Contacts of the strand formed by residues 297 - 300 (chain E) 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 THR 297 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151E  ILE*     3.4    11.0    -      -       +      +
    153E  MET*     5.5     2.5    -      -       +      -
    278E  THR*     3.9    27.3    -      -       +      +
    282E  ILE*     5.1     1.9    -      -       -      +
    293E  LEU      3.2    14.9    +      -       -      -
    294E  TYR*     3.8     9.4    +      -       -      -
    296E  ASN*     1.3    73.8    -      -       -      +
    298E  VAL*     1.3    53.8    +      -       -      +
    299E  LEU*     4.7    12.1    -      -       +      -
    313E  MET*     5.2     0.9    -      -       +      -
    317E  ILE*     4.2     6.0    -      -       +      +
    327E  ILE*     5.3     0.9    -      -       -      +
    328E  LYS      3.2    11.6    +      -       -      -
    329E  ILE*     3.3    25.9    -      -       +      +
    330E  ILE*     2.5    35.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 298 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  MET*     4.9     0.2    -      -       -      -
     45C  VAL*     3.0    38.6    -      -       +      +
     46C  GLY*     4.2     0.4    -      -       -      -
    142E  LEU*     4.6     0.2    -      -       +      -
    145E  SER*     5.2     4.0    -      -       -      +
    147E  ARG*     4.2    18.4    -      -       -      +
    151E  ILE      2.9    12.2    +      -       -      +
    152E  VAL*     3.2     6.9    -      -       +      -
    153E  MET*     2.8    28.6    +      -       -      +
    296E  ASN      4.3     5.2    -      -       -      +
    297E  THR*     1.3    74.8    -      -       -      +
    299E  LEU*     1.3    75.2    +      -       -      +
    300E  SER*     5.4     1.3    -      -       -      -
    330E  ILE*     3.4    30.3    -      -       +      +
    332E  PRO*     4.3     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 299 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153E  MET*     3.5    14.4    -      -       +      -
    297E  THR*     4.7    10.5    -      -       +      -
    298E  VAL*     1.3    89.4    -      -       -      +
    300E  SER*     1.3    64.6    +      -       -      +
    304E  THR*     3.8    19.7    -      -       +      +
    309E  ILE*     3.8    34.3    -      -       +      +
    310E  ALA*     4.4    14.8    -      -       -      -
    313E  MET*     3.9    32.1    -      -       +      -
    329E  ILE*     4.6     8.7    -      -       +      -
    330E  ILE      3.1    15.7    +      -       -      +
    331E  ALA*     4.6     7.9    -      -       +      -
    332E  PRO*     4.2     3.1    -      -       -      +
    335E  ARG*     3.9    19.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 300 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141E  SER*     2.8    30.4    +      -       -      -
    152E  VAL*     3.5     9.4    -      -       -      +
    153E  MET      2.9     8.7    +      -       -      +
    154E  ASP*     2.6    31.3    +      -       -      -
    155E  SER      3.0    22.0    +      -       -      -
    298E  VAL*     4.1     2.2    +      -       -      -
    299E  LEU*     1.3    76.4    -      -       -      +
    301E  GLY*     1.3    59.4    +      -       -      +
    304E  THR*     3.1     9.3    -      -       -      +
    335E  ARG*     3.8    10.5    -      -       -      -
    338E  SER*     5.0     1.8    -      -       -      -
----------------------------------------------------------
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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