Contacts of the strand formed by residues 156 - 165 (chain B) in PDB entry 2WLJ


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 LYS 156 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152B  ASP*     4.0     3.4    -      -       -      -
    153B  PHE      2.8    31.2    +      -       -      +
    154B  GLU      3.3     6.4    +      -       -      +
    155B  GLY*     1.3    80.0    -      -       -      +
    157B  PRO*     1.3    77.5    -      -       +      +
    158B  THR*     3.0     7.1    +      -       -      +
    217B  PRO*     4.1    17.7    -      -       +      -
    218B  ILE      4.8     2.2    -      -       -      +
    219B  ASP*     3.6    37.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  ILE*     4.3    14.8    -      -       +      -
    151B  SER*     3.7     8.1    -      -       -      +
    152B  ASP*     3.7    15.4    -      -       -      +
    155B  GLY      4.4     3.4    -      -       -      +
    156B  LYS*     1.3    86.8    -      -       +      +
    158B  THR*     1.3    59.2    +      -       -      +
    218B  ILE*     2.9    43.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  VAL      3.5     1.0    -      -       -      +
    150B  ILE*     3.2     8.0    -      -       -      +
    151B  SER      2.8    35.1    +      -       -      +
    153B  PHE*     3.8    16.5    +      -       +      +
    156B  LYS*     3.0    16.1    +      -       -      +
    157B  PRO*     1.3    73.0    +      -       -      +
    159B  LEU*     1.3    64.5    +      -       -      +
    160B  MET*     3.7    18.1    +      -       +      +
    215B  MET*     3.6    31.2    -      -       +      -
    216B  HIS      3.4    17.5    -      -       -      +
    217B  PRO*     3.7    11.2    -      -       +      +
    218B  ILE*     4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  MET*     3.6    36.8    -      -       +      -
    149B  VAL      3.4    15.3    -      -       -      +
    150B  ILE*     3.6    22.7    -      -       +      -
    158B  THR*     1.3    71.1    -      -       -      +
    160B  MET*     1.3    61.2    +      -       -      +
    178B  LEU*     4.1     7.9    -      -       +      +
    198B  LEU*     4.1    13.2    -      -       +      -
    214B  VAL      3.9     0.2    -      -       -      +
    215B  MET*     3.3     2.3    -      -       -      -
    216B  HIS*     2.7    49.9    +      -       +      +
    218B  ILE*     4.1     2.6    -      -       -      +
    224B  ILE*     4.2    12.1    -      -       +      -
    239B  PHE*     3.6    37.0    -      -       +      -
    265B  ILE*     4.4     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  MET*     3.2    11.2    -      -       -      +
    149B  VAL*     2.9    44.4    +      -       +      -
    151B  SER*     3.7    38.1    -      -       -      +
    152B  ASP      4.6     1.6    -      -       -      +
    153B  PHE*     4.0    18.4    -      -       +      -
    158B  THR*     3.7    17.0    -      -       +      +
    159B  LEU*     1.3    82.2    -      -       -      +
    161B  MET*     1.3    64.0    -      -       -      +
    178B  LEU*     5.6     0.9    -      -       -      -
    213B  THR*     4.3    11.7    -      -       +      -
    214B  VAL      3.2    11.2    -      -       -      +
    215B  MET*     3.8    21.5    -      -       +      +
    271B  PHE*     4.1     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  PHE*     3.8    21.3    -      -       +      -
    145B  SER*     3.7     9.0    -      -       -      +
    147B  ARG      4.1     4.7    -      -       -      +
    148B  MET*     3.9    22.0    -      -       +      -
    160B  MET*     1.3    76.0    -      -       -      +
    162B  ARG*     1.3    86.3    +      -       -      +
    163B  LEU*     3.9     5.2    -      -       +      -
    178B  LEU*     4.8     5.4    -      -       +      -
    213B  THR*     3.6     4.3    -      -       -      +
    214B  VAL*     2.9    51.3    +      -       +      +
    241B  VAL*     4.1    24.5    -      -       +      -
    260B  TYR*     3.4    21.5    -      -       +      +
    271B  PHE*     3.6    13.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  PHE*     3.8     0.2    -      -       -      -
    145B  SER*     3.0    36.8    +      -       -      -
    161B  MET*     1.3    86.1    -      -       -      +
    163B  LEU*     1.3    63.2    +      -       -      +
    211B  SER*     4.2     5.8    -      -       -      +
    212B  TRP      3.2    14.8    -      -       -      +
    213B  THR*     3.8    19.3    +      -       +      +
    271B  PHE*     3.6    27.2    -      -       +      +
    272B  VAL      2.9    30.1    +      -       -      -
    273B  ASP*     4.6     1.2    -      -       -      +
    274B  VAL*     3.6    22.3    -      -       -      +
    289B  LYS      3.2    14.8    +      -       -      -
    290B  PHE*     2.7    52.6    +      -       +      +
    292B  GLU      3.8    10.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 163 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  VAL*     3.9    13.0    -      -       +      -
    143B  LEU      3.2     6.7    -      -       -      +
    144B  PHE*     3.1    43.7    -      -       +      -
    161B  MET*     3.9     9.9    -      -       +      -
    162B  ARG*     1.3    76.1    -      -       -      +
    164B  ALA*     1.3    60.8    +      -       -      +
    176B  VAL*     4.7     6.7    -      -       +      -
    208B  PHE*     3.8    10.2    -      -       +      -
    211B  SER*     3.2     4.7    +      -       -      -
    212B  TRP*     2.8    61.7    +      -       +      +
    214B  VAL*     4.1    14.1    -      -       +      -
    241B  VAL*     4.6     3.6    -      -       +      -
    243B  PHE*     3.9    20.6    -      -       +      -
    290B  PHE*     3.6     2.7    -      -       -      -
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Residues in contact with ALA 164 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  VAL*     3.3     7.7    -      -       -      +
    143B  LEU*     2.8    41.1    +      -       +      +
    163B  LEU*     1.3    75.8    -      -       -      +
    165B  ASN*     1.3    60.2    +      -       -      +
    166B  LEU*     3.5     1.1    +      -       +      -
    208B  PHE*     3.9     4.5    -      -       -      -
    210B  LEU      3.2     9.9    -      -       -      +
    211B  SER*     4.7     1.3    -      -       -      -
    287B  LEU*     3.7    29.8    -      -       +      -
    290B  PHE*     3.5    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ARG*     6.1     1.0    -      -       -      -
    141B  GLY      4.0     6.2    -      -       -      +
    142B  VAL*     5.0     1.1    -      -       -      +
    164B  ALA*     1.3    70.3    -      -       -      +
    166B  LEU*     1.3    59.9    +      -       -      +
    167B  ARG*     2.9    35.3    +      -       -      +
    169B  GLU      2.7    26.1    +      -       -      +
    170B  GLN*     4.0     1.4    -      -       -      +
    171B  ILE*     4.1    13.1    -      -       -      +
    208B  PHE*     3.5    36.2    +      -       +      -
    209B  SER*     3.4    24.1    +      -       -      +
    210B  LEU*     2.9    11.0    +      -       -      +
    247B  HIS*     4.4     4.7    +      -       -      -
    285B  LEU*     5.7     1.7    -      -       -      +
    287B  LEU*     4.6     8.3    -      -       -      +
----------------------------------------------------------
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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