Contacts of the strand formed by residues 73 - 77 (chain A) in PDB entry 4ERO


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 MET 73 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  PHE*     3.5    31.9    -      -       +      -
     53A  PHE*     4.6     8.1    -      -       +      -
     67A  LEU*     3.4    26.7    -      -       +      -
     72A  SER*     1.3    72.3    -      -       -      +
     74A  ALA*     1.3    62.1    +      -       -      +
     75A  HIS*     4.0     0.4    +      -       +      -
     84A  LYS*     3.5     1.4    -      -       -      -
     85A  MET*     2.7    52.2    +      -       +      +
    103A  GLU*     3.8    44.2    -      -       +      +
    104A  MET      3.7     7.4    -      -       -      +
    105A  PRO      3.9     8.5    -      -       -      -
    106A  CYS*     3.7     3.8    -      -       -      -
    111A  ALA*     3.7    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  MET*     1.3    78.1    -      -       -      +
     75A  HIS*     1.3    62.6    +      -       -      +
     83A  GLY      3.5    10.5    -      -       -      +
     84A  LYS*     4.5     2.0    -      -       +      +
    103A  GLU*     3.3     5.9    -      -       -      +
    104A  MET*     2.7    36.8    +      -       +      +
    106A  CYS*     3.6    24.7    -      -       +      -
    288A  ILE*     3.7    25.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  MET      5.6     0.2    -      -       -      -
     74A  ALA*     1.3    77.1    -      -       -      +
     76A  GLU*     1.3    61.7    +      -       -      +
     81A  HIS*     4.0     7.0    +      +       -      -
     82A  THR*     3.2    14.5    -      -       -      +
     83A  GLY*     3.1    63.0    +      -       -      +
     84A  LYS      4.3     0.8    +      -       -      -
     85A  MET*     4.1    27.2    -      -       +      +
     91A  GLN*     3.4    32.9    +      -       -      +
    101A  HIS*     5.5     3.4    -      -       -      +
    102A  ALA      3.3    11.7    -      -       -      +
    103A  GLU*     4.4    10.8    -      -       +      -
    131A  TYR*     5.0     3.0    +      -       -      -
    133A  GLU*     3.4    21.3    +      -       -      +
    288A  ILE*     3.8     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  HIS*     1.3    75.7    +      -       -      +
     77A  ASP*     1.3    66.2    +      -       -      +
     80A  GLY*     5.5     2.1    -      -       -      +
     81A  HIS      3.5     5.8    -      -       -      -
     82A  THR*     3.4    21.8    -      -       +      -
    101A  HIS*     3.2     4.6    -      -       -      +
    102A  ALA      2.9    30.7    +      -       -      -
    131A  TYR*     5.6     0.7    -      -       -      -
    284A  TRP*     4.0    10.9    +      -       -      -
    285A  LYS      4.5     0.5    -      -       -      +
    286A  SER*     3.2    15.3    -      -       -      -
    287A  LYS*     2.8    42.4    +      -       -      +
    288A  ILE*     3.1    31.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  GLU*     1.3    77.7    -      -       -      +
     78A  PHE*     1.3    59.7    +      -       -      +
     79A  CYS*     2.9    20.2    +      -       -      +
     80A  GLY*     3.1    17.8    +      -       -      -
     81A  HIS*     3.0    36.0    +      -       -      +
     99A  ILE*     3.2    20.8    -      -       +      +
    100A  LEU      3.3    13.2    -      -       -      +
    101A  HIS*     3.7     7.0    -      -       +      -
    131A  TYR*     3.1    35.1    +      -       -      +
    284A  TRP*     3.4    17.0    +      -       -      -
----------------------------------------------------------
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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