Contacts of the strand formed by residues 8 - 12 (chain F) 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 LEU 8 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7F  ALA*     1.3    74.1    -      -       -      +
      9F  VAL*     1.3    62.1    +      -       -      +
     10F  VAL*     3.7     5.2    +      -       +      +
     20F  GLY      3.1    10.8    -      -       -      +
     21F  PHE*     3.2    33.0    -      -       +      -
     90F  PHE*     3.3    39.9    -      -       +      -
     94F  LEU*     4.7    10.1    -      -       +      -
     96F  VAL*     3.3    17.3    -      -       +      -
     97F  ALA      5.5     0.4    -      -       -      +
     98F  PRO*     5.7     1.3    -      -       +      -
    101F  HIS*     3.7    34.5    -      -       +      +
    102F  PRO      3.1     5.6    +      -       -      +
    103F  VAL*     3.6    11.7    -      -       +      +
    104F  LEU      3.2    20.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 9 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  LEU*     1.3    72.8    -      -       -      +
     10F  VAL*     1.3    63.1    +      -       -      +
     19F  ALA*     3.2     5.5    -      -       -      -
     20F  GLY      2.9    26.9    +      -       -      -
     22F  ALA*     4.2    15.9    -      -       +      +
    104F  LEU*     3.7    31.0    -      -       +      +
    106F  THR*     5.1     4.3    -      -       +      -
    340F  TRP*     3.2    28.5    +      -       +      +
    343F  GLY*     3.8    14.1    -      -       -      +
    344F  SER*     3.4    33.0    -      -       -      +
    347F  ALA*     4.8     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 10 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  LEU*     4.5    10.3    -      -       +      +
      9F  VAL*     1.3    76.3    -      -       -      +
     11F  ASP*     1.3    62.2    -      -       -      +
     12F  ASN*     3.6    24.7    +      -       -      +
     17F  CYS*     5.9     3.6    -      -       +      -
     18F  LYS      3.7     3.8    -      -       -      +
     19F  ALA*     4.4     3.1    -      -       +      +
     86F  TRP*     3.7    18.6    -      -       +      +
     89F  THR*     3.9    28.3    -      -       +      +
     90F  PHE*     4.5    17.0    -      -       +      -
    103F  VAL*     5.5     1.8    -      -       +      -
    104F  LEU      3.0     8.1    +      -       -      +
    105F  LEU*     3.4    18.0    -      -       +      -
    106F  THR*     2.9    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 11 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9F  VAL*     4.1     1.0    -      -       +      -
     10F  VAL*     1.3    73.7    -      -       -      +
     12F  ASN*     1.3    65.7    +      -       -      +
     13F  GLY*     3.7     1.0    +      -       -      -
     17F  CYS*     3.3     9.9    -      -       -      +
     18F  LYS*     2.8    65.0    +      -       +      +
    106F  THR*     2.7    25.5    +      -       +      +
    137F  GLN*     4.1     7.1    -      -       -      +
    339F  VAL*     3.4    33.5    -      -       +      +
    340F  TRP*     4.1    13.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 12 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10F  VAL*     3.6    22.0    +      -       -      +
     11F  ASP*     1.3    75.1    +      -       -      +
     13F  GLY*     1.3    60.3    -      -       -      +
     14F  SER      4.3     0.3    +      -       -      -
     17F  CYS*     4.3     6.1    -      -       -      -
     71F  ILE*     4.0    23.7    -      -       +      +
     74F  GLY*     5.0     3.3    -      -       -      +
     76F  VAL*     6.0     1.1    -      -       +      -
     82F  MET*     3.2    11.3    -      -       +      +
     86F  TRP*     2.9    40.8    +      -       -      -
    105F  LEU*     4.3     4.6    -      -       -      +
    106F  THR*     3.4    25.1    +      -       -      +
    119F  MET*     5.7     0.6    -      -       -      -
    137F  GLN*     4.0    17.8    +      -       -      -
    157F  ASP*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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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