Contacts of the strand formed by residues 5 - 10 (chain A) 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 LEU 5 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  LYS*     3.6    17.0    -      -       +      +
      4A  LYS*     1.3    74.9    -      -       -      +
      6A  LEU*     1.3    60.5    +      -       -      +
      7A  PHE*     4.0    15.5    -      -       +      -
     30A  HIS*     3.6    26.2    -      -       +      +
     32A  THR*     6.2     0.2    -      -       -      +
     53A  ARG*     3.6    23.6    -      -       -      +
     60A  SER      2.8    10.7    +      -       -      +
     61A  THR*     3.3     7.0    -      -       -      +
     62A  ALA      3.0    25.5    +      -       -      +
    268A  PHE*     3.6     2.9    -      -       -      -
     21B  VAL*     3.9    35.2    -      -       +      -
     24B  TYR*     3.7    34.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 6 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LYS      4.0     0.8    +      -       -      -
      5A  LEU*     1.3    73.9    -      -       -      +
      7A  PHE*     1.3    63.7    +      -       -      +
      8A  GLN*     3.9     3.0    +      -       +      -
     19A  ASP      5.6     1.8    -      -       -      +
     23A  GLY*     4.6     4.9    -      -       -      -
     28A  ALA*     4.1     5.4    -      -       +      -
     30A  HIS      2.9    12.3    +      -       -      +
     31A  ILE*     3.3    31.7    -      -       +      +
     32A  THR*     2.9    25.5    +      -       -      -
     62A  ALA*     3.5    23.8    -      -       +      +
     64A  PHE*     4.0    26.9    -      -       +      -
    264A  ILE*     4.2    17.7    -      -       +      -
    267A  LEU*     4.0    23.1    -      -       +      -
    268A  PHE*     4.1    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 7 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  LEU*     4.0    21.8    -      -       +      -
      6A  LEU*     1.3    75.9    -      -       -      +
      8A  GLN*     1.3    59.4    +      -       -      +
      9A  PHE*     3.8    20.9    +      -       +      -
     32A  THR*     3.5    31.0    -      -       +      -
     34A  TYR*     4.1    11.0    -      +       -      -
     49A  THR*     4.0     9.0    -      -       +      -
     61A  THR*     3.9    19.7    -      -       +      -
     62A  ALA      2.9    12.9    +      -       -      +
     63A  ILE*     3.4     8.2    -      -       +      +
     64A  PHE      2.9    26.3    +      -       -      +
     17B  VAL*     3.6    23.8    -      -       +      -
     20B  VAL*     3.8    22.9    -      -       +      -
     21B  VAL*     3.7    32.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 8 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     3.9     3.7    +      -       +      -
      7A  PHE*     1.3    69.4    -      -       -      +
      9A  PHE*     1.3    68.5    +      -       -      +
     10A  ASP*     4.5     3.7    +      -       +      +
     15A  PRO*     3.5    24.1    -      -       +      +
     16A  SER*     3.2    30.5    +      -       -      +
     19A  ASP*     3.7    18.4    +      -       -      +
     20A  VAL*     3.3    20.8    -      -       -      +
     31A  ILE*     3.8    17.6    -      -       +      +
     32A  THR      3.0     7.2    +      -       -      +
     33A  GLY*     3.4     9.6    -      -       -      -
     34A  TYR      2.8    29.3    +      -       -      +
     64A  PHE*     3.5    23.1    -      -       +      -
     66A  GLY*     5.9     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 9 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PHE*     4.0    26.0    -      +       +      -
      8A  GLN*     1.3    77.3    -      -       -      +
     10A  ASP*     1.3    59.9    +      -       -      +
     11A  THR*     5.5     0.6    -      -       -      +
     34A  TYR*     4.0    20.9    -      +       +      -
     37A  VAL*     3.8    20.0    -      -       +      -
     42A  VAL*     3.6    25.1    -      -       +      -
     45A  TYR*     3.6    40.6    -      +       +      -
     46A  VAL*     4.4     3.6    -      -       +      -
     49A  THR*     5.1     0.9    -      -       +      -
     63A  ILE*     3.8    42.8    -      -       +      -
     64A  PHE      2.9    10.8    +      -       -      +
     65A  VAL*     3.3    13.4    -      -       +      +
     66A  GLY      3.0    23.8    +      -       -      +
     76A  VAL*     4.7     1.6    -      -       +      -
     80A  VAL*     4.4     4.9    -      -       +      -
     17B  VAL*     4.8     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 10 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLN*     3.9     6.9    +      -       +      -
      9A  PHE*     1.3    74.4    -      -       -      +
     11A  THR*     1.3    65.1    +      -       -      +
     12A  ASP*     2.7    33.3    +      -       -      +
     14A  THR      3.9    11.8    -      -       -      +
     15A  PRO*     3.8    15.0    -      -       +      -
     16A  SER*     3.0    31.5    +      -       -      -
     19A  ASP*     4.8     1.0    -      -       -      +
     34A  TYR      2.9    15.2    +      -       -      +
     35A  GLY      3.4     2.1    -      -       -      -
     36A  ASN      3.3     7.6    +      -       -      -
     37A  VAL*     3.2    19.7    +      -       -      +
     66A  GLY*     3.4     4.3    -      -       -      -
     67A  GLY*     3.2    22.8    +      -       -      -
----------------------------------------------------------
 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