Contacts of the strand formed by residues 20 - 27 (chain E) in PDB entry 1LNU


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 ILE 20 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13E  VAL*     4.4     1.0    -      -       -      +
     14E  TYR*     3.1     8.9    -      -       -      -
     15E  GLN*     2.8    57.2    +      -       +      +
     17E  PRO      3.3    23.1    -      -       -      +
     18E  GLY*     3.0    17.9    -      -       -      +
     19E  ASP*     1.3    71.3    -      -       -      +
     21E  GLY*     1.3    63.3    +      -       -      +
    116E  PRO      5.2     3.8    -      -       -      +
    117E  VAL*     4.3    19.5    -      -       +      -
    169E  TRP*     5.9     2.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 21 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13E  VAL      3.3     8.3    -      -       -      -
     14E  TYR*     3.9     9.4    -      -       -      -
     19E  ASP      3.8     4.4    +      -       -      -
     20E  ILE*     1.3    79.6    -      -       -      +
     22E  GLN*     1.3    62.1    +      -       -      +
     37E  LEU*     3.3    30.3    -      -       -      +
     64E  ILE*     4.9     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 22 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  ILE*     3.5     4.4    -      -       -      +
     12E  SER*     3.6     1.0    -      -       -      -
     13E  VAL*     3.0    49.1    +      -       +      +
     21E  GLY*     1.3    74.5    -      -       -      +
     23E  TYR*     1.3    60.9    +      -       -      +
     24E  THR*     3.4    27.4    +      -       +      +
     34E  TYR*     5.6     2.5    -      -       +      -
     35E  VAL      5.8     0.4    -      -       -      -
     37E  LEU*     3.9     3.3    -      -       -      +
     64E  ILE*     3.9     4.3    -      -       -      +
    137E  SER*     3.9     8.6    -      -       -      +
    138E  PHE*     3.0    68.2    +      -       +      +
    146E  PHE*     5.7     1.2    -      -       -      -
    148E  LYS*     5.6     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 23 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  GLY*     2.9    26.8    -      -       -      -
     11E  ILE      3.3     2.9    -      -       -      -
     12E  SER*     3.1    29.8    -      -       -      -
     22E  GLN*     1.3    74.2    -      -       -      +
     24E  THR*     1.3    67.5    +      -       -      +
     25E  PHE*     3.3    25.8    -      +       -      -
     33E  PHE*     5.0     0.4    -      +       -      -
     34E  TYR*     3.4     1.4    -      -       -      +
     35E  VAL*     3.1    39.9    +      -       +      -
     37E  LEU*     4.3    14.7    -      -       +      +
     55E  PHE*     4.0    11.9    -      +       -      -
     59E  GLY      4.7     0.2    -      -       -      -
     60E  GLY*     3.6    33.2    -      -       -      -
     63E  ASN*     3.4    17.7    -      -       +      -
     64E  ILE*     4.2     9.6    -      -       +      +
      5F  LYS*     3.3    27.5    -      -       -      +
      6F  ALA      4.1     0.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 24 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  GLY      3.7     1.6    +      -       -      -
     11E  ILE*     2.8    67.3    +      -       +      +
     22E  GLN*     3.4    37.0    +      -       +      +
     23E  TYR*     1.3    82.7    -      -       -      +
     25E  PHE*     1.3    67.4    +      -       -      +
     26E  GLU*     4.6     7.2    +      -       -      +
     31E  GLU*     5.3     2.7    -      -       -      -
     33E  PHE*     3.7     9.4    -      -       -      -
     34E  TYR*     4.0    13.2    -      -       +      +
    137E  SER*     4.0     8.7    -      -       -      -
    138E  PHE      4.8     2.1    +      -       -      +
    140E  VAL*     5.5     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 25 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  THR      3.5     3.4    -      -       -      -
      9E  TYR*     3.2    32.8    -      +       +      -
     10E  GLY      3.5    12.8    -      -       -      -
     23E  TYR*     3.3    35.0    -      +       -      -
     24E  THR*     1.3    73.1    -      -       -      +
     26E  GLU*     1.3    61.2    +      -       -      +
     31E  GLU*     3.7     4.2    -      -       -      +
     32E  LEU*     2.9    30.6    +      -       +      +
     33E  PHE*     3.1    46.1    +      +       +      +
     55E  PHE*     3.4    29.4    -      +       -      -
      3F  ALA*     4.4     7.2    -      -       +      -
      4F  GLN      3.4    23.3    -      -       -      -
      5F  LYS*     3.7     7.6    -      -       -      -
    108F  ASN*     4.0     6.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 26 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  THR*     2.6    57.0    +      -       -      +
      9E  TYR*     3.8     5.5    -      -       -      -
     11E  ILE*     3.8    11.4    -      -       +      +
     24E  THR*     4.6     5.0    +      -       -      +
     25E  PHE*     1.3    77.0    -      -       -      +
     27E  PHE*     1.3    65.1    +      -       -      +
     29E  GLY*     4.2    14.4    -      -       -      +
     30E  ASP      3.4     9.4    -      -       -      +
     31E  GLU*     4.4     8.7    -      -       +      -
     32E  LEU*     4.0     2.2    -      -       -      +
    138E  PHE      4.1     3.7    -      -       -      +
    139E  PHE*     3.5    27.6    -      -       +      +
    140E  VAL*     2.9    45.1    +      -       -      +
    147E  HIS*     5.9     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 27 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  HIS*     3.8    17.7    -      +       +      -
      6E  VAL      3.0    37.5    -      -       -      -
      7E  GLY*     3.6    11.2    -      -       -      -
      8E  THR*     4.9     0.2    -      -       -      -
      9E  TYR*     4.3     1.3    -      -       -      -
     26E  GLU*     1.3    75.7    -      -       -      +
     28E  ASP*     1.3    93.9    +      -       +      +
     29E  GLY      3.2     0.7    -      -       -      -
     30E  ASP*     2.6    30.9    +      -       -      +
     32E  LEU*     3.9    10.3    -      -       +      -
     43F  PHE*     4.6     4.5    -      +       -      -
    109F  TYR*     5.2     1.6    -      +       -      -
    113F  GLU*     3.4    33.4    -      -       +      +
    117F  SER*     3.0    37.7    -      -       -      -
    118F  LEU*     3.7    14.4    -      -       +      -
    150F  TYR*     5.0     2.2    -      -       -      -
    180F  TRP*     4.2     8.2    -      +       +      -
----------------------------------------------------------
 Back to top of page


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