    -      -       +      +
     64A  VAL*     4.1     5.4    -      -       +      +
    211A  PHE*     3.2     5.1    -      -       -      +
    212A  SER*     2.8    46.1    +      -       -      +
    234A  SER*     4.0     6.3    -      -       -      -
    235A  MET*     1.3    73.0    -      -       -      +
    237A  ILE*     1.3    62.0    -      -       -      +
    239A  GLY      3.5    19.5    -      -       -      +
    240A  ILE      4.5     0.4    -      -       -      +
    241A  ASP*     4.1     3.8    -      -       +      +
    244A  LEU*     3.7    31.6    -      -       +      -
    403A  TYR*     3.8     8.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  PHE*     4.3     4.3    -      -       -      -
     63A  MET*     3.4    25.9    -      -       -      +
     66A  ASN*     5.3     0.4    -      -       -      +
    148A  ILE*     3.5    33.2    -      -       +      -
    151A  GLY*     4.5     6.3    -      -       -      -
    152A  PRO*     3.6    33.1    -      -       +      +
    198A  PHE*     3.8    13.5    -      -       +      -
    201A  LEU*     3.7    22.9    -      -       +      -
    207A  VAL*     3.9     7.2    -      -       +      +
    211A  PHE*     4.2     8.3    -      -       +      -
    235A  MET*     3.7    35.9    -      -       +      +
    236A  ILE*     1.3    73.0    -      -       -      +
    238A  GLY*     1.3    64.3    +      -       -      +
    239A  GLY      3.4     0.8    +      -       -      -
----------------------------------------------------------
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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