Contacts of the strand formed by residues 233 - 237 (chain V) in PDB entry 3EXG


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 CYS 233 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202V  ARG*     2.9    24.7    +      -       -      +
    203V  GLN      3.2    12.0    -      -       -      +
    204V  GLY*     3.2     1.2    -      -       -      -
    207V  ILE*     3.6    26.0    -      -       +      +
    209V  VAL*     4.4     8.5    -      -       +      -
    223V  ALA*     4.0    30.5    -      -       +      -
    226V  LEU*     4.1    24.9    -      -       -      -
    231V  VAL*     3.6     8.2    +      -       -      -
    232V  GLU*     1.3    74.1    -      -       -      +
    234V  GLU*     1.3    59.5    +      -       -      +
    235V  VAL*     3.7     4.5    -      -       +      -
    323V  ILE*     4.1     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 234 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200V  ILE*     3.5    30.0    -      -       +      +
    202V  ARG      3.3    10.8    -      -       -      +
    203V  GLN*     3.3     7.1    -      -       -      +
    204V  GLY      2.8    39.3    +      -       -      +
    207V  ILE      2.8    16.8    +      -       -      +
    208V  THR*     4.0     1.0    -      -       -      -
    209V  VAL      3.3    18.1    +      -       -      +
    232V  GLU      4.0     0.2    +      -       -      -
    233V  CYS*     1.3    71.7    -      -       -      +
    235V  VAL*     1.3    65.1    +      -       -      +
    236V  ILE*     3.3     7.9    +      -       +      +
    252V  SER*     3.1    33.6    +      -       -      +
    255V  LYS*     2.8    23.8    +      -       -      -
    256V  THR*     4.6     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 235 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200V  ILE*     3.7     1.4    -      -       -      -
    201V  GLU*     2.9    27.0    +      -       +      -
    202V  ARG*     3.4    33.7    +      -       +      +
    209V  VAL*     3.4    12.8    -      -       +      +
    211V  SER*     5.8     0.7    -      -       -      -
    216V  VAL*     4.6     8.5    -      -       +      +
    219V  CYS*     3.6    28.5    -      -       +      -
    220V  LEU*     3.8    30.3    -      -       +      +
    223V  ALA*     4.0    14.1    -      -       +      -
    233V  CYS*     3.7     5.8    -      -       +      -
    234V  GLU*     1.3    71.6    -      -       -      +
    236V  ILE*     1.3    68.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 236 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198V  ALA*     4.2    21.8    -      -       +      -
    199V  LYS      3.8     4.5    -      -       -      +
    200V  ILE*     4.1    16.2    -      -       +      -
    208V  THR*     3.6    17.7    -      -       +      -
    209V  VAL      2.7    14.2    +      -       -      +
    210V  VAL*     3.8    10.3    -      -       +      -
    211V  SER*     3.2    24.6    +      -       -      +
    216V  VAL*     4.7     0.5    -      -       -      +
    234V  GLU*     3.7     7.0    -      -       +      +
    235V  VAL*     1.3    83.1    -      -       -      +
    237V  ASN*     1.3    65.3    +      -       -      +
    238V  MET*     4.5     1.6    -      -       -      +
    248V  THR*     4.3    17.7    -      -       +      -
    249V  ILE*     4.4    17.3    -      -       +      -
    252V  SER*     3.6    31.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 237 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146V  SER      5.0     1.6    +      -       -      -
    148V  TRP*     4.0     9.0    +      -       -      +
    152V  ASP*     3.0    28.9    -      -       -      +
    198V  ALA*     3.4     2.5    -      -       -      +
    199V  LYS*     2.8    34.3    +      -       +      +
    201V  GLU*     3.2    32.0    -      -       +      +
    211V  SER      3.6     8.3    +      -       -      -
    212V  HIS*     4.3     4.6    -      -       -      +
    213V  SER      4.9     0.8    -      -       -      +
    216V  VAL*     3.8    20.3    -      -       +      +
    235V  VAL      4.3     0.4    +      -       -      -
    236V  ILE*     1.3    71.7    -      -       -      +
    238V  MET*     1.3    65.9    +      -       -      +
    239V  ARG*     3.5    21.6    +      -       -      +
----------------------------------------------------------
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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