Contacts of the strand formed by residues 163 - 167 (chain A) in PDB entry 3IE7


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 PHE 163 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  LYS      4.5     1.2    +      -       -      -
    133A  ASP      3.1    12.9    +      -       -      +
    134A  MSE      3.6    35.0    -      -       +      -
    135A  VAL*     2.9    30.3    +      -       -      +
    136A  VAL*     6.0     0.2    -      -       +      -
    161A  GLY      3.8     1.0    +      -       -      -
    162A  ALA*     1.3    75.2    -      -       -      +
    164A  LEU*     1.3    66.2    +      -       -      +
    165A  GLY      4.1     1.8    -      -       -      -
    182A  ASP*     3.5    28.5    -      -       +      -
    183A  PHE*     3.8    26.7    -      -       +      -
    215A  TYR*     3.8    23.3    -      +       -      -
    258A  ILE*     4.0    14.1    -      -       +      -
    261A  LEU*     3.7    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  VAL*     3.5     9.6    -      -       +      +
    137A  ILE*     4.0    22.2    -      -       +      -
    154A  LEU*     4.1    16.2    -      -       +      +
    157A  VAL*     3.7    30.3    -      -       +      -
    158A  LYS*     4.1    23.3    -      -       +      -
    162A  ALA      4.3     3.1    -      -       -      +
    163A  PHE*     1.3    78.5    -      -       -      +
    165A  GLY*     1.3    69.5    +      -       -      +
    166A  CYS*     4.2     2.5    -      -       -      -
    180A  GLY      4.6     0.9    -      -       -      +
    181A  VAL*     3.6    29.1    -      -       +      +
    182A  ASP*     2.8    44.6    +      -       -      +
    183A  PHE      3.2     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  VAL      2.9    11.2    +      -       -      +
    136A  VAL*     3.4    10.4    -      -       -      -
    137A  ILE      2.9    25.3    +      -       -      -
    163A  PHE*     4.1     6.0    -      -       -      -
    164A  LEU*     1.3    75.8    -      -       -      +
    166A  CYS*     1.3    64.7    +      -       -      -
    167A  ASP      4.3     0.2    -      -       -      -
    183A  PHE*     3.3    26.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  ILE*     3.3     9.2    -      -       -      -
    150A  PHE*     5.0     0.4    -      -       -      -
    154A  LEU*     3.7    29.4    -      -       -      -
    164A  LEU*     4.2     6.7    -      -       -      -
    165A  GLY*     1.3    78.8    -      -       -      -
    167A  ASP*     1.3    60.8    +      -       -      +
    168A  ASN*     3.5    19.9    +      -       +      +
    173A  LEU*     4.9     2.3    -      -       +      +
    176A  ALA*     3.9    16.8    -      -       +      -
    181A  VAL*     3.9    17.0    -      -       +      -
    183A  PHE*     2.8    14.6    +      -       -      +
    184A  ILE*     3.3    30.7    -      -       +      +
    185A  LYS      3.9     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LYS*     2.6    48.3    +      -       -      +
    136A  VAL*     5.4     1.9    -      -       +      +
    137A  ILE      2.9     8.9    +      -       -      -
    138A  ALA*     3.5    12.4    -      -       +      +
    139A  GLY      3.2    14.7    +      -       -      -
    166A  CYS*     1.3    70.6    -      -       -      +
    168A  ASN*     1.3    59.6    +      -       -      +
    183A  PHE*     5.6     1.1    -      -       +      -
    185A  LYS*     3.6    31.5    -      -       +      +
    190A  GLU*     4.4     5.9    -      -       -      +
    250A  GLY      4.4     0.7    -      -       -      +
    251A  ASP*     4.3     4.9    -      -       -      +
    254A  VAL*     3.4    34.1    -      -       +      +
    319A   MG      4.1     8.5    -      -       -      -
----------------------------------------------------------
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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