Contacts of the strand formed by residues 224 - 230 (chain A) in PDB entry 3RJH


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 ILE 224 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215A  VAL*     4.1    14.1    -      -       +      +
    218A  LEU*     3.0    39.6    +      -       +      +
    219A  GLN*     3.4    44.3    -      -       +      +
    222A  HIS*     4.0     4.2    -      -       -      -
    223A  PHE*     1.3    86.1    +      -       +      +
    225A  THR*     1.3    62.5    +      -       -      +
    226A  ASP      4.0    14.1    -      -       -      +
    235A  PHE*     3.6    32.3    -      -       +      -
    238A  VAL      3.2    12.6    -      -       -      +
    239A  CYS*     4.1     0.2    -      -       -      +
    255A  ILE*     4.6     7.9    -      -       +      -
    257A  ILE*     4.6     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  TYR*     4.4     1.8    -      -       -      -
    219A  GLN*     6.2     0.4    -      -       -      -
    222A  HIS*     4.3    11.2    -      -       +      +
    223A  PHE      4.0     9.6    -      -       -      +
    224A  ILE*     1.3    78.4    -      -       -      +
    226A  ASP*     1.3    82.5    +      -       -      +
    238A  VAL*     2.7    29.1    +      -       -      +
    240A  GLN*     4.5    12.6    -      -       +      +
    252A  HIS*     3.5    21.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  HIS*     5.9     0.7    -      -       +      +
    138A  ILE*     4.0    22.6    -      -       +      +
    141A  LYS*     3.4    20.4    +      -       -      -
    142A  TYR*     2.4    34.6    +      -       -      -
    219A  GLN*     5.8     0.4    -      -       -      +
    224A  ILE*     4.0     7.5    -      -       -      +
    225A  THR*     1.3   101.7    +      -       -      +
    227A  THR*     1.3    63.6    +      -       -      +
    235A  PHE*     4.0     0.3    -      -       -      -
    237A  GLY*     3.4     2.9    -      -       -      -
    238A  VAL*     2.9    37.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  HIS*     2.6    36.9    +      -       +      -
    138A  ILE*     4.4     0.7    -      -       -      +
    219A  GLN*     3.9    16.3    +      -       -      -
    226A  ASP*     1.3    76.4    +      -       -      +
    228A  LEU*     1.3    65.0    +      -       -      +
    229A  SER*     3.6    20.6    -      -       -      +
    230A  LYS*     4.0    10.3    -      -       +      +
    235A  PHE*     3.5    30.1    -      -       +      -
    236A  MET      4.0     2.0    -      -       -      -
    237A  GLY*     4.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  SER*     4.3     2.2    -      -       -      +
    134A  HIS*     4.2     9.7    -      -       -      -
    135A  HIS*     3.6    57.6    +      -       +      +
    138A  ILE*     3.5    39.9    -      -       +      -
    139A  GLY*     4.7     2.5    -      -       -      +
    146A  PHE*     5.2     1.3    -      -       +      -
    227A  THR*     1.3    74.9    -      -       -      +
    229A  SER*     1.3    60.0    +      -       -      +
    236A  MET*     2.6    24.9    +      -       +      +
    237A  GLY*     4.2     7.2    -      -       -      +
    238A  VAL*     4.7     2.2    -      -       +      -
    254A  ARG*     3.5    44.6    -      -       -      +
     11T    A      4.4     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  HIS*     5.7     2.0    -      -       -      -
    227A  THR*     3.6     6.5    -      -       -      +
    228A  LEU*     1.3    80.2    -      -       -      +
    230A  LYS*     1.3    65.0    +      -       -      +
    234A  LYS*     4.8     1.2    -      -       -      -
    235A  PHE*     3.8     0.5    -      -       -      -
    236A  MET*     2.9    60.2    +      -       -      +
     10T    C      3.4    23.2    +      -       -      -
     11T    A      3.5    17.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  LEU*     5.5     1.1    -      -       +      -
    212A  HIS*     2.8    47.9    +      -       -      +
    215A  VAL*     4.2    24.0    -      -       +      -
    219A  GLN*     6.0     0.4    -      -       -      +
    227A  THR*     4.0    10.5    -      -       +      +
    229A  SER*     1.3    77.1    -      -       -      +
    231A  GLY*     1.3    71.1    +      -       -      +
    234A  LYS      3.7     5.4    -      -       -      +
    235A  PHE*     3.8    26.2    -      -       +      -
     10T    C      3.4     4.2    +      -       -      +
     11T    A      3.0    22.1    +      -       -      +
----------------------------------------------------------
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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