Contacts of the strand formed by residues 154 - 158 (chain A) in PDB entry 1E1A


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 SER 154 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  ARG*     4.7     1.0    +      -       -      -
    117A  GLN*     2.7    30.0    +      -       -      -
    134A  ALA*     2.7    39.4    +      -       -      +
    152A  PHE      3.7     2.6    +      -       -      -
    153A  GLY*     1.3    74.5    +      -       -      -
    155A  ILE*     1.3    68.8    +      -       -      +
    156A  TYR*     4.1     8.5    -      -       -      -
    166A  GLN*     3.4    17.0    +      -       -      -
    168A  ASP      3.4    11.4    -      -       -      -
    169A  THR*     3.5    12.9    -      -       -      +
    171A  PHE*     5.2     0.2    -      -       -      -
    174A  PRO*     3.5     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  TRP*     5.2     0.4    -      -       +      -
    132A  ILE      3.3     9.9    -      -       -      +
    133A  THR*     4.0     8.3    -      -       +      -
    154A  SER*     1.3    85.1    -      -       -      +
    156A  TYR*     1.3    68.3    +      -       -      +
    166A  GLN*     3.5     5.5    -      -       -      +
    167A  VAL*     2.8    42.5    +      -       +      -
    168A  ASP*     3.0    17.4    +      -       +      +
    171A  PHE*     3.8    23.3    -      -       +      -
    174A  PRO*     3.6    23.6    -      -       +      -
    177A  ILE*     4.4    13.0    -      -       +      -
    190A  LEU*     4.5    11.9    -      -       +      -
    192A  VAL*     3.7    21.3    -      -       +      -
    203A  TYR*     4.6     3.1    -      -       +      +
    211A  ILE*     5.1     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  ASP*     3.9    13.4    +      -       +      -
    114A  ARG*     3.6     3.6    +      -       -      -
    115A  ARG      4.2     0.3    +      -       -      -
    116A  MET*     3.7    33.5    -      -       +      -
    117A  GLN*     3.4    25.4    +      -       +      +
    119A  CYS*     4.6     2.7    -      -       -      -
    131A  TRP*     3.5     5.0    -      -       -      -
    132A  ILE*     2.8    39.2    +      -       +      +
    134A  ALA*     3.3    34.1    -      -       +      -
    154A  SER*     4.1     6.7    -      -       -      -
    155A  ILE*     1.3    78.3    -      -       -      +
    157A  CYS*     1.3    61.3    +      -       -      +
    158A  PHE      4.2     0.2    -      -       -      -
    164A  MET*     3.9    23.6    -      -       +      -
    165A  ILE      3.2     7.9    -      -       -      -
    166A  GLN*     3.4    49.1    +      -       +      -
    167A  VAL*     4.1     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  ASN*     3.9    19.1    -      -       -      -
    130A  LEU      3.2     4.9    -      -       -      -
    131A  TRP*     3.8    36.8    -      -       +      -
    156A  TYR*     1.3    77.0    -      -       -      +
    158A  PHE*     1.3    59.3    +      -       -      +
    159A  THR*     3.5     7.5    +      -       -      +
    163A  GLN      3.2     3.8    -      -       -      +
    164A  MET*     4.8     0.2    -      -       -      -
    165A  ILE*     2.8    33.0    +      -       -      +
    167A  VAL*     4.0     4.5    -      -       +      -
    209A  ALA*     3.5    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  PHE*     4.1    24.7    -      +       -      -
     94A  LEU*     3.9    12.8    -      -       +      -
    106A  ILE*     3.6    29.6    -      -       +      -
    124A  PHE*     5.6     1.3    -      +       -      -
    128A  GLY      4.4     1.2    -      -       -      +
    129A  ASN*     3.8     0.7    -      -       -      -
    130A  LEU*     2.8    41.7    +      -       +      +
    132A  ILE*     4.0    21.9    -      -       +      +
    156A  TYR      4.2     0.4    -      -       -      -
    157A  CYS*     1.3    70.1    -      -       -      +
    159A  THR*     1.3    68.6    +      -       -      +
    162A  GLY*     3.6    33.7    -      -       -      -
    163A  GLN      3.2    13.9    -      -       -      -
    164A  MET*     3.9    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