Contacts of the strand formed by residues 466 - 473 (chain A) 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 TYR 466 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192A  PRO*     3.3    19.9    +      -       +      +
    193A  PRO      3.0    26.0    +      -       -      -
    194A  ASP*     4.5     0.2    -      -       -      -
    196A  TYR*     3.5    20.4    -      -       +      +
    197A  GLN*     3.4    41.4    +      -       +      +
    200A  ALA*     4.7     1.8    -      -       +      -
    323A  LEU*     4.5    15.7    -      -       +      -
    324A  GLU      3.2     9.6    -      -       -      +
    325A  LEU*     3.2    33.9    -      -       +      -
    326A  ALA*     4.7     0.6    -      -       -      +
    464A  GLY*     3.5    25.4    -      -       -      -
    465A  ARG*     1.3    74.7    -      -       -      +
    467A  ASN*     1.3    62.5    +      -       -      +
    485A  HIS*     3.1     5.5    -      -       -      +
    486A  TRP*     2.7    51.7    +      +       +      +
----------------------------------------------------------
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Residues in contact with ASN 467 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  LEU*     3.2     8.2    -      -       -      +
    324A  GLU*     2.7    35.1    +      -       -      +
    325A  LEU      3.7     5.6    +      -       -      +
    326A  ALA*     3.4    29.2    -      -       -      +
    327A  SER      4.1     6.5    +      -       -      +
    328A  HIS*     6.2     0.6    -      -       -      -
    466A  TYR*     1.3    74.7    -      -       -      +
    468A  VAL*     1.3    61.6    +      -       -      +
    469A  PHE*     3.2    27.0    -      -       +      -
    482A  LYS*     3.4    32.6    +      -       -      +
    484A  GLY      3.9     3.6    -      -       -      +
    485A  HIS*     3.6    10.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 468 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  ILE*     3.4    31.0    -      -       +      -
    321A  ILE*     4.1    15.3    -      -       +      -
    323A  LEU*     3.5    18.6    -      -       +      -
    467A  ASN*     1.3    69.6    -      -       -      +
    469A  PHE*     1.3    71.1    +      -       -      +
    482A  LYS*     3.8     0.5    -      -       -      -
    483A  VAL*     2.9    37.7    +      -       +      +
    484A  GLY      2.7    24.3    +      -       -      +
    485A  HIS*     3.6    21.1    -      -       -      +
    486A  TRP*     4.5     1.8    -      -       +      +
    490A  LEU*     4.0     9.9    -      -       +      -
    491A  SER      4.3     0.4    -      -       -      +
    492A  LEU*     4.6     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  GLY      6.0     0.4    -      -       -      -
    305A  ALA*     3.8    21.5    -      -       +      -
    321A  ILE*     3.1    13.9    -      -       -      +
    322A  THR*     2.8    49.6    +      -       -      +
    324A  GLU*     4.7    11.2    -      -       +      -
    467A  ASN*     3.2    40.2    -      -       +      -
    468A  VAL*     1.3    83.9    -      -       -      +
    470A  ASN*     1.3    59.6    +      -       -      +
    480A  TYR*     3.7    31.0    -      -       +      -
    481A  LEU      3.6     8.3    -      -       -      -
    482A  LYS*     4.2    21.3    -      -       +      -
    483A  VAL*     4.0     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 470 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  GLY      4.0     2.8    -      -       -      -
    320A  ALA      3.0    17.4    +      -       -      -
    321A  ILE*     4.5     2.2    -      -       +      +
    469A  PHE*     1.3    75.1    -      -       -      +
    471A  LEU*     1.3    68.9    +      -       -      +
    472A  GLN*     3.2    18.4    +      -       -      +
    480A  TYR*     3.7     1.7    -      -       -      -
    481A  LEU      2.9    33.3    +      -       -      +
    483A  VAL*     3.7    22.2    -      -       +      -
    497A  ILE*     3.1    18.0    -      -       +      +
    498A  HIS*     2.6    45.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  TRP*     4.4     5.8    -      -       +      -
    310A  VAL*     3.3    39.9    -      -       +      -
    314A  GLU      4.9     1.8    -      -       -      +
    317A  ALA*     3.4    22.4    -      -       +      +
    318A  TYR*     4.0     5.0    -      -       +      +
    319A  GLY*     2.9    27.5    +      -       -      -
    320A  ALA*     2.9    22.8    +      -       +      +
    322A  THR*     5.8     1.7    +      -       +      +
    469A  PHE      4.3     0.2    -      -       -      -
    470A  ASN*     1.3    69.8    -      -       -      +
    472A  GLN*     1.3    61.6    +      -       -      +
    478A  TYR*     4.6    10.8    -      -       +      -
    479A  SER      3.2    31.0    -      -       -      +
    480A  TYR*     3.9    28.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  TYR*     3.8     7.0    -      -       +      -
    470A  ASN*     3.2    30.2    +      -       -      +
    471A  LEU*     1.3    77.4    -      -       -      +
    473A  GLN*     1.3    60.9    +      -       -      +
    474A  THR*     4.2    12.2    -      -       -      +
    478A  TYR*     4.6     0.9    -      -       -      -
    479A  SER*     2.9    41.1    +      -       -      +
    481A  LEU*     3.7    33.1    -      -       +      +
    496A  SER      3.5    16.8    +      -       -      -
    498A  HIS*     3.5    42.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314A  GLU      5.9     1.6    -      -       -      +
    318A  TYR*     3.5    26.2    +      -       +      -
    472A  GLN*     1.3    77.5    -      -       -      +
    474A  THR*     1.3    89.4    +      -       -      +
    476A  GLY*     2.7    33.9    -      -       -      +
    477A  LYS      3.2    32.3    -      -       -      +
    478A  TYR*     3.9     8.7    -      -       +      +
    498A  HIS*     5.1     1.7    -      -       -      -
----------------------------------------------------------
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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