Contacts of the strand formed by residues 379 - 386 (chain L) in PDB entry 1LWU


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 MET 379 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196L  HIS*     4.8     6.3    -      -       -      +
    197L  ARG*     3.5     6.1    -      -       -      +
    198L  HIS*     4.0    36.3    -      -       +      +
    247L  ASP      4.3     0.7    -      -       -      -
    248L  LEU*     3.8     1.4    -      -       -      -
    249L  THR*     3.3    47.9    +      -       +      +
    253L  ASN*     4.5     6.1    -      -       -      +
    255L  HIS*     5.2     4.7    -      -       -      +
    377L  LEU*     4.0     3.6    -      -       -      +
    378L  LYS*     1.3   112.4    -      -       +      +
    380L  THR*     1.3    70.7    +      -       -      +
    381L  THR*     6.0     1.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 380 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195L  GLN*     3.0    21.1    -      -       -      +
    196L  HIS*     2.8    12.3    -      -       -      -
    197L  ARG*     2.8    40.3    +      -       +      +
    247L  ASP      3.3     8.7    +      -       -      -
    248L  LEU*     3.8     9.6    -      -       +      +
    342L  LEU*     3.8    34.0    -      -       +      +
    365L  ILE*     3.7    20.3    -      -       -      +
    377L  LEU*     4.3     0.7    -      -       -      +
    379L  MET*     1.3    84.1    +      -       -      +
    381L  THR*     1.3    69.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 381 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184L  GLU*     5.2     1.2    +      -       -      +
    193L  VAL*     4.4     8.5    -      -       -      +
    195L  GLN      3.1    10.4    +      -       -      -
    196L  HIS*     3.6    17.9    -      -       +      +
    222L  LEU*     4.9     6.8    -      -       +      +
    245L  ARG      3.4     0.9    -      -       -      +
    246L  ILE*     3.3     6.6    -      -       -      +
    247L  ASP*     3.0    57.3    +      -       +      +
    379L  MET*     6.0     0.9    -      -       +      -
    380L  THR*     1.3    84.8    -      -       -      +
    382L  MET*     1.3    64.7    +      -       -      +
    383L  LYS*     3.7    19.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 382 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194L  ILE*     2.7    44.3    +      -       +      +
    195L  GLN*     2.9    23.8    +      -       -      +
    227L  TRP*     4.1    24.2    -      -       +      -
    244L  LEU*     4.0    28.9    -      -       +      -
    245L  ARG      3.3     5.6    -      -       -      -
    246L  ILE*     4.4     7.6    -      -       +      -
    263L  PHE*     4.7     7.2    -      -       +      -
    288L  PHE*     5.1     3.1    -      -       +      -
    332L  TRP*     4.1    10.1    -      -       +      -
    333L  TRP*     4.4    24.7    -      -       +      -
    342L  LEU*     3.6    32.1    -      -       +      -
    381L  THR*     1.3    74.9    -      -       -      +
    383L  LYS*     1.3    54.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 383 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184L  GLU*     3.1    40.6    +      -       -      -
    186L  GLU*     4.9     1.8    +      -       -      -
    191L  TRP*     3.2    53.7    -      -       +      +
    192L  THR      3.9     4.0    -      -       -      -
    193L  VAL*     4.1    13.2    -      -       +      +
    243L  ARG      3.8     0.5    -      -       -      +
    244L  LEU*     3.4     0.2    -      -       -      -
    245L  ARG*     2.7    58.8    +      -       +      +
    247L  ASP*     3.0    30.0    +      -       -      +
    381L  THR*     3.7    11.0    -      -       -      +
    382L  MET*     1.3    74.3    -      -       -      +
    384L  LEU*     1.3    65.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 384 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191L  TRP*     3.5     5.9    -      -       -      -
    192L  THR*     2.9    45.2    +      -       +      +
    194L  ILE*     3.7    30.1    -      -       +      -
    233L  ILE*     4.9     0.2    -      -       +      -
    236L  LEU*     4.4    12.3    -      -       +      -
    237L  THR*     3.3    31.6    -      -       +      -
    242L  TYR*     4.0    24.2    -      -       +      -
    243L  ARG      3.6     1.1    -      -       -      -
    244L  LEU*     3.5    30.1    -      -       +      -
    263L  PHE*     3.8    10.8    -      -       +      -
    383L  LYS*     1.3    83.6    -      -       -      +
    385L  LEU*     1.3    60.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 385 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155L  GLN*     4.5     3.4    -      -       -      +
    189L  ASN*     3.8    22.4    -      -       +      +
    190L  GLY      4.5     6.7    -      -       -      +
    191L  TRP*     3.2    54.5    -      -       +      +
    242L  TYR*     3.3     5.7    -      -       -      -
    243L  ARG*     2.6    46.2    +      -       +      +
    384L  LEU*     1.3    73.0    -      -       -      +
    386L  PRO*     1.3   104.8    -      -       +      +
    389L  ARG*     3.3    23.8    -      -       +      +
    390L  ASP*     6.2     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 386 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153L  ASP*     3.6    22.4    -      -       -      +
    155L  GLN*     3.6    28.0    -      -       +      -
    190L  GLY      4.5     3.1    -      -       -      +
    192L  THR*     5.6     0.2    -      -       +      -
    240L  GLN*     3.7    18.2    -      -       -      +
    241L  ALA      3.5     5.4    -      -       -      +
    242L  TYR*     3.6    10.1    -      -       +      -
    243L  ARG*     4.9     1.2    -      -       -      +
    385L  LEU*     1.3   106.8    -      -       +      +
    387L  MET*     1.3    69.0    +      -       -      +
    388L  GLY      2.9     6.7    +      -       -      +
    389L  ARG*     3.3    15.4    +      -       +      +
----------------------------------------------------------
 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