Contacts of the strand formed by residues 242 - 249 (chain C) 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 TYR 242 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153C  ASP*     2.4    40.6    +      -       +      +
    192C  THR*     4.7     2.5    -      -       +      -
    236C  LEU*     2.9    34.6    -      -       +      +
    237C  THR*     3.7    15.5    -      -       +      -
    239C  GLN*     3.0    18.0    +      -       -      -
    240C  GLN*     3.5    24.9    +      -       +      -
    241C  ALA*     1.3    75.8    -      -       -      +
    243C  ARG*     1.3    60.4    +      -       -      +
    262C  HIS*     3.0     8.2    +      -       -      +
    263C  PHE*     2.8    42.5    +      -       -      +
    384C  LEU*     4.0    27.6    -      -       +      -
    385C  LEU*     3.3    25.4    -      -       -      -
    386C  PRO*     3.6    12.3    -      -       +      -
    387C  MET*     4.1     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 243 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191C  TRP*     3.7    22.1    -      -       -      -
    242C  TYR*     1.3    72.5    -      -       -      +
    244C  LEU*     1.3    66.3    +      -       -      +
    245C  ARG*     4.5     4.2    -      -       -      +
    259C  ASP*     3.1    25.5    +      -       +      +
    260C  TYR      3.4    11.2    -      -       -      +
    280C  LEU*     4.0    28.0    +      -       +      +
    281C  ASP*     5.4     3.8    -      -       -      +
    384C  LEU*     3.6     2.1    -      -       -      -
    385C  LEU*     2.6    40.2    +      -       +      +
    386C  PRO      4.9     0.9    -      -       -      -
    387C  MET*     3.1    50.2    +      -       +      +
    389C  ARG      4.7     1.6    +      -       -      -
    390C  ASP*     4.0    33.7    +      -       -      +
    391C  LEU*     5.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 244 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194C  ILE*     5.8     0.4    -      -       +      -
    242C  TYR      3.7     2.6    +      -       -      -
    243C  ARG*     1.3    73.4    -      -       -      +
    245C  ARG*     1.3    77.0    +      -       -      +
    246C  ILE*     4.2    11.7    -      -       +      -
    258C  ALA      3.8     0.3    -      -       -      +
    259C  ASP*     3.3     6.8    -      -       -      +
    260C  TYR*     2.7    43.8    +      -       +      +
    263C  PHE*     3.3    47.8    -      -       +      -
    288C  PHE*     4.2    21.5    -      -       +      -
    382C  MET*     4.0    28.0    -      -       +      -
    383C  LYS      3.4    11.7    -      -       -      +
    384C  LEU*     3.6    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 245 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186C  GLU*     4.6    10.9    +      -       -      -
    191C  TRP*     3.6    32.8    -      -       +      -
    243C  ARG*     3.8     4.8    +      -       -      +
    244C  LEU*     1.3    74.9    -      -       -      +
    246C  ILE*     1.3    68.9    +      -       -      +
    247C  ASP*     3.4    27.1    -      -       -      +
    257C  TYR*     3.7    20.4    +      -       +      -
    258C  ALA      3.4     3.1    -      -       -      +
    259C  ASP*     3.0    33.9    +      -       -      +
    381C  THR      3.5     1.2    -      -       -      +
    382C  MET*     3.3     4.5    -      -       -      -
    383C  LYS*     2.7    63.6    +      -       +      +
    390C  ASP*     5.6     5.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 246 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244C  LEU*     4.2    17.0    -      -       +      -
    245C  ARG*     1.3    79.2    -      -       -      +
    247C  ASP*     1.3    61.9    +      -       -      +
    248C  LEU*     3.4    34.9    -      -       +      +
    257C  TYR*     3.1     8.7    -      -       -      +
    258C  ALA*     2.9    33.9    +      -       +      +
    260C  TYR*     4.4     6.5    -      -       +      -
    288C  PHE*     3.9    19.5    -      -       +      -
    342C  LEU*     3.6    20.9    -      -       +      -
    367C  TRP*     3.6    35.4    -      -       +      -
    381C  THR      3.3     6.1    -      -       -      +
    382C  MET*     4.5     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 247 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  GLU*     4.9     0.7    -      -       -      +
    245C  ARG*     3.4    22.7    -      -       -      +
    246C  ILE*     1.3    75.9    -      -       -      +
    248C  LEU*     1.3    63.4    +      -       -      +
    249C  THR*     4.9     2.1    +      -       -      +
    255C  HIS*     6.3     2.2    -      -       +      -
    256C  ARG      3.8     4.7    -      -       -      +
    257C  TYR*     3.5     9.4    -      -       -      +
    379C  MET*     4.4     0.5    -      -       -      +
    380C  THR*     3.3     7.4    +      -       -      -
    381C  THR*     3.0    44.8    +      -       +      +
    383C  LYS*     3.1    33.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 248 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246C  ILE*     3.4    41.7    -      -       +      +
    247C  ASP*     1.3    80.1    -      -       -      +
    249C  THR*     1.3    69.0    +      -       -      +
    254C  THR      3.5     0.8    -      -       -      +
    255C  HIS*     3.5    19.9    -      -       -      +
    256C  ARG      3.2    13.6    +      -       -      +
    284C  ALA*     4.3    17.7    -      -       +      -
    342C  LEU*     3.6    22.0    -      -       +      -
    367C  TRP*     4.3    17.0    -      -       +      +
    370C  TRP*     3.9    14.6    -      -       +      -
    377C  LEU*     3.5    22.7    -      -       +      -
    379C  MET      3.9     2.7    -      -       -      -
    380C  THR*     3.9    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 249 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247C  ASP*     4.9     2.3    +      -       -      +
    248C  LEU*     1.3    81.4    +      -       -      +
    250C  ASP*     1.3    67.0    +      -       -      +
    253C  ASN*     4.0     7.4    -      -       -      +
    254C  THR      3.1    10.5    -      -       -      +
    255C  HIS*     3.2    32.5    -      -       -      +
    377C  LEU*     3.6     6.0    -      -       -      +
    378C  LYS*     2.8    48.3    +      -       -      +
    379C  MET*     3.3    32.6    +      -       +      +
----------------------------------------------------------
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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