Contacts of the strand formed by residues 225 - 238 (chain A) in PDB entry 5OAQ


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 TRP 225 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  ARG*     3.3    44.7    -      -       +      +
    218A  SER      4.1     2.0    -      -       -      +
    219A  VAL      3.3    16.2    -      -       -      -
    220A  ALA*     3.6    19.3    -      -       +      -
    224A  LEU*     1.3    75.3    -      -       -      +
    226A  MET*     1.3    80.8    +      -       -      +
    227A  LEU*     3.5    46.0    -      -       +      +
    320A  TYR*     3.0     9.4    -      -       -      -
    321A  GLU*     2.9    61.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  VAL*     2.8    33.8    +      -       +      +
    225A  TRP*     1.3    84.4    +      -       -      +
    227A  LEU*     1.3    59.8    +      -       -      +
    228A  GLU      3.5    16.6    -      -       -      +
    229A  PHE*     3.8    34.8    -      -       +      -
    250A  ILE*     4.2    22.6    -      -       +      +
    319A  GLN      3.5     4.3    -      -       -      +
    320A  TYR*     3.4    32.3    -      -       +      -
    397A  GLN*     4.0    10.3    -      -       -      -
    409A  LEU*     3.9    10.1    -      -       +      +
    411A  ILE*     4.0    12.6    -      -       +      -
    413A  TYR*     3.6    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  TRP*     3.5    47.0    -      -       +      +
    226A  MET*     1.3    73.0    -      -       -      +
    228A  GLU*     1.3    62.0    +      -       +      +
    250A  ILE*     4.0     5.1    -      -       -      +
    251A  GLY*     3.4    22.0    +      -       -      +
    319A  GLN*     2.9    22.7    +      -       +      +
    320A  TYR*     3.6     7.6    -      -       -      +
    321A  GLU*     3.5    48.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  MET*     3.5     9.0    -      -       -      +
    227A  LEU*     1.3    82.4    -      -       +      +
    229A  PHE*     1.3    63.0    +      -       -      +
    230A  SER*     3.3    23.8    +      -       -      -
    250A  ILE*     3.3    11.0    -      -       -      +
    251A  GLY*     4.9     4.5    -      -       -      -
    317A  SER*     3.0    23.5    -      -       -      +
    318A  SER*     3.1    18.5    +      -       -      -
    319A  GLN*     3.1    33.3    +      -       +      +
    360A  ARG*     2.9    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  MET*     3.8    22.2    -      -       +      -
    228A  GLU*     1.3    76.2    -      -       -      +
    230A  SER*     1.3    67.2    +      -       -      +
    248A  VAL*     4.2    12.3    -      -       +      -
    249A  HIS*     3.2     2.8    -      -       -      -
    250A  ILE*     2.8    40.3    +      -       +      +
    298A  PHE*     4.0    33.0    -      +       -      -
    316A  VAL*     4.0    24.0    -      -       +      -
    317A  SER      3.3     6.5    -      -       -      -
    318A  SER*     4.2    10.5    -      -       -      -
    332A  THR*     6.3     2.2    -      -       +      -
    397A  GLN*     3.6    21.8    -      -       -      -
    413A  TYR*     3.6    22.4    -      +       -      -
    502A  MYR      4.2    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  GLU*     3.3    14.1    +      -       -      -
    229A  PHE*     1.3    80.9    -      -       -      +
    231A  ALA*     1.3    59.1    +      -       -      +
    232A  PHE*     4.0    13.7    -      -       -      -
    246A  LEU*     4.3    15.7    -      -       -      +
    248A  VAL      3.3    13.0    -      -       -      -
    249A  HIS*     4.0    10.1    -      -       -      -
    250A  ILE      5.5     0.2    -      -       -      -
    315A  GLY      3.9     0.2    -      -       -      +
    316A  VAL*     3.1     9.1    -      -       -      +
    317A  SER*     2.8    39.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  PHE*     5.1     0.2    -      -       +      -
    230A  SER*     1.3    72.1    -      -       -      +
    232A  PHE*     1.3    61.4    +      -       -      +
    246A  LEU*     3.6     1.7    -      -       -      +
    247A  PHE*     2.8    30.9    +      -       +      -
    248A  VAL*     3.2    30.4    +      -       +      +
    315A  GLY      3.3     8.5    -      -       -      +
