Contacts of the strand formed by residues 161 - 167 (chain A) in PDB entry 3MEU


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 LYS 161 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  SER*     4.3    14.5    +      -       -      +
    159A  GLY      4.0     7.0    +      -       -      +
    160A  ASP*     1.3    76.8    -      -       -      +
    162A  VAL*     1.3    64.3    +      -       -      +
    177A  LEU*     4.5     5.2    -      -       +      -
    178A  ALA      3.4    12.8    -      -       -      +
    179A  GLU*     3.1    30.5    +      -       +      +
    195A  ILE*     4.4    18.6    -      -       +      -
    212A  PRO*     4.0     1.2    -      -       -      +
    213A  LEU*     3.0    42.7    +      -       +      +
    215A  GLN*     5.8     0.2    -      -       -      +
    282A  ARG*     3.3    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  ALA*     4.5     7.2    -      -       +      -
    160A  ASP      4.1     0.9    -      -       -      +
    161A  LYS*     1.3    81.7    -      -       -      +
    163A  ALA*     1.3    64.1    +      -       -      +
    164A  ALA*     4.2     5.4    -      -       +      -
    176A  ILE      3.6     0.5    -      -       -      +
    177A  LEU*     3.7     6.6    -      -       -      +
    178A  ALA*     2.9    53.0    +      -       +      +
    180A  VAL*     3.7    20.6    -      -       +      -
    192A  VAL*     4.3    11.2    -      -       +      -
    210A  VAL*     3.7    30.7    -      -       +      -
    211A  ILE      3.3    12.3    -      -       -      +
    212A  PRO*     4.0     7.4    -      -       +      -
    213A  LEU*     3.9     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  VAL*     1.3    73.4    -      -       -      +
    164A  ALA*     1.3    58.8    +      -       -      +
    175A  TRP*     3.5    18.1    -      -       +      -
    176A  ILE      3.4     5.2    -      -       -      -
    210A  VAL*     3.4     3.8    -      -       -      -
    211A  ILE*     2.8    47.6    +      -       +      +
    213A  LEU*     3.8     5.1    -      -       +      +
    235A  LEU*     5.6     0.4    -      -       +      -
    244A  PHE*     3.7    33.7    -      -       +      -
    285A  VAL*     4.7     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  VAL*     3.9     5.6    -      -       +      -
    163A  ALA*     1.3    74.0    -      -       -      +
    165A  ARG*     1.3    60.1    +      -       -      +
    166A  VAL*     3.4     3.8    +      -       +      -
    174A  GLN      3.3     2.9    -      -       -      +
    175A  TRP*     3.6     3.5    -      -       -      -
    176A  ILE*     2.8    43.3    +      -       +      +
    178A  ALA*     4.0    15.0    -      -       +      -
    192A  VAL*     4.0    15.7    -      -       +      -
    205A  LEU*     3.7    23.1    -      -       +      -
    209A  ARG      3.3     4.7    -      -       -      +
    210A  VAL*     4.8     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  ALA*     1.3    68.7    -      -       -      +
    166A  VAL*     1.3    60.4    +      -       -      +
    173A  GLU*     3.5    45.4    +      -       +      +
    174A  GLN      3.4    11.0    -      -       -      +
    175A  TRP*     3.4    47.0    -      -       +      +
    205A  LEU*     3.6     7.5    -      -       -      +
    208A  ARG      5.8     0.4    -      -       -      -
    209A  ARG*     2.8    66.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  ALA*     3.9     8.5    -      -       +      +
    165A  ARG*     1.3    78.8    -      -       -      +
    167A  LYS*     1.3    63.8    +      -       -      +
    172A  ASP      3.8     0.7    -      -       -      +
    173A  GLU*     3.5     5.4    -      -       -      -
    174A  GLN*     2.9    34.7    +      -       +      +
    176A  ILE*     3.7    39.0    -      -       +      -
    203A  HIS*     3.8    42.0    -      -       +      +
    205A  LEU*     4.1    18.2    -      -       +      -
    209A  ARG*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  VAL*     1.3    81.3    -      -       -      +
    168A  ALA*     1.3    70.4    +      -       -      +
    171A  GLY*     4.5    11.9    -      -       -      +
    172A  ASP      3.6     7.4    -      -       -      +
    173A  GLU*     2.6    38.0    +      -       +      +
    203A  HIS*     5.2     7.1    +      -       -      -
    209A  ARG*     3.1    21.1    -      -       -      +
----------------------------------------------------------
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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