Contacts of the strand formed by residues 356 - 359 (chain W) 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 LYS 356 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347W  GLU*     3.4    37.0    -      -       +      +
    348W  VAL      3.7     5.8    -      -       -      +
    349W  ARG*     5.1     0.7    -      -       -      +
    353W  GLN      3.8    20.4    +      -       -      +
    354W  TRP*     3.6    12.7    +      -       -      +
    355W  ILE*     1.3    79.0    -      -       -      +
    357W  PHE*     1.3    64.0    +      -       -      +
    358W  LYS      4.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 357 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298V  ALA*     5.1     0.4    -      -       +      -
    311V  ASN*     4.7    12.1    -      -       +      -
    332W  LEU*     3.5    48.2    -      -       +      -
    333W  GLU*     4.5    11.0    -      -       -      -
    335W  LEU*     3.4    31.9    -      -       +      -
    336W  GLY*     4.4    15.5    -      -       -      -
    347W  GLU*     3.3     5.6    -      -       -      -
    348W  VAL*     2.6    50.4    +      -       +      +
    349W  ARG      5.0     1.3    -      -       -      -
    350W  GLY*     4.4    11.0    -      -       -      -
    355W  ILE*     3.4    28.9    -      -       +      -
    356W  LYS*     1.3    75.5    -      -       -      +
    358W  LYS*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 358 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333W  GLU      4.4     4.5    +      -       -      +
    336W  GLY*     3.6    10.5    +      -       -      -
    337W  TYR*     3.3    33.4    +      -       +      +
    345W  PRO*     4.4    12.2    -      -       +      +
    346W  PHE*     3.7     9.6    -      -       -      +
    347W  GLU*     4.6     7.4    -      -       +      +
    356W  LYS      4.3     0.4    +      -       -      -
    357W  PHE*     1.3    73.5    -      -       -      +
    359W  SER*     1.3    61.1    +      -       -      +
    360W  VAL*     3.3    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 359 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336W  GLY      3.1    23.3    +      -       -      -
    338W  HIS      4.3     0.2    +      -       -      -
    339W  ILE*     3.6    13.3    +      -       -      +
    340W  TYR      4.9     0.3    +      -       -      -
    345W  PRO*     3.3     5.0    -      -       -      +
    346W  PHE*     2.6    64.7    +      -       -      -
    348W  VAL*     3.5    19.7    -      -       -      -
    357W  PHE      3.7     0.2    +      -       -      -
    358W  LYS*     1.3    73.2    -      -       -      +
    360W  VAL*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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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