    316A  VAL*     4.3     8.3    -      -       +      +
    366A  LEU*     5.5     3.4    -      -       +      -
    502A  MYR      3.9    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  SER*     4.0    14.6    -      -       -      -
    231A  ALA*     1.3    76.1    -      -       -      +
    233A  LEU*     1.3    61.5    +      -       -      +
    234A  GLU*     4.1    11.9    -      -       +      -
    244A  LYS*     3.9    27.8    -      -       +      -
    245A  HIS      3.1    14.6    -      -       -      +
    246A  LEU*     3.6    14.6    -      -       +      -
    247A  PHE*     3.6    11.0    -      -       -      -
    313A  PHE*     4.0    21.8    -      +       -      -
    314A  TYR*     3.4     4.0    -      -       -      +
    315A  GLY*     2.8    56.0    +      -       -      +
    316A  VAL      3.9     1.1    -      -       -      -
    317A  SER*     3.7    22.2    -      -       -      -
    363A  ARG*     3.9    35.2    -      -       +      -
    366A  LEU*     5.5     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  PHE*     1.3    75.6    -      -       -      +
    234A  GLU*     1.3    66.1    +      -       -      +
    235A  GLN*     3.9    23.4    -      -       +      +
    243A  ASN      3.7     1.6    -      -       -      +
    244A  LYS*     3.4     1.4    -      -       -      -
    245A  HIS*     2.8    39.0    +      -       +      +
    247A  PHE*     3.6    17.4    -      -       +      -
    304A  THR*     3.9    25.4    -      -       +      +
    305A  ASN      4.1    13.7    -      -       -      +
    312A  SER*     3.6    33.2    -      -       -      +
    313A  PHE      3.5     6.5    -      -       -      +
    314A  TYR*     3.9    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  PHE*     4.1    13.2    -      -       +      -
    233A  LEU*     1.3    73.0    -      -       -      +
    235A  GLN*     1.3    63.6    +      -       -      +
    236A  GLN      4.2     0.2    +      -       -      -
    242A  TYR*     3.9    39.6    -      -       +      +
    243A  ASN      3.3     9.0    -      -       -      +
    244A  LYS*     4.3    13.4    +      -       +      +
    311A  SER      3.7     0.7    -      -       -      +
    312A  SER*     3.4     3.1    -      -       -      -
    313A  PHE*     2.7    51.0    +      -       +      +
    363A  ARG*     2.7    44.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  LEU*     3.9    17.7    -      -       +      +
    234A  GLU*     1.3    75.7    -      -       -      +
    236A  GLN*     1.3    61.7    +      -       -      +
    237A  GLN      3.4     3.3    +      -       -      +
    242A  TYR*     3.3     3.9    -      -       -      -
    243A  ASN*     2.7    53.2    +      -       +      +
    245A  HIS*     5.9     0.5    -      -       -      +
    304A  THR*     4.0     6.9    +      -       -      -
    305A  ASN*     3.3    49.3    +      -       -      +
    311A  SER*     3.3     7.9    -      -       -      +
    312A  SER*     3.6    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  GLU*     4.2     1.0    -      -       -      +
    235A  GLN*     1.3    69.1    -      -       -      +
    237A  GLN*     1.3    67.6    +      -       -      +
    238A  ASP*     3.3    16.3    -      -       -      +
    239A  PRO*     3.3    30.9    -      -       -      +
    241A  THR      3.6     3.8    -      -       -      -
    242A  TYR*     3.6    34.5    +      -       +      -
    311A  SER*     2.9    40.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  GLN*     3.4     3.8    +      -       -      +
    236A  GLN*     1.3    74.9    -      -       -      +
    238A  ASP*     1.3    68.6    +      -       -      +
    241A  THR*     2.8    34.2    +      -       +      +
    243A  ASN*     2.9    34.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  GLN*     3.3    13.1    -      -       -      +
    237A  GLN*     1.3    85.6    +      -       -      +
    239A  PRO*     1.4    71.4    -      -       +      +
    240A  ASP*     2.8    22.0    +      -       -      +
    241A  THR*     2.7    43.4    +      -       -      +
    242A  TYR*     4.4     0.2    -      -       -      -
----------------------------------------------------------
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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