Contacts of the strand formed by residues 241 - 246 (chain A) in PDB entry 2E4H


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 TRP 241 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  LEU*     3.6     1.4    -      -       -      +
    232A  GLY      2.5    46.5    +      -       -      +
    234A  THR*     3.4    33.7    -      -       +      -
    236A  PHE*     5.2     1.1    -      +       -      -
    237A  ALA*     3.2    28.7    -      -       +      +
    238A  LYS      3.5    16.7    +      -       -      -
    239A  GLY      3.6    12.1    -      -       -      -
    240A  GLU*     1.3    84.3    +      -       -      +
    242A  CYS*     1.3    60.6    +      -       -      +
    272A  PHE*     3.5    26.2    -      -       +      -
    273A  ALA*     3.8     1.1    -      -       -      -
    274A  PRO*     3.6    24.7    -      -       +      -
    275A  VAL*     4.8     2.8    -      -       -      +
    449B  GLU*     2.8    38.1    -      -       +      -
    450B  GLU*     3.9     1.8    -      -       -      -
    451B  TYR*     4.2    20.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with CYS 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  LEU*     4.8     2.9    -      -       -      -
    228A  VAL*     3.5    18.8    -      -       -      -
    230A  PHE      3.5     7.4    -      -       -      -
    231A  LEU*     3.2    33.9    -      -       +      +
    232A  GLY      4.6     0.2    -      -       -      +
    241A  TRP*     1.3    77.1    -      -       -      +
    243A  GLY*     1.3    73.8    +      -       -      +
    244A  VAL*     4.1    10.2    +      -       -      +
    271A  LEU      3.8     0.2    -      -       -      +
    272A  PHE*     3.2    10.8    -      -       -      +
    273A  ALA      2.8    41.1    +      -       -      +
    274A  PRO      4.3     9.0    -      -       -      +
    275A  VAL*     4.4     4.9    -      -       +      +
    278A  VAL*     4.6     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  VAL*     3.2     5.0    -      -       -      -
    229A  ARG      2.7    31.7    +      -       -      -
    230A  PHE      2.6    15.9    +      -       -      +
    242A  CYS*     1.3    73.6    -      -       -      +
    244A  VAL*     1.3    59.1    +      -       -      +
    263A  PHE*     3.4    33.0    -      -       -      -
    271A  LEU      3.7     2.0    -      -       -      -
    272A  PHE*     4.7     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  VAL*     3.4    24.7    -      -       +      -
    220A  VAL*     3.3    35.2    -      -       +      -
    226A  GLY*     3.0    42.0    -      -       -      -
    227A  VAL      3.0    10.1    -      -       -      +
    228A  VAL*     4.5     0.7    -      -       -      -
    229A  ARG*     4.4     1.6    -      -       -      -
    242A  CYS*     4.2     7.6    -      -       -      +
    243A  GLY*     1.3    80.8    -      -       -      +
    245A  GLU*     1.3    60.6    +      -       -      +
    246A  LEU*     3.4     2.1    +      -       -      +
    263A  PHE*     4.1     3.2    -      -       -      -
    270A  GLY*     4.1     0.5    -      -       -      -
    271A  LEU*     3.0    32.4    +      -       -      +
    278A  VAL*     4.1    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  GLY*     2.7    26.4    -      -       -      -
    227A  VAL*     2.6    27.6    +      -       +      +
    229A  ARG*     2.8    40.3    +      -       +      +
    244A  VAL*     1.3    70.0    -      -       -      +
    246A  LEU*     1.3    66.5    +      -       -      +
    247A  ASP*     3.6     1.0    +      -       -      -
    263A  PHE*     5.2     0.2    -      -       -      -
    264A  GLN      3.5     1.4    -      -       -      +
    265A  CYS*     3.5    30.7    -      -       +      +
    266A  GLN*     4.4     8.5    +      -       -      +
    269A  TYR*     3.5    13.2    -      -       +      +
    270A  GLY*     5.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  VAL*     3.4    33.4    -      -       +      -
    224A  LYS*     3.6     1.3    -      -       +      -
    225A  ALA      3.2     8.3    -      -       -      +
    245A  GLU*     1.3    76.9    -      -       -      +
    247A  ASP*     1.3    57.5    +      -       -      +
    248A  GLU      3.3    13.2    -      -       -      +
    250A  LEU*     3.0    27.6    -      -       +      +
    251A  GLY*     2.9    45.1    -      -       -      +
    268A  LYS      4.0     1.1    -      -       -      +
    269A  TYR*     2.7    54.6    +      -       -      +
    271A  LEU*     3.6    18.6    -      -       +      -
----------------------------------------------------------
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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