Contacts of the strand formed by residues 16 - 21 (chain J) in PDB entry 3LUE


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 MET 16 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13J  GLY*     3.0    19.2    +      -       -      -
     14J  SER      3.7     0.4    -      -       -      -
     15J  GLY*     1.3    86.5    -      -       -      +
     17J  CYS*     1.3    57.6    +      -       -      +
     18J  LYS*     2.9    32.7    +      -       +      +
     30J  VAL*     3.5    28.9    -      -       +      +
     31J  PHE*     3.5    23.3    -      -       -      +
     32J  PRO*     4.1    12.1    -      -       +      -
     33J  SER*     3.7     5.2    -      -       -      -
    210J  ARG*     4.8    10.5    -      -       -      +
    336J  LYS*     4.3    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 17 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10J  VAL*     5.9     3.4    -      -       +      -
     11J  ASP      3.3    12.8    -      -       -      +
     12J  ASN*     4.3    13.0    -      -       -      -
     16J  MET*     1.3    72.9    -      -       -      +
     18J  LYS*     1.3    63.2    +      -       -      +
     19J  ALA*     6.1     0.4    -      -       +      -
     29J  ALA      3.7     0.8    -      -       -      +
     30J  VAL*     3.3     3.6    -      -       -      +
     31J  PHE*     2.8    57.4    +      -       +      -
     33J  SER*     3.0    24.7    -      -       -      -
     71J  ILE*     4.4     7.0    -      -       -      -
     85J  ILE*     3.9    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 18 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10J  VAL*     5.0     0.3    -      -       -      +
     11J  ASP*     2.8    61.9    +      -       +      +
     13J  GLY*     4.4     5.7    -      -       -      -
     16J  MET*     2.9    32.6    +      -       +      +
     17J  CYS*     1.3    77.2    -      -       -      +
     19J  ALA*     1.3    59.2    +      -       -      +
     27J  PRO*     3.6    22.4    -      -       +      -
     29J  ALA      3.2     6.5    -      -       -      -
     30J  VAL*     4.0     8.7    -      -       +      +
    336J  LYS*     3.5    28.0    -      -       -      +
    337J  TYR*     3.9    20.9    -      -       +      -
    340J  TRP*     3.3    17.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 19 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9J  VAL      3.2    10.5    -      -       -      +
     10J  VAL*     4.4     5.2    -      -       +      -
     17J  CYS*     6.1     0.7    -      -       +      -
     18J  LYS*     1.3    74.5    -      -       -      +
     20J  GLY*     1.3    59.0    +      -       -      +
     27J  PRO*     4.3     1.0    -      -       -      +
     28J  ARG      3.1     4.7    +      -       -      -
     29J  ALA*     3.0    36.3    +      -       +      +
     31J  PHE*     4.9     4.9    -      -       +      -
     89J  THR*     3.7    20.2    -      -       +      -
     94J  LEU*     3.6    26.2    -      -       +      +
    340J  TRP*     3.7     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 20 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8J  LEU*     3.1    11.6    -      -       -      +
      9J  VAL      2.9    25.8    +      -       -      -
     19J  ALA*     1.3    76.9    -      -       -      +
     21J  PHE*     1.3    69.4    +      -       -      -
     24J  ASP*     5.2     0.2    -      -       -      -
     28J  ARG*     4.2     9.0    -      -       -      -
     94J  LEU*     3.9    11.9    -      -       -      +
    340J  TRP*     3.4    16.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 21 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3J  ASP*     3.4    34.5    -      -       -      -
      4J  ASP*     5.9     0.7    -      -       -      -
      6J  ALA*     4.5     6.5    -      -       +      -
      7J  ALA      3.6     2.9    -      -       -      +
      8J  LEU*     3.2    35.4    -      -       +      -
     20J  GLY*     1.3    78.9    -      -       -      -
     22J  ALA*     1.3    69.9    -      -       -      +
     24J  ASP*     3.1    36.6    +      -       -      +
     28J  ARG*     3.3    40.4    -      -       -      +
     94J  LEU*     4.3    26.9    -      -       +      -
     96J  VAL*     3.8    21.5    -      -       +      -
    101J  HIS*     5.3     0.9    -      +       -      -
    340J  TRP*     3.8     9.4    -      -       -      -
----------------------------------------------------------
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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