Contacts of the strand formed by residues 297 - 300 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151D  ILE*     3.4    10.3    -      -       +      +
    153D  MET*     5.5     2.2    -      -       +      -
    278D  THR*     3.9    27.8    -      -       +      +
    282D  ILE*     5.1     1.6    -      -       -      +
    293D  LEU      3.2    14.6    +      -       -      -
    294D  TYR*     3.8    10.2    +      -       -      -
    296D  ASN*     1.3    73.6    -      -       -      +
    298D  VAL*     1.3    53.1    +      -       -      +
    299D  LEU*     4.7    12.3    -      -       +      -
    313D  MET*     5.2     0.9    -      -       +      -
    317D  ILE*     4.2     5.9    -      -       +      +
    327D  ILE*     5.3     0.9    -      -       -      +
    328D  LYS      3.2    11.4    +      -       -      -
    329D  ILE*     3.2    25.6    -      -       +      +
    330D  ILE*     2.5    35.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 298 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  VAL*     3.0    38.4    -      -       +      +
     46B  GLY*     4.2     0.4    -      -       -      -
    142D  LEU*     4.6     0.2    -      -       +      -
    145D  SER*     5.2     4.5    -      -       -      +
    147D  ARG*     4.2    18.6    -      -       -      +
    151D  ILE      2.9    12.1    +      -       -      +
    152D  VAL*     3.2     7.1    -      -       +      -
    153D  MET*     2.8    28.6    +      -       -      +
    296D  ASN      4.3     5.4    -      -       -      +
    297D  THR*     1.3    76.0    -      -       -      +
    299D  LEU*     1.3    75.6    +      -       -      +
    300D  SER*     5.4     1.6    -      -       -      -
    330D  ILE*     3.4    29.4    -      -       +      +
    332D  PRO*     4.3     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 299 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153D  MET*     3.5    15.0    -      -       +      -
    297D  THR*     4.7    10.8    -      -       +      -
    298D  VAL*     1.3    88.6    -      -       -      +
    300D  SER*     1.3    64.3    +      -       -      +
    304D  THR*     3.8    20.2    -      -       +      +
    309D  ILE*     3.8    34.1    -      -       +      +
    310D  ALA*     4.4    14.8    -      -       -      -
    313D  MET*     3.9    31.4    -      -       +      -
    329D  ILE*     4.6     9.4    -      -       +      -
    330D  ILE      3.1    14.1    +      -       -      +
    331D  ALA*     4.6     6.7    -      -       +      -
    332D  PRO*     4.2     3.8    -      -       -      +
    335D  ARG*     3.9    18.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 300 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141D  SER*     2.8    31.3    +      -       -      -
    152D  VAL*     3.5     9.0    -      -       -      +
    153D  MET      2.9     8.3    +      -       -      +
    154D  ASP*     2.6    31.2    +      -       -      -
    155D  SER      3.0    21.3    +      -       -      -
    298D  VAL*     4.1     2.0    +      -       -      -
    299D  LEU*     1.3    76.2    -      -       -      +
    301D  GLY*     1.3    60.6    +      -       -      +
    304D  THR*     3.1     9.4    -      -       -      +
    335D  ARG*     3.8     9.4    -      -       -      -
    338D  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