Contacts of the strand formed by residues 233 - 237 (chain 6) 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 6).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2026  ARG*     2.8    32.5    +      -       -      +
    2046  GLY*     3.4     4.7    -      -       -      -
    2076  ILE*     3.2    26.9    -      -       -      +
    2096  VAL*     3.7    15.5    -      -       +      -
    2236  ALA*     4.2    17.5    -      -       +      +
    2266  LEU*     3.8    27.4    -      -       -      -
    2316  VAL*     3.9     6.2    +      -       -      -
    2326  GLU*     1.3    74.3    -      -       -      +
    2346  GLU*     1.3    63.4    +      -       -      +
    2356  VAL*     3.4    11.1    +      -       +      -
    3236  ILE*     4.2     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 234 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2006  ILE*     3.9    26.6    -      -       +      +
    2026  ARG      3.1    11.9    -      -       -      +
    2036  GLN*     3.6     6.9    -      -       -      +
    2046  GLY*     2.8    28.6    +      -       -      +
    2076  ILE      2.8    10.0    +      -       -      +
    2086  THR*     3.6     2.0    -      -       -      +
    2096  VAL      2.8    25.6    +      -       -      +
    2336  CYS*     1.3    71.4    -      -       -      +
    2356  VAL*     1.3    58.6    +      -       -      +
    2366  ILE*     3.9     5.6    +      -       +      -
    2526  SER*     2.9    44.5    +      -       -      +
    2556  LYS*     2.6    34.0    +      -       -      -
    2566  THR*     4.7     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 235 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2006  ILE*     3.6     5.7    -      -       -      +
    2016  GLU*     2.9    30.7    +      -       +      -
    2026  ARG*     3.0    14.3    +      -       +      -
    2096  VAL*     3.3    20.0    -      -       +      +
    2116  SER*     6.1     0.9    -      -       -      +
    2166  VAL*     4.7     8.3    -      -       +      -
    2196  CYS*     4.0    33.7    -      -       +      +
    2206  LEU*     3.6    30.5    -      -       +      -
    2236  ALA*     4.2    13.5    -      -       +      -
    2336  CYS*     3.4     5.7    +      -       +      -
    2346  GLU*     1.3    74.5    -      -       -      +
    2366  ILE*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 236 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1986  ALA*     3.9    24.2    -      -       +      -
    1996  LYS      3.5    11.0    -      -       -      +
    2006  ILE*     4.6     5.4    -      -       +      +
    2086  THR*     3.7    27.4    -      -       +      -
    2096  VAL      2.7    16.0    +      -       -      +
    2106  VAL*     3.6    10.7    -      -       +      +
    2116  SER*     3.0    28.1    +      -       -      +
    2166  VAL*     5.0     0.3    -      -       -      +
    2346  GLU*     4.3    10.1    -      -       +      +
    2356  VAL*     1.3    83.2    -      -       -      +
    2376  ASN*     1.3    64.4    +      -       -      +
    2386  MET      3.6     0.8    +      -       -      +
    2486  THR*     4.1    11.2    -      -       +      +
    2496  ILE*     4.1    23.6    -      -       +      -
    2526  SER*     3.9    16.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 237 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1466  SER      5.0     1.6    +      -       -      -
    1486  TRP*     4.0     6.7    -      -       -      +
    1526  ASP*     3.0    29.4    +      -       -      +
    1986  ALA*     3.4     0.3    -      -       -      -
    1996  LYS*     2.7    39.7    +      -       +      +
    2016  GLU*     3.3    33.8    -      -       +      +
    2116  SER      3.7     3.5    +      -       -      -
    2126  HIS*     4.6     4.0    -      -       -      +
    2136  SER      4.9     1.0    -      -       -      +
    2166  VAL*     3.9    25.0    -      -       +      +
    2356  VAL      4.3     0.6    +      -       -      -
    2366  ILE*     1.3    73.1    -      -       -      +
    2386  MET*     1.3    65.9    +      -       -      +
    2396  ARG*     3.1    22.2    +      -       -      +
----------------------------------------------------------
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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