Contacts of the strand formed by residues 238 - 247 (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 GLU 238 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180B  LEU*     3.5     5.5    -      -       -      +
    181B  VAL*     2.7    45.4    +      -       +      +
    193B  ARG*     4.4    14.8    +      -       -      +
    236B  HIS      4.5     1.9    -      -       -      +
    237B  SER*     1.3    77.5    -      -       -      +
    239B  PHE*     1.3    68.0    +      -       -      +
    240B  LEU*     4.2    12.1    -      -       +      +
    259B  ALA*     4.9     7.7    -      -       +      +
    260B  TYR      3.5    13.2    -      -       -      +
    261B  SER*     4.3    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 239 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  MET*     3.8    22.2    -      -       -      -
    159B  LEU*     3.6    28.7    -      -       +      -
    178B  LEU*     4.2     8.7    -      -       +      -
    179B  VAL      3.4     2.9    -      -       -      -
    180B  LEU*     3.6    31.4    -      -       +      -
    198B  LEU*     3.8    20.4    -      -       +      -
    224B  ILE*     4.2    17.3    -      -       +      -
    232B  LEU*     4.6     8.3    -      -       +      -
    237B  SER*     4.6     9.6    -      -       -      -
    238B  GLU*     1.3    78.7    -      -       -      +
    240B  LEU*     1.3    63.7    +      -       -      +
    258B  HIS      3.7     0.3    -      -       -      +
    259B  ALA*     3.3     2.3    -      -       -      -
    260B  TYR*     2.6    49.0    +      -       +      +
    261B  SER      5.4     1.3    -      -       -      -
    262B  CYS*     5.5     1.6    -      -       -      -
    265B  ILE*     3.6    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 240 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  HIS      3.4     1.4    -      -       -      +
    178B  LEU*     3.3     5.8    -      -       -      +
    179B  VAL*     2.8    49.8    +      -       +      +
    181B  VAL*     4.1    22.7    -      -       +      -
    195B  PHE*     4.6    11.9    -      -       +      -
    238B  GLU*     4.7    10.3    -      -       +      +
    239B  PHE*     1.3    74.8    -      -       -      +
    241B  VAL*     1.3    62.8    +      -       -      +
    242B  LEU*     3.8    23.7    -      -       +      +
    257B  ARG*     6.2     0.4    -      -       +      -
    258B  HIS      3.4     4.3    -      -       -      +
    259B  ALA*     3.9    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 241 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  PHE*     4.0    23.6    -      -       +      -
    161B  MET*     4.1    22.4    -      -       +      -
    163B  LEU*     4.6     2.0    -      -       +      -
    176B  VAL*     3.5    27.4    -      -       +      -
    177B  HIS      3.2     4.3    -      -       -      +
    178B  LEU*     4.2    13.0    -      -       +      -
    240B  LEU*     1.3    76.1    -      -       -      +
    242B  LEU*     1.3    65.5    +      -       -      +
    257B  ARG*     3.1     8.9    -      -       -      +
    258B  HIS*     2.9    28.5    +      -       +      +
    260B  TYR*     3.6    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 242 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  ASP      3.7     0.5    -      -       -      +
    176B  VAL*     3.1     7.5    -      -       -      +
    177B  HIS*     2.8    46.6    +      -       +      +
    179B  VAL*     4.3    15.5    -      -       +      -
    240B  LEU*     3.8    32.3    -      -       +      +
    241B  VAL*     1.3    79.7    -      -       -      +
    243B  PHE*     1.3    61.8    +      -       -      +
    244B  THR*     5.4     0.7    -      -       -      +
    256B  ALA      3.6     3.4    -      -       -      +
    257B  ARG*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 243 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  ALA*     4.8     1.6    -      -       +      -
    142B  VAL*     3.8    24.7    -      -       +      -
    144B  PHE*     4.6    11.7    -      -       +      -
    163B  LEU*     3.9    24.2    -      -       +      -
    171B  ILE*     3.9    17.9    -      -       +      -
    174B  ALA*     3.7    27.6    -      -       +      -
    175B  ASP      3.3    11.4    -      -       -      -
    176B  VAL*     4.8     2.0    -      -       +      -
    208B  PHE*     3.8    33.7    -      +       -      -
    212B  TRP*     4.5     4.9    -      +       -      -
    242B  LEU*     1.3    76.4    -      -       -      +
    244B  THR*     1.3    74.0    +      -       -      +
    245B  GLY      4.3     2.5    -      -       -      -
    254B  VAL*     4.4     7.0    -      -       +      -
    255B  HIS*     3.3     6.6    -      -       -      +
    256B  ALA*     2.8    47.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 244 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173B  GLU      4.4     0.7    -      -       -      +
    174B  ALA*     3.0     5.4    -      -       -      +
    175B  ASP*     2.8    46.4    +      -       -      +
    242B  LEU*     5.4     1.2    -      -       -      +
    243B  PHE*     1.3    82.2    +      -       -      +
    245B  GLY*     1.3    67.6    +      -       -      +
    253B  ASN*     4.8     9.6    -      -       +      +
    254B  VAL      3.4    14.1    -      -       -      +
    255B  HIS*     4.1    22.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  ILE*     3.6    17.5    -      -       -      -
    172B  ILE      3.8     0.2    -      -       -      -
    173B  GLU      3.7    14.1    -      -       -      -
    174B  ALA*     4.1     0.4    -      -       -      -
    243B  PHE*     4.3     2.0    -      -       -      -
    244B  THR*     1.3    80.9    -      -       -      +
    246B  HIS*     1.3    62.1    +      -       -      -
    253B  ASN*     3.1     8.1    -      -       -      +
    254B  VAL*     2.7    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 246 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  HIS*     3.6    35.8    +      +       +      -
    171B  ILE*     3.3     2.7    -      -       -      +
    172B  ILE*     2.8    60.2    +      -       +      +
    173B  GLU*     4.6     6.0    +      -       +      +
    245B  GLY*     1.3    72.3    -      -       -      -
    247B  HIS*     1.3    69.7    +      -       -      +
    248B  GLU*     3.6     7.4    +      -       +      +
    251B  ALA*     3.4    41.1    -      -       +      +
    252B  GLN*     4.0     4.9    +      -       -      -
    253B  ASN*     3.4    21.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 247 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  ALA      3.6    14.0    +      -       -      -
    165B  ASN*     4.4     4.2    +      -       -      -
    167B  ARG*     3.4    30.7    +      -       +      -
    169B  GLU*     3.8    25.0    +      -       +      -
    170B  GLN      3.9     2.2    +      -       -      -
    171B  ILE*     3.4    30.2    -      -       +      +
    245B  GLY      3.7     2.2    +      -       -      -
    246B  HIS*     1.3    73.6    -      -       -      +
    248B  GLU*     1.3    62.5    +      -       -      +
    249B  ALA*     3.0    37.6    +      -       +      +
    250B  PHE*     3.6    22.2    -      +       +      -
    251B  ALA*     2.8    28.8    +      -       -      -
    252B  GLN      3.2    12.6    +      -       -      +
    254B  VAL*     3.9    11.4    -      -       +      -
----------------------------------------------------------
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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