Contacts of the strand formed by residues 288 - 297 (chain A) in PDB entry 4LL4


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 VAL 288 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  LYS*     3.9    30.3    -      -       +      +
    166A  LYS*     3.6    34.3    -      -       +      +
    168A  VAL*     5.6     0.4    -      -       +      -
    178A  VAL*     4.1    26.5    -      -       +      +
    179A  SER*     5.1     0.4    -      -       -      -
    180A  VAL*     3.8    26.3    -      -       +      +
    278A  ILE      4.0     0.3    -      -       -      +
    279A  TYR*     3.0     3.1    -      -       -      -
    280A  VAL*     2.7    43.9    +      -       +      +
    282A  VAL*     4.5     7.2    -      -       +      -
    287A  LYS*     1.3    73.1    -      -       -      +
    289A  ILE*     1.3    60.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  LYS*     2.5    36.7    +      -       -      +
    277A  LEU*     4.6    14.6    -      -       +      -
    278A  ILE      3.6     4.0    -      -       -      -
    279A  TYR*     3.7    10.8    -      -       +      -
    287A  LYS*     3.6    32.2    +      -       +      +
    288A  VAL*     1.3    73.4    -      -       -      +
    290A  LEU*     1.3    76.1    +      -       -      +
    291A  ASP*     4.2     7.0    +      -       +      +
     79C  GLU      4.1    16.6    -      -       -      +
     80C  ASP*     4.6     4.3    -      -       -      +
     82C  PRO*     4.1    24.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  ALA*     3.8    16.8    -      -       +      +
    163A  LYS*     3.5    36.3    -      -       -      +
    164A  LYS*     3.5    19.7    -      -       +      +
    180A  VAL*     3.8    22.4    -      -       +      +
    182A  ALA*     3.3    34.3    -      -       +      +
    276A  LEU      3.5     0.7    -      -       -      +
    277A  LEU*     3.1     6.8    -      -       -      -
    278A  ILE*     2.6    48.2    +      -       +      +
    288A  VAL      4.3     0.2    -      -       -      -
    289A  ILE*     1.3    77.3    -      -       -      +
    291A  ASP*     1.3    59.2    +      -       -      +
    292A  LEU*     4.0    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  ARG*     3.1    24.7    +      -       -      -
    275A  SER*     2.6    25.7    +      -       -      -
    276A  LEU      3.6     2.9    -      -       -      -
    277A  LEU*     3.6    12.6    -      -       +      +
    289A  ILE*     4.1     7.4    +      -       +      -
    290A  LEU*     1.3    72.1    -      -       -      +
    292A  LEU*     1.3    66.7    +      -       -      +
    293A  PRO*     3.5    13.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  VAL*     4.1    24.9    -      -       +      +
    162A  ALA*     3.8    26.5    -      -       +      +
    182A  ALA*     4.6    12.3    -      -       +      +
    184A  ILE*     4.7    15.5    -      -       +      +
    276A  LEU*     2.6    45.5    +      -       +      +
    278A  ILE*     3.8    29.8    -      -       +      -
    290A  LEU*     4.6     4.7    -      -       +      -
    291A  ASP*     1.3    83.6    +      -       -      +
    293A  PRO*     1.3    70.3    -      -       +      +
    294A  LEU*     3.7     3.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  VAL*     5.4     7.7    -      -       +      +
    184A  ILE*     5.7     0.2    -      -       -      +
    187A  LYS*     3.1    40.5    -      -       -      +
    274A  TYR      3.8     8.3    -      -       -      +
    275A  SER*     4.0     3.8    -      -       -      +
    291A  ASP*     3.5    13.9    -      -       -      +
    292A  LEU*     1.3    86.7    -      -       +      +
    294A  LEU*     1.3    64.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  GLN*     4.9     0.5    -      -       -      +
    184A  ILE*     4.1    16.8    -      -       +      -
    187A  LYS*     3.4     9.3    -      -       -      +
    189A  PHE*     4.0    24.9    -      -       +      -
    195A  ILE*     3.9    17.3    -      -       +      -
    215A  ILE*     4.3     6.5    -      -       +      -
    273A  GLU*     5.5     0.7    -      -       -      -
    274A  TYR*     3.0    26.0    +      -       +      +
    275A  SER*     3.6    10.1    -      -       -      +
    276A  LEU*     3.6    24.9    -      -       +      +
    292A  LEU      3.7    10.5    -      -       -      +
    293A  PRO*     1.3    82.4    -      -       -      +
    295A  VAL*     1.3    65.7    +      -       -      +
    296A  ILE*     3.7    30.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 295 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  VAL*     4.0    17.5    -      -       +      -
     56A  TRP*     3.7    26.2    -      -       +      -
     65A  GLN*     3.3    22.9    -      -       +      +
    114A  PHE*     4.2    31.9    -      -       +      -
    156A  LEU*     4.6     7.0    -      -       +      -
    187A  LYS*     3.0    13.1    +      -       -      +
    188A  GLY*     3.4     4.3    -      -       -      -
    189A  PHE      2.8    26.3    +      -       -      +
    294A  LEU*     1.3    76.3    -      -       -      +
    296A  ILE*     1.3    66.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  GLN*     3.4    26.9    +      -       -      +
    189A  PHE*     3.2    19.1    -      -       +      +
    191A  GLU*     4.4    13.7    -      -       +      +
    195A  ILE*     5.3     0.2    -      -       +      -
    215A  ILE*     5.0     3.8    -      -       +      -
    257A  VAL*     3.8    33.7    -      -       +      -
    258A  GLN      5.5     1.6    -      -       -      +
    274A  TYR*     3.7    48.0    +      -       +      +
    294A  LEU*     3.7    35.4    -      -       +      -
    295A  VAL*     1.3    79.4    -      -       -      +
    297A  GLY*     1.3    64.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  TRP*     3.8    10.2    -      -       -      -
     63A  CYS*     4.1     5.6    -      -       -      -
     64A  LYS*     3.3    24.5    -      -       -      -
     65A  GLN*     3.8     2.5    -      -       -      -
    189A  PHE      3.1     8.3    +      -       -      -
    190A  CYS*     3.5     3.6    -      -       -      -
    191A  GLU*     3.0    31.1    +      -       -      +
    296A  ILE*     1.3    74.9    -      -       -      +
    298A  SER*     1.3    60.7    +      -       -      -
----------------------------------------------------------
 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