Contacts of the strand formed by residues 179 - 185 (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 PHE 179 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168L  TYR      3.6     0.2    -      -       -      +
    169L  TYR*     3.1     9.5    -      -       -      -
    170L  ILE*     2.9    40.1    +      -       +      +
    172L  PRO*     3.4    40.6    -      -       +      -
    175L  ALA*     4.5     6.3    -      -       +      -
    177L  GLN      3.9    11.7    -      -       -      +
    178L  PRO*     1.3    73.1    -      -       -      +
    180L  LEU*     1.3    66.4    +      -       -      +
    181L  VAL*     3.2    36.7    +      -       +      -
    228L  LEU*     4.1     6.7    -      -       +      -
    232L  LYS*     3.6    62.1    -      -       +      +
    235L  LEU*     5.3     2.7    -      -       +      -
    236L  LEU*     5.1     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 180 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224K  VAL*     3.6    41.3    -      -       +      -
    247K  TYR*     6.0     1.6    -      -       +      -
    146L  ILE*     3.6    41.1    -      -       +      -
    167L  LEU*     3.9    15.7    -      -       +      -
    168L  TYR      3.4    12.6    -      -       -      +
    169L  TYR*     3.6    26.7    -      -       +      +
    179L  PHE*     1.3    79.9    -      -       -      +
    181L  VAL*     1.3    67.0    +      -       -      +
    218L  LEU*     3.5    25.1    -      -       +      +
    228L  LEU*     3.9     6.1    -      -       -      +
    232L  LYS*     4.6     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 181 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154L  CYS*     4.0    15.3    -      -       -      -
    167L  LEU*     3.4     7.2    -      -       -      -
    168L  TYR      2.9    33.1    +      -       -      +
    170L  ILE*     3.4    39.3    -      -       +      -
    179L  PHE*     3.2    34.5    -      -       +      -
    180L  LEU*     1.3    81.5    -      -       -      +
    182L  PHE*     1.3    61.3    +      -       -      +
    183L  CYS*     3.7     1.7    +      -       -      -
    192L  THR*     5.1     2.5    -      -       -      +
    193L  VAL      5.0     4.3    -      -       -      +
    218L  LEU*     4.2     7.0    -      -       -      -
    228L  LEU*     3.8    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 182 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154L  CYS*     4.4     0.7    -      -       -      -
    165L  SER*     4.1    15.0    -      -       -      -
    166L  GLY*     3.4    11.4    -      -       -      -
    167L  LEU*     4.2     7.0    -      -       +      -
    181L  VAL*     1.3    73.6    -      -       -      +
    183L  CYS*     1.3    79.3    +      -       -      +
    184L  GLU*     4.0    12.3    -      -       +      -
    192L  THR      4.1     0.3    -      -       -      -
    193L  VAL*     3.2    46.7    +      -       +      +
    218L  LEU*     4.3    14.5    -      -       +      +
    219L  ALA      3.3    20.9    -      -       -      -
    220L  PRO      3.7     6.3    -      -       -      -
    221L  THR*     3.4    13.9    -      -       -      -
    222L  LEU*     3.1    53.2    -      -       +      -
    226L  PHE*     4.8     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 183 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154L  CYS*     2.0    57.7    -      -       +      +
    157L  VAL*     4.5     5.4    -      -       -      -
    165L  SER*     3.2     4.7    -      -       -      -
    166L  GLY      2.7    30.1    +      -       -      -
    168L  TYR*     3.7    40.4    -      -       +      -
    181L  VAL*     3.7     5.1    +      -       -      -
    182L  PHE*     1.3    77.9    -      -       -      +
    184L  GLU*     1.3    60.0    +      -       -      +
    185L  ILE*     4.5     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 184 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165L  SER*     3.4     7.4    -      -       -      +
    182L  PHE*     3.8    12.2    +      -       +      -
    183L  CYS*     1.3    72.2    -      -       -      +
    185L  ILE*     1.3    63.2    +      -       -      +
    186L  GLU*     4.0    18.7    -      -       +      +
    189L  ASN      3.1     1.6    -      -       -      +
    190L  GLY      3.7     0.3    -      -       -      -
    191L  TRP*     2.6    54.9    +      -       +      +
    193L  VAL*     4.6     6.8    -      -       +      +
    222L  LEU*     4.5    14.6    -      -       -      +
    247L  ASP*     4.9     0.7    -      -       -      +
    381L  THR*     5.2     1.7    +      -       -      +
    383L  LYS*     3.1    36.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 185 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157L  VAL*     5.2     2.0    -      -       +      -
    158L  VAL*     3.7    33.2    -      -       +      -
    162L  GLY*     3.9    13.5    -      -       -      +
    163L  LYS*     3.5    24.6    -      -       -      +
    164L  ASP      3.4    22.9    -      -       -      +
    165L  SER*     2.7    20.1    +      -       -      +
    168L  TYR*     3.9    14.4    -      -       +      +
    183L  CYS*     4.5    10.8    -      -       +      +
    184L  GLU*     1.3    78.0    -      -       -      +
    186L  GLU*     1.3    72.5    +      -       -      +
    188L  GLY*     4.7     1.6    -      -       -      +
    189L  ASN      3.1    10.1    -      -       -      +
    190L  GLY*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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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