Contacts of the strand formed by residues 198 - 204 (chain B) in PDB entry 5EWL


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 198 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  TYR      2.9     9.4    +      -       -      -
    168B  ILE*     3.6    23.7    -      -       +      -
    169B  PHE*     3.1    29.6    +      -       -      +
    196B  GLY      3.8     2.9    +      -       -      +
    197B  TRP*     1.3    76.6    -      -       -      +
    199B  LEU*     1.3    59.5    +      -       -      +
    200B  GLU*     3.3    10.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  PHE*     3.4    30.4    -      -       +      +
    171B  ILE*     3.7    33.7    -      -       +      +
    186B  ILE*     4.9     2.9    -      -       +      -
    187B  ARG*     3.8    35.5    +      -       +      +
    190B  ILE*     5.4    10.4    -      -       +      +
    197B  TRP*     4.2     0.8    -      -       -      +
    198B  GLU*     1.3    68.2    -      -       -      +
    200B  GLU*     1.3    61.1    +      -       -      +
    201B  GLU      3.3    25.6    -      -       -      +
    202B  VAL*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168B  ILE*     3.2    24.5    -      -       +      +
    169B  PHE      2.9     7.5    +      -       -      +
    170B  SER*     3.6     1.6    -      -       -      +
    198B  GLU*     3.8    15.7    -      -       +      +
    199B  LEU*     1.3    72.6    -      -       -      +
    201B  GLU*     1.3    66.6    +      -       +      +
    224B  GLN*     4.2     9.6    -      -       +      +
    225B  SER*     2.7    40.3    +      -       -      +
    226B  PRO*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170B  SER*     3.2    16.6    +      -       -      +
    171B  ILE      2.9    24.9    +      -       -      -
    199B  LEU*     3.3     6.7    -      -       -      +
    200B  GLU*     1.3    84.8    -      -       +      +
    202B  VAL*     1.3    82.7    +      -       -      +
    203B  LEU*     4.0    17.0    -      -       +      +
    222B  LYS*     4.3    23.3    -      -       +      +
    223B  LEU*     4.5    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  ILE*     3.2    12.3    -      -       +      +
    173B  THR*     5.6     1.3    -      -       -      +
    183B  VAL*     4.0    32.1    -      -       +      -
    187B  ARG*     3.6    31.6    -      -       -      +
    199B  LEU*     3.8    20.4    -      -       +      -
    201B  GLU*     1.3    90.6    +      -       -      +
    203B  LEU*     1.3    69.2    +      -       -      +
    204B  LEU*     4.1     1.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  ILE      2.8    10.7    +      -       -      -
    172B  VAL*     3.6    13.9    -      -       +      -
    173B  THR*     2.9    33.8    +      -       -      -
    201B  GLU*     4.0    22.9    -      -       +      +
    202B  VAL*     1.3    84.3    -      -       -      +
    204B  LEU*     1.4    59.5    +      -       -      +
    205B  LEU*     4.2    10.8    -      -       +      -
    219B  GLN*     3.3    43.7    -      -       +      +
    220B  LEU*     4.2     7.4    -      -       +      +
    222B  LYS*     4.5     6.1    -      -       +      -
    223B  LEU*     3.7    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173B  THR*     3.5    12.3    -      -       -      +
    174B  THR      3.2    33.4    -      -       -      +
    175B  TYR*     3.3    43.1    +      -       +      +
    179B  TYR*     3.7    24.7    -      -       +      +
    202B  VAL*     4.1     1.6    +      -       +      +
    203B  LEU*     1.4    72.5    -      -       -      +
    205B  LEU*     1.3    59.7    -      -       -      +
    206B  ASP      4.1     0.9    +      -       -      -
    219B  GLN*     2.9    19.5    +      -       -      +
----------------------------------------------------------
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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