Contacts of the strand formed by residues 229 - 238 (chain A) in PDB entry 5DQE


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 GLN 229 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  LEU      3.9     5.4    -      -       -      +
    224A  GLY*     4.6     2.9    -      -       -      -
    225A  THR      2.9    29.4    +      -       -      +
    226A  ALA*     3.4    15.6    +      -       -      +
    227A  ARG      4.1     0.6    -      -       -      -
    228A  LEU*     1.3    77.8    -      -       -      +
    230A  LEU*     1.3    66.3    +      -       -      +
    231A  VAL*     3.6     0.7    +      -       -      +
    333A  TYR*     3.1     9.1    -      -       -      +
    334A  GLU*     2.8    63.8    +      -       +      +
    335A  SER*     4.9     4.2    -      -       -      +
    336A  LEU      5.9     0.2    -      -       -      +
    422A  LEU*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  LEU*     2.9    53.7    +      -       +      +
    224A  GLY*     4.5     0.2    -      -       -      -
    228A  LEU      4.3     0.4    +      -       -      -
    229A  GLN*     1.3    74.5    -      -       -      +
    231A  VAL*     1.3    61.1    +      -       -      +
    232A  GLU      3.8    17.0    -      -       -      +
    233A  PHE*     4.2    21.3    -      -       +      -
    254A  ILE*     4.2    19.1    -      -       +      -
    256A  GLN*     3.0    25.4    -      -       -      +
    331A  SER*     4.9     2.5    -      -       -      -
    332A  GLN      3.6    16.2    -      -       -      +
    333A  TYR*     3.8    33.4    -      -       +      +
    422A  LEU*     4.7     1.6    -      -       +      +
    426A  TYR*     5.0     6.3    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    229A  GLN*     3.6     3.1    +      -       +      +
    230A  LEU*     1.3    78.0    -      -       -      +
    232A  GLU*     1.3    64.7    +      -       +      +
    255A  SER*     3.7     0.9    +      -       -      -
    256A  GLN*     2.8    44.1    +      -       -      +
    332A  GLN*     2.7    40.1    +      -       +      +
    333A  TYR      4.5     0.7    -      -       -      -
    334A  GLU*     3.1    48.2    -      -       +      +
    369A  ARG*     6.3     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  LEU*     3.8     5.6    -      -       -      +
    231A  VAL*     1.3    84.0    -      -       +      +
    233A  PHE*     1.3    62.8    +      -       -      +
    234A  SER*     5.7     1.6    -      -       -      -
    253A  HIS*     2.9    28.0    +      -       +      +
    254A  ILE      3.1    18.8    -      -       -      +
    255A  SER*     3.5    17.5    +      -       -      +
    330A  SER      3.9     0.4    -      -       -      +
    331A  SER*     3.3     4.2    -      -       -      -
    332A  GLN*     2.9    40.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  LEU*     4.2    21.1    -      -       +      -
    232A  GLU*     1.3    75.8    -      -       -      +
    234A  SER*     1.3    66.5    +      -       -      +
    252A  VAL*     3.9    20.4    -      -       +      -
    253A  HIS*     3.2     5.4    -      -       -      -
    254A  ILE*     2.7    48.6    +      -       +      +
    302A  PHE*     4.3    16.8    -      +       -      -
    329A  VAL*     3.6    25.8    -      -       +      -
    330A  SER      3.5    10.3    -      -       -      -
    331A  SER*     3.9    14.1    -      -       -      -
    333A  TYR*     6.0     0.2    -      -       -      -
    410A  GLN*     4.5    15.3    -      -       -      -
    426A  TYR*     4.6     9.2    -      -       -      -
    501A  5E4      3.4    47.6    -      +       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    232A  GLU*     5.7     2.2    -      -       -      -
    233A  PHE*     1.3    83.8    -      -       -      +
    235A  ALA*     1.3    60.4    +      -       -      +
    236A  PHE*     3.6    17.8    -      -       -      -
    248A  ARG*     4.3     5.5    +      -       -      -
    250A  LEU*     4.1    13.5    -      -       -      -
    252A  VAL      3.3     9.0    -      -       -      -
    253A  HIS*     3.8    17.0    -      -       -      -
    329A  VAL*     3.5     5.0    -      -       -      +
    330A  SER*     3.0    37.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  PHE*     4.6     1.3    -      -       +      -
    234A  SER*     1.3    72.8    -      -       -      +
    236A  PHE*     1.3    58.4    +      -       -      +
    250A  LEU*     3.6     1.6    -      -       -      +
    251A  PHE*     2.8    38.6    +      -       +      -
    252A  VAL*     3.1    22.6    +      -       +      +
    328A  GLY      3.5     8.5    -      -       -      +
    329A  VAL*     4.2     7.2    -      -       +      -
    379A  MET*     4.2     6.1    -      -       +      -
    501A  5E4      3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  SER*     3.6    20.2    -      -       -      -
    235A  ALA*     1.3    74.1    -      -       -      +
    237A  VAL*     1.3    67.1    +      -       -      +
    238A  GLU*     3.9    18.8    -      -       +      -
    248A  ARG*     3.5    51.1    -      -       -      -
    249A  HIS      3.1    15.5    -      -       -      +
    250A  LEU*     3.8    12.8    -      -       +      -
    251A  PHE*     3.7    12.4    -      -       -      -
    326A  PHE*     4.5     7.0    -      +       -      -
    327A  TYR*     3.5     3.3    -      -       -      -
    328A  GLY*     3.0    58.3    +      -       -      +
    329A  VAL      4.1     1.1    -      -       -      -
    330A  SER*     3.7    20.4    -      -       -      -
    376A  ARG*     4.1     9.2    -      -       +      -
    379A  MET*     4.2     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  PHE*     1.3    75.8    -      -       -      +
    238A  GLU*     1.3    76.4    +      -       -      +
    239A  PRO*     4.7     0.5    -      -       -      +
    247A  GLN      4.4     0.2    -      -       -      +
    248A  ARG*     3.7     3.6    -      -       -      +
    249A  HIS*     3.0    43.9    +      -       +      +
    251A  PHE*     3.6    20.6    -      -       +      -
    308A  TRP*     4.0    24.5    -      -       +      +
    325A  GLY*     5.0     1.8    -      -       -      -
    326A  PHE      3.4     9.6    -      -       -      +
    327A  TYR*     3.7    37.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  PHE*     4.0     8.5    -      -       +      -
    237A  VAL*     1.3    82.3    -      -       -      +
    239A  PRO*     1.3    72.9    -      -       +      +
    247A  GLN      4.0     5.8    -      -       -      +
    248A  ARG*     2.7    49.0    +      -       +      +
    325A  GLY*     3.8     2.4    -      -       -      -
    326A  PHE*     2.9    38.3    +      -       +      +
    376A  ARG*     2.3    34.8    +      -       -      -
----------------------------------------------------------
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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