Contacts of the strand formed by residues 61 - 66 (chain B) in PDB entry 1LUA


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 61 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LEU*     3.4    14.2    -      -       -      +
      7B  PHE*     4.0    19.3    -      -       +      -
     49B  THR*     3.8    36.5    +      -       +      +
     52B  THR*     5.3     0.2    +      -       -      -
     53B  ARG*     3.0    31.7    +      -       -      +
     58B  LYS*     3.1    17.4    +      -       -      +
     59B  GLN*     4.0     4.9    -      -       -      +
     60B  SER*     1.3    77.8    -      -       -      +
     62B  ALA*     1.3    67.7    +      -       -      +
     90B  VAL*     3.5    17.3    -      -       +      +
     91B  SER      4.4     1.7    +      -       -      -
    267B  LEU      4.9     0.7    -      -       -      +
    268B  PHE*     4.1     0.4    -      -       -      -
     21C  VAL*     4.6     4.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LEU      3.0     7.4    +      -       -      +
      6B  LEU*     3.6    10.9    -      -       +      -
      7B  PHE*     2.9    27.7    +      -       -      +
     61B  THR*     1.3    76.4    -      -       -      +
     63B  ILE*     1.3    66.4    +      -       -      +
     90B  VAL*     4.3     2.9    -      -       -      -
     91B  SER      3.5    13.7    -      -       -      +
    267B  LEU*     3.8    32.1    -      -       +      +
    268B  PHE*     3.8    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     4.3     2.7    -      -       -      -
      7B  PHE*     3.5     4.0    -      -       +      +
      9B  PHE*     3.6    34.8    -      -       +      -
     46B  VAL*     4.0    25.4    -      -       +      -
     49B  THR*     3.8    22.9    -      -       +      +
     62B  ALA*     1.3    80.4    -      -       -      +
     64B  PHE*     1.3    67.3    +      -       -      +
     65B  VAL*     4.2     9.2    -      -       +      -
     80B  VAL*     4.1    13.9    -      -       +      -
     84B  PHE*     4.6     1.3    -      -       +      -
     90B  VAL*     3.7    22.7    -      -       +      -
     91B  SER      3.0    10.6    +      -       -      +
     92B  CYS*     3.1    12.5    -      -       +      -
     93B  MET*     2.9    25.8    +      -       -      +
    267B  LEU*     4.2     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     4.1    24.2    -      -       +      +
      7B  PHE      3.0     8.8    +      -       -      +
      8B  GLN*     3.4    16.0    -      -       +      -
      9B  PHE*     2.9    27.0    +      -       -      +
     19B  ASP*     3.4    42.6    -      -       +      -
     63B  ILE*     1.3    74.5    -      -       -      +
     65B  VAL*     1.3    72.3    +      -       -      +
     66B  GLY*     3.9     7.0    -      -       -      -
     93B  MET*     3.4    29.8    -      -       +      -
     95B  ASP*     3.8    31.6    -      -       +      -
    260B  HIS*     3.7    20.6    -      +       -      -
    264B  ILE*     4.0    10.1    -      -       +      -
    267B  LEU*     5.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  PHE*     3.3    14.4    -      -       +      +
     11B  THR*     5.2     1.6    -      -       +      -
     63B  ILE*     4.2    14.8    -      -       +      -
     64B  PHE*     1.3    79.5    -      -       -      +
     66B  GLY*     1.3    63.8    +      -       -      +
     73B  GLY*     3.7    30.5    -      -       -      +
     76B  VAL*     4.1    26.0    -      -       +      -
     77B  PHE*     4.0    18.4    -      -       +      -
     80B  VAL*     4.3     8.1    -      -       +      -
     93B  MET      2.8    12.9    +      -       -      +
     94B  LEU*     3.5    12.4    -      -       +      +
     95B  ASP      2.9    27.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  GLN*     5.9     0.4    -      -       -      +
      9B  PHE      3.0     8.4    +      -       -      +
     10B  ASP*     3.3     8.5    -      -       -      -
     11B  THR*     3.1    26.5    +      -       -      +
     19B  ASP*     4.4     3.4    -      -       -      -
     64B  PHE*     3.9    17.1    -      -       -      -
     65B  VAL*     1.3    75.0    -      -       -      +
     67B  GLY*     1.3    58.4    +      -       -      -
     95B  ASP      4.4     0.7    -      -       -      -
     96B  SER*     3.7    20.2    +      -       -      -
----------------------------------------------------------
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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