Contacts of the strand formed by residues 271 - 275 (chain B) in PDB entry 2E4Y


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 VAL 271 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  LEU*     4.3    22.0    -      -       +      -
    210B  TRP*     3.6    30.7    -      -       +      +
    213B  VAL*     3.0    42.7    -      -       +      +
    214B  SER*     3.1     8.5    +      -       -      -
    269B  ALA*     3.3     1.3    -      -       -      +
    270B  ARG*     1.3    82.8    -      -       +      +
    272B  VAL*     1.3    64.1    +      -       -      +
    296B  THR*     3.6    24.5    -      -       -      +
    298B  VAL*     4.4    10.1    -      -       +      -
    505B  PRO*     4.6     2.7    -      -       +      -
    507B  SER*     3.4    16.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 272 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214B  SER*     3.2    11.7    -      -       -      +
    216B  VAL*     3.4    32.3    -      -       +      -
    263B  LEU*     3.9    20.9    -      -       +      -
    269B  ALA      4.9     2.0    -      -       -      +
    270B  ARG      3.8     0.4    +      -       -      -
    271B  VAL*     1.3    74.8    -      -       -      +
    273B  VAL*     1.3    64.1    +      -       -      +
    274B  LEU*     3.8     0.8    +      -       +      +
    295B  PHE*     3.3    37.0    -      -       +      -
    296B  THR      3.1     7.6    +      -       -      +
    297B  TRP*     3.3    27.5    -      -       +      -
    298B  VAL*     2.9    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 273 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201B  MET*     4.7     9.2    -      -       +      -
    205B  LEU*     3.7    16.2    -      -       +      -
    213B  VAL*     4.4     4.5    -      -       +      -
    214B  SER      2.7    14.2    +      -       -      +
    215B  THR*     3.5     8.6    -      -       +      -
    216B  VAL*     3.1    28.9    +      -       -      +
    227B  ILE*     4.4     7.6    -      -       +      -
    230B  PHE*     3.6    46.9    -      -       +      -
    271B  VAL*     4.0     0.6    +      -       +      -
    272B  VAL*     1.3    72.5    -      -       -      +
    274B  LEU*     1.3    67.5    +      -       -      +
    275B  PHE*     4.2     1.3    +      -       +      -
    298B  VAL*     3.2    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 274 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201B  MET*     3.8     2.8    -      -       -      +
    216B  VAL*     3.1    37.0    -      -       +      +
    272B  VAL*     4.1     4.9    -      -       +      -
    273B  VAL*     1.3    76.5    -      -       -      +
    275B  PHE*     1.3    58.2    +      -       -      +
    276B  MET*     3.4    32.5    -      -       +      +
    281B  SER*     5.4     0.9    -      -       -      +
    284B  LEU*     4.5     5.8    -      -       +      -
    285B  ILE*     5.3     0.2    -      -       +      -
    297B  TRP*     3.8    27.8    -      -       +      -
    298B  VAL      2.5    12.4    +      -       -      +
    299B  ALA*     3.2    13.6    -      -       +      -
    300B  SER*     2.7    34.0    +      -       -      -
    303B  TRP*     3.6    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 275 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194B  ASP*     3.8    28.7    -      -       +      -
    197B  GLN*     4.2    11.9    -      -       +      -
    198B  ALA*     4.5    10.5    -      -       -      -
    201B  MET*     3.7    29.4    -      -       -      -
    216B  VAL      3.4     7.1    +      -       -      -
    217B  ALA*     3.3     3.0    -      -       +      -
    218B  SER      3.1    15.9    +      -       -      -
    222B  TYR*     4.0    17.7    -      +       -      -
    223B  GLY*     3.2    13.8    -      -       -      +
    226B  GLY*     3.0    44.9    -      -       -      -
    227B  ILE*     3.8    24.9    -      -       +      -
    230B  PHE*     4.6     6.3    -      -       +      -
    273B  VAL*     4.2     2.6    -      -       +      +
    274B  LEU*     1.3    70.5    -      -       -      +
    276B  MET*     1.3    60.3    +      -       -      +
    300B  SER*     3.2    20.4    -      -       -      -
----------------------------------------------------------
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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