Contacts of the strand formed by residues 237 - 243 (chain A) in PDB entry 6EBT


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 237 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  ARG*     3.3     5.7    -      -       -      -
    234A  THR*     2.9    32.5    +      -       -      +
    235A  HIS*     4.2    12.7    -      -       +      +
    236A  THR*     1.3    86.7    +      -       -      +
    238A  ASP*     1.3    72.2    +      -       -      +
    239A  ALA*     4.0     0.3    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    231A  ILE*     4.1    10.6    -      -       +      +
    232A  GLY      3.7     5.8    -      -       -      -
    233A  ARG*     5.1     7.7    +      -       -      +
    234A  THR*     4.9     0.9    +      -       -      -
    236A  THR      4.9     2.3    -      -       -      +
    237A  GLN*     1.3    80.4    -      -       -      +
    239A  ALA*     1.3    60.3    +      -       -      +
    452A  SER*     4.9     7.0    +      -       -      +
    453A  LEU*     5.5     3.5    +      -       -      +
    454A  MET*     3.5    27.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  ILE*     3.2    18.6    -      -       -      +
    232A  GLY      2.8    18.2    +      -       -      +
    234A  THR*     3.7    22.4    -      -       +      +
    237A  GLN      4.0     0.7    -      -       -      +
    238A  ASP*     1.3    76.1    -      -       -      +
    240A  VAL*     1.3    68.1    +      -       -      +
    454A  MET*     3.3    19.1    -      -       -      +
    278B  ALA*     5.7     2.7    -      -       +      -
    279B  VAL*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  GLY*     3.1    14.6    +      -       -      -
    239A  ALA*     1.3    81.2    -      -       -      +
    241A  PRO*     1.3    75.7    -      -       +      +
    454A  MET*     3.9    23.1    -      -       +      +
    457A  THR*     5.6     3.6    -      -       -      +
    506A  MET*     5.4     2.7    -      -       +      -
    278B  ALA*     4.1    17.9    -      -       +      -
    279B  VAL*     3.7    32.0    -      -       +      +
    281B  THR*     4.7     3.4    -      -       -      +
    283B  LEU*     3.7    29.6    -      -       +      -
    284B  ASN*     5.7     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  ILE*     3.7    19.1    -      -       +      -
    230A  LYS      3.1    18.2    -      -       -      +
    231A  ILE*     4.4     2.7    -      -       +      -
    232A  GLY      4.1     0.9    -      -       -      +
    240A  VAL*     1.3    94.9    -      -       +      +
    242A  LEU*     1.3    65.7    +      -       -      +
    449A  MET*     4.6     6.3    -      -       +      -
    454A  MET      6.0     0.2    -      -       -      +
    455A  LEU*     3.6    31.4    -      -       +      -
    503A  PRO*     4.7     1.8    -      -       +      -
    506A  MET*     4.0    34.0    -      -       +      +
    507A  LEU*     4.1     5.2    -      -       +      -
    279B  VAL*     3.8     3.5    -      -       -      +
    281B  THR*     3.6    13.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  ILE*     4.6     0.2    -      -       -      -
    230A  LYS*     3.0    54.7    +      -       -      +
    232A  GLY*     4.5     4.5    -      -       -      +
    241A  PRO*     1.3    75.2    -      -       -      +
    243A  THR*     1.3    91.1    +      -       -      +
    246A  GLN*     3.4    13.9    -      -       +      +
    247A  GLU*     3.7    16.8    -      -       +      +
    507A  LEU*     3.7     9.2    -      -       -      -
    279B  VAL*     3.7    23.6    -      -       +      +
    281B  THR*     3.6     8.5    -      -       +      -
    312B  PHE*     3.8    10.8    -      -       +      -
    404B  GLU*     3.3    34.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  PHE      4.2     0.4    -      -       -      -
    226A  ALA*     3.3    27.1    +      -       -      +
    227A  GLN      4.8     0.7    -      -       -      -
    228A  ILE      3.2    12.8    -      -       -      +
    229A  ILE*     4.3     9.0    -      -       +      +
    242A  LEU*     1.3    90.7    -      -       -      +
    244A  LEU*     1.3    65.4    +      -       -      +
    245A  GLY*     3.7     3.9    +      -       -      -
    246A  GLN*     2.8    59.0    +      -       -      +
    247A  GLU      3.0     0.7    +      -       -      -
    507A  LEU*     4.0    23.6    -      -       +      -
----------------------------------------------------------
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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