Contacts of the strand formed by residues 234 - 239 (chain A) in PDB entry 3SRG


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 TYR 234 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  ILE*     3.3     8.2    -      -       -      +
    229A  SER*     2.9    39.2    +      -       -      +
    231A  ASP*     4.3     8.1    -      -       -      -
    232A  GLY      3.6     0.6    -      -       -      -
    233A  LYS*     1.4   105.4    -      -       +      +
    235A  VAL*     1.3    63.1    +      -       -      +
    236A  TYR*     4.0    25.6    -      -       +      +
    247A  VAL*     4.3     2.2    -      -       +      -
    248A  TYR      3.1    14.4    -      -       -      +
    249A  GLU*     3.9    17.7    +      -       +      -
    250A  LYS      4.2     0.2    -      -       -      +
    259A  LEU*     3.7    30.2    -      -       +      +
    311A  LEU*     3.6    34.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  VAL*     5.5     1.3    -      -       +      -
    179A  TYR*     4.6    10.8    -      -       +      -
    226A  ILE*     4.0    14.8    -      -       +      -
    227A  ASN      3.4     9.2    -      -       -      +
    228A  ILE*     4.2     9.9    -      -       +      -
    234A  TYR*     1.3    79.2    -      -       -      +
    236A  TYR*     1.3    64.8    -      -       -      +
    237A  ILE*     3.9    21.1    -      -       +      -
    246A  HIS      3.7     0.5    -      -       -      +
    247A  VAL*     3.5     3.5    -      -       -      -
    248A  TYR*     2.8    34.0    +      -       +      +
    250A  LYS*     3.7    28.0    -      -       +      -
    256A  LEU*     4.0    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  ILE*     3.2     5.9    -      -       -      +
    227A  ASN*     2.9    34.8    +      -       +      +
    228A  ILE      3.9     1.8    -      -       -      -
    229A  SER*     3.6    36.0    -      -       -      -
    234A  TYR*     4.0    18.2    -      -       +      +
    235A  VAL*     1.3    75.1    -      -       -      +
    237A  ILE*     1.3    65.6    +      -       -      +
    245A  ILE*     4.4     1.6    -      -       +      -
    246A  HIS      3.2     4.5    -      -       -      +
    247A  VAL*     3.9    29.4    -      -       +      -
    271A  ILE*     3.7    18.6    -      -       +      +
    273A  VAL*     3.9    22.7    -      -       +      -
    278A  GLY      4.5     4.6    +      -       -      -
    280A  LEU*     3.8    32.9    -      -       +      +
    310A  ILE*     3.8    28.5    -      -       +      +
    311A  LEU*     5.7     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  THR*     4.1    13.9    -      -       +      -
    205A  VAL*     3.8    29.4    -      -       +      -
    217A  ALA*     4.7     1.1    -      -       +      -
    220A  PHE*     4.0    21.8    -      -       +      -
    223A  ALA*     4.2     3.1    -      -       +      -
    225A  GLY      3.4     7.6    -      -       -      +
    226A  ILE*     4.0     7.6    -      -       +      -
    235A  VAL*     3.9    17.3    -      -       +      -
    236A  TYR*     1.3    81.7    -      -       -      +
    238A  ALA*     1.3    71.9    +      -       -      +
    245A  ILE*     3.3     2.7    -      -       -      +
    246A  HIS*     2.8    41.0    +      -       +      +
    248A  TYR*     3.8    30.5    -      -       +      -
    256A  LEU*     4.4     5.6    -      -       +      -
    271A  ILE*     3.9     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  ALA*     3.3     4.2    -      -       -      -
    224A  ASN*     2.8    26.6    +      -       +      -
    225A  GLY      2.8    13.2    +      -       -      +
    237A  ILE*     1.3    76.2    -      -       -      +
    239A  GLU*     1.3    59.5    +      -       -      +
    240A  LEU      3.7     0.4    -      -       -      -
    244A  LYS      3.6     5.4    -      -       -      -
    245A  ILE*     4.3     2.5    -      -       +      -
    268A  VAL*     3.8    20.4    -      -       +      +
    269A  ASP      3.3    26.9    -      -       -      +
    271A  ILE*     3.6    15.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  ALA*     5.4     0.2    -      -       -      +
    219A  GLY      4.2     3.5    -      -       -      +
    220A  PHE*     3.4    19.5    -      -       +      -
    221A  ASP*     2.6    45.5    +      -       -      +
    222A  PHE      3.8     2.7    -      -       -      -
    223A  ALA*     4.3     1.3    -      -       -      +
    238A  ALA*     1.3    71.6    -      -       -      +
    240A  LEU*     1.3    65.6    +      -       -      +
    242A  ALA*     3.2    23.9    +      -       +      +
    243A  HIS*     3.0    18.7    +      -       -      -
    244A  LYS*     2.8    24.5    +      -       +      +
    246A  HIS*     2.6    40.0    +      -       +      +
    268A  VAL*     3.9     1.0    -      -       -      +
----------------------------------------------------------
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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