Contacts of the strand formed by residues 163 - 168 (chain M) in PDB entry 2ZHX


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 LEU 163 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60M  VAL*     4.5     2.9    -      -       +      -
     61M  ARG*     3.3    27.6    -      -       -      +
     62M  VAL      3.8     1.1    -      -       -      +
     63M  LEU*     3.7    20.4    -      -       +      +
    153M  ILE*     5.1     1.1    -      -       +      +
    156M  LEU*     3.9    46.0    -      -       +      +
    157M  ALA      4.3     1.6    -      -       -      +
    159M  ARG*     4.1     8.5    -      -       -      +
    161M  ALA      4.0     1.1    +      -       -      +
    162M  PRO*     1.3    76.3    -      -       -      +
    164M  VAL*     1.3    77.9    +      -       -      +
    165M  ALA*     4.0     2.0    +      -       +      +
    179M  LEU*     4.2    22.7    -      -       +      -
    183M  ASN      3.3     6.4    +      -       -      +
    184M  CYS*     3.4    15.7    -      -       -      +
    185M  VAL      3.1    25.1    +      -       -      +
    217M  MET*     4.5     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 164 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61M  ARG      2.8    12.9    +      -       -      +
     62M  VAL*     2.9    16.5    -      -       +      +
     63M  LEU      2.8    22.6    +      -       -      -
    163M  LEU*     1.3    76.4    -      -       -      +
    165M  ALA*     1.3    62.4    +      -       -      +
    166M  ILE*     4.5     8.1    -      -       +      -
    185M  VAL      3.4     6.5    -      -       -      +
    187M  ILE*     4.6     2.7    -      -       +      -
    210M  ALA*     3.7    35.4    -      -       +      +
    213M  LEU*     3.8    17.3    -      -       +      -
    214M  LEU*     3.8    22.9    -      -       +      -
    217M  MET*     3.7    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 165 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63M  LEU*     3.3    23.1    -      -       +      +
    163M  LEU*     4.0     2.2    -      -       +      -
    164M  VAL*     1.3    75.1    -      -       -      +
    166M  ILE*     1.3    62.6    +      -       -      +
    167M  LEU*     3.4    16.5    -      -       +      +
    179M  LEU*     3.9    28.0    -      -       +      -
    185M  VAL      3.0     9.3    +      -       -      +
    186M  ALA*     3.3     3.9    -      -       +      -
    187M  ILE*     2.8    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 166 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62M  VAL*     4.2    19.1    -      -       +      -
     63M  LEU      2.7    17.2    +      -       -      +
     64M  ILE*     3.5    29.7    -      -       +      +
     65M  VAL*     3.7    15.8    +      -       -      +
    164M  VAL*     4.5     5.8    -      -       +      -
    165M  ALA*     1.3    75.4    -      -       -      +
    167M  LEU*     1.3    62.4    +      -       -      +
    168M  TRP*     3.2    44.5    +      -       +      +
    187M  ILE*     3.4    31.9    -      -       +      -
    206M  PRO*     4.3    12.6    -      -       +      -
    207M  PHE*     5.0     5.4    -      -       +      -
    210M  ALA*     4.6     5.8    -      -       +      -
    224M  TRP*     5.6     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 167 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65M  VAL*     4.2    11.4    -      -       +      -
    165M  ALA*     3.4    35.9    -      -       +      +
    166M  ILE*     1.3    76.5    -      -       -      +
    168M  TRP*     1.3    64.1    +      -       -      +
    169M  GLY      3.8     3.8    +      -       -      +
    172M  ALA*     3.0    41.5    -      -       +      +
    173M  SER*     4.1     7.6    -      -       -      +
    175M  LEU*     4.5     5.2    -      -       +      -
    176M  LYS*     4.3    20.0    -      -       +      +
    179M  LEU*     5.5     3.6    -      -       +      -
    186M  ALA*     4.1    11.9    -      -       +      -
    187M  ILE      2.8    13.1    +      -       -      +
    188M  GLU*     3.6    15.2    -      -       +      +
    189M  SER      3.5    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 168 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64M  ILE*     3.6    27.8    -      -       +      -
     65M  VAL      4.7     8.5    +      -       -      +
     67M  GLN*     5.1     3.1    +      -       -      -
     81M  PHE*     3.3    29.5    -      +       +      -
     97M  ILE*     3.1    44.2    -      -       +      -
    118M  TRP*     5.6     2.0    -      +       -      -
    166M  ILE*     3.2    36.1    +      -       +      +
    167M  LEU*     1.3    74.3    -      -       -      +
    169M  GLY*     1.3    59.3    +      -       -      +
    172M  ALA*     3.8    11.3    +      -       -      +
    187M  ILE      5.7     0.7    -      -       -      -
    188M  GLU      5.7     0.2    -      -       -      -
    189M  SER*     3.2    25.3    +      -       -      -
    191M  HIS*     3.6    15.8    -      -       +      -
    192M  PRO*     3.4    27.1    -      -       +      -
    201M  PHE*     3.8    23.0    -      +       -      -
    204M  SER*     5.5     0.4    +      -       -      -
    206M  PRO*     4.6    14.6    -      -       +      +
    207M  PHE*     4.8     3.6    -      +       -      -
----------------------------------------------------------
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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