Contacts of the strand formed by residues 224 - 228 (chain A) in PDB entry 1RP1


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 224 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  PHE*     3.7    31.2    -      -       +      -
    199A  VAL      3.4     2.1    +      -       -      +
    200A  ASP*     3.3     4.3    -      -       +      +
    201A  VAL      2.8    31.0    +      -       -      -
    222A  GLY      4.4     0.3    -      -       -      -
    223A  HIS*     1.3    90.0    +      -       +      +
    225A  ASP*     1.3    57.9    +      -       -      +
    226A  PHE*     3.8    26.6    -      -       +      -
    305A  PRO*     4.3     3.6    -      -       +      -
    311A  ALA*     4.0     9.6    -      -       +      +
    314A  PHE*     3.8    35.4    -      -       +      +
    323A  GLN      5.6     0.4    -      -       -      -
    325A  TYR*     3.8    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  VAL*     3.3    10.5    -      -       -      +
    203A  HIS*     2.7    22.4    +      -       -      +
    220A  GLN*     3.7    21.5    +      -       +      +
    221A  MET      2.8    21.8    +      -       -      -
    222A  GLY      2.9    29.7    +      -       -      +
    223A  HIS      4.8     0.2    -      -       -      -
    224A  LEU*     1.3    73.4    -      -       -      +
    226A  PHE*     1.3    62.3    +      -       -      +
    227A  PHE*     3.5    20.4    -      -       +      -
    323A  GLN      4.8     2.2    +      -       -      +
    324A  LYS*     4.0     0.9    -      -       -      -
    325A  TYR*     3.1    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  ASP*     4.4     5.4    -      -       +      -
    201A  VAL      2.7    22.5    +      -       -      +
    202A  ILE*     4.5     4.3    -      -       +      -
    203A  HIS*     2.9    31.9    +      -       -      -
    224A  LEU*     3.8    37.9    -      -       +      -
    225A  ASP*     1.3    73.6    -      -       -      +
    227A  PHE*     1.3    64.1    +      -       -      +
    228A  PRO*     3.4     2.7    -      -       +      +
    282A  SER*     3.2    39.0    -      -       -      -
    305A  PRO*     4.1    11.4    -      -       +      -
    306A  GLN      3.6    17.3    -      -       -      -
    307A  MET*     3.6    39.3    -      -       +      -
    308A  GLY      4.9     1.1    -      -       -      -
    311A  ALA*     4.2    15.3    -      -       +      -
    325A  TYR*     3.6    10.5    -      +       +      +
    327A  LEU*     4.7     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  HIS*     3.6    39.9    -      +       +      -
    206A  ALA*     5.7     1.8    -      -       +      -
    218A  SER*     3.5    26.2    -      -       -      -
    220A  GLN*     4.2     4.3    -      -       +      -
    225A  ASP*     3.5    24.9    -      -       +      -
    226A  PHE*     1.3    72.9    -      -       -      +
    228A  PRO*     1.3    69.9    -      -       -      +
    229A  ASN      3.3     0.7    +      -       -      -
    230A  GLY      3.0    25.0    +      -       -      +
    231A  GLY*     3.8     3.1    -      -       -      +
    324A  LYS*     3.2    45.5    -      -       +      -
    325A  TYR      2.9    19.6    +      -       -      -
    326A  PHE*     3.5    31.7    -      +       +      -
    327A  LEU*     3.9     4.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  ILE*     4.2     2.5    -      -       +      -
    203A  HIS      3.3    18.4    -      -       -      +
    204A  THR*     3.9     6.1    -      -       +      -
    226A  PHE      3.4     7.0    -      -       -      +
    227A  PHE*     1.3    85.9    -      -       -      +
    229A  ASN*     1.3    70.2    +      -       -      +
    231A  GLY      3.0    10.6    +      -       -      -
    234A  MET*     3.1    13.0    -      -       -      +
    269A  TYR*     3.8    19.5    -      -       +      -
    307A  MET*     3.8    23.3    -      -       -      -
    327A  LEU*     3.3    22.1    -      -       +      +
    329A  THR*     4.0    21.8    -      -       +      -
----------------------------------------------------------
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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