Contacts of the strand formed by residues 222 - 227 (chain A) in PDB entry 3DB4


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 VAL 222 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  GLY      3.6     5.8    +      -       -      +
    221A  GLN*     1.3    74.8    -      -       -      +
    223A  VAL*     1.3    61.9    +      -       -      +
    240A  ASP*     5.9     2.0    -      -       +      -
    241A  ALA      3.2    11.7    -      -       -      +
    242A  GLU*     4.4    18.8    -      -       +      +
    280A  ILE*     3.6    18.3    +      -       +      +
    282A  ARG*     3.4    39.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  ILE*     3.8    27.6    -      -       +      -
    221A  GLN*     4.0     7.6    -      -       +      -
    222A  VAL*     1.3    80.6    -      -       -      +
    224A  MSE      1.3    59.2    +      -       -      +
    225A  LEU*     3.6    26.7    -      -       +      -
    240A  ASP*     3.2     4.9    -      -       -      -
    241A  ALA      2.8    39.7    +      -       -      +
    243A  ILE*     3.7    29.4    -      -       +      -
    277A  VAL*     3.5    14.4    -      -       +      -
    278A  PHE      3.4     9.0    -      -       -      +
    280A  ILE*     3.7     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with MSE 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  ASP*     4.6     9.9    -      -       -      +
    151A  TRP*     3.8    22.0    -      -       -      +
    205A  ARG*     3.6    19.7    -      -       -      +
    208A  ALA*     3.8    25.1    -      -       +      -
    223A  VAL*     1.3    72.3    -      -       -      +
    225A  LEU*     1.3    63.5    +      -       -      +
    238A  TRP*     3.8    37.7    -      -       +      +
    239A  TYR      3.4    13.5    -      -       -      +
    240A  ASP*     3.7    13.0    -      -       -      +
    277A  VAL*     3.7     0.2    -      -       -      -
    278A  PHE*     2.7    58.5    +      -       +      +
    279A  LYS      5.7     0.2    -      -       -      +
    280A  ILE*     3.8     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  VAL*     3.6    23.8    -      -       +      -
    224A  MSE      1.3    76.4    -      -       -      +
    226A  ASN*     1.3    64.3    +      -       -      +
    227A  TYR*     3.7    11.8    +      -       +      -
    238A  TRP*     3.4    12.3    -      -       -      -
    239A  TYR*     2.9    36.1    +      -       +      +
    241A  ALA*     3.7    27.1    -      -       +      -
    243A  ILE*     5.2     1.1    -      -       +      -
    255A  LEU*     5.0     4.3    -      -       +      -
    257A  ALA*     4.4     4.5    -      -       +      -
    259A  VAL*     4.4     2.7    -      -       +      -
    271A  ILE*     3.7    44.4    -      -       +      -
    273A  PHE      5.3     0.4    -      -       -      +
    276A  GLU      4.6     1.3    -      -       -      -
    277A  VAL*     4.1    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  LEU*     1.3    75.4    -      -       -      +
    227A  TYR*     1.3    65.2    +      -       -      +
    235A  ARG*     3.6    15.3    -      -       -      +
    236A  GLY      2.9    38.7    +      -       -      -
    237A  PHE      3.6     2.7    -      -       -      -
    238A  TRP*     3.1    49.6    -      -       +      +
    271A  ILE*     4.2    11.3    -      -       -      +
    272A  ILE      5.0     0.7    +      -       -      -
    273A  PHE*     3.7    33.8    +      -       +      +
    276A  GLU      5.0     1.0    +      -       -      -
    301A  SO4      3.6    15.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  LEU*     3.7    14.1    +      -       +      -
    226A  ASN*     1.3    76.7    +      -       -      +
    228A  ASN*     1.3    69.6    +      -       -      +
    229A  PRO*     3.7    30.2    +      -       +      +
    232A  PRO*     3.5    39.1    -      -       +      +
    234A  GLU      4.8     2.0    -      -       -      -
    236A  GLY*     4.0     3.4    -      -       -      -
    237A  PHE      2.9    31.0    +      -       -      +
    239A  TYR*     3.5    14.5    -      +       +      -
    259A  VAL*     4.1    15.5    -      -       +      -
    266A  LEU*     4.2    10.7    -      -       +      +
    269A  CYS*     3.5    37.3    -      -       +      +
    270A  ARG      3.7    20.9    +      -       -      -
    271A  ILE*     3.7    18.2    -      -       +      -
    272A  ILE*     5.6     0.9    -      -       +      -
    273A  PHE*     5.4     1.6    -      -       -      -
----------------------------------------------------------
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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