Contacts of the strand formed by residues 169 - 178 (chain F) in PDB entry 3ZWG


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 HIS 169 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23F  LEU*     3.8    20.5    -      -       +      +
     28F  ASN*     4.4    13.0    -      -       -      -
     29F  VAL      3.0    21.5    +      -       -      -
     30F  LYS*     3.7    12.7    +      -       -      -
     32F  LYS*     3.4    34.5    +      -       +      -
    165F  ASN*     3.0    20.4    +      -       -      -
    167F  SER*     3.3     6.1    -      -       -      -
    168F  GLY*     1.3    83.3    -      -       -      +
    170F  ALA*     1.3    59.2    +      -       -      +
    171F  ILE*     5.0     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 170 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23F  LEU*     3.6     3.9    -      -       -      +
     32F  LYS      2.8    11.2    +      -       -      +
     33F  ILE*     3.3    19.6    -      -       +      -
     34F  ALA      2.9    26.0    +      -       -      -
    106F  VAL*     3.8    22.2    -      -       +      -
    115F  ASN*     4.2     7.2    -      -       -      +
    164F  MET*     4.1    10.8    -      -       +      -
    165F  ASN*     3.2    10.1    -      -       -      +
    167F  SER      4.3     1.3    -      -       -      +
    169F  HIS*     1.3    73.7    -      -       -      +
    171F  ILE*     1.3    67.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 171 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16F  PHE*     4.7    10.8    -      -       +      +
     19F  LEU*     3.7    30.3    -      -       +      -
     20F  LYS*     4.1    35.9    -      -       +      +
     23F  LEU*     4.2    15.9    -      -       +      -
     34F  ALA*     3.7     5.8    -      -       +      -
    163F  PHE*     3.5     7.2    -      -       +      +
    164F  MET*     3.4    25.2    -      -       -      +
    165F  ASN*     2.8    20.0    +      -       +      +
    169F  HIS      5.0     1.1    -      -       -      +
    170F  ALA*     1.3    78.9    -      -       -      +
    172F  LEU*     1.3    62.7    +      -       -      +
    173F  GLU*     4.7     4.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 172 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19F  LEU*     4.0     3.7    -      -       -      +
     33F  ILE*     4.2    12.3    -      -       +      +
     34F  ALA      3.0    12.9    +      -       -      +
     35F  VAL*     3.5    16.4    -      -       +      -
     36F  GLY      3.0    25.5    +      -       -      +
    102F  VAL*     4.3     6.1    -      -       +      -
    104F  PHE*     4.2    19.7    -      -       +      -
    117F  TRP*     3.7    39.9    -      -       +      -
    163F  PHE      3.3    15.5    -      -       -      +
    164F  MET*     4.0     8.3    -      -       +      -
    170F  ALA      4.1     0.4    -      -       -      -
    171F  ILE*     1.3    73.4    -      -       -      +
    173F  GLU*     1.3    59.3    +      -       -      +
    174F  ILE*     3.7    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 173 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14F  LEU*     4.1    18.3    -      -       +      +
     15F  GLY*     4.2    11.7    -      -       -      -
     16F  PHE*     4.1    17.8    +      -       -      +
     19F  LEU*     3.8    13.3    -      -       +      +
     36F  GLY      3.7     3.4    -      -       -      -
    149F  TRP*     3.9    22.4    -      -       +      -
    161F  ARG      3.8     0.3    -      -       -      +
    162F  GLY*     3.0     3.6    -      -       -      -
    163F  PHE*     2.8    40.2    +      -       +      +
    171F  ILE*     4.1     4.8    -      -       +      +
    172F  LEU*     1.3    70.6    -      -       -      +
    174F  ILE*     1.3    62.7    +      -       -      +
    175F  HIS*     2.9    30.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 174 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14F  LEU*     4.1     1.0    -      -       -      +
     36F  GLY      3.0    11.1    +      -       -      +
     37F  ILE*     3.3    17.5    -      -       +      -
     38F  ASP*     2.9    24.1    +      -       -      +
    102F  VAL*     3.6    34.1    -      -       +      -
    117F  TRP*     4.0    11.4    -      -       +      -
    119F  VAL*     3.8    24.9    -      -       +      -
    160F  SER*     4.7     3.1    -      -       -      -
    161F  ARG      3.2     9.4    -      -       -      +
    162F  GLY*     4.2     0.4    -      -       -      -
    172F  LEU*     3.7    28.7    -      -       +      -
    173F  GLU*     1.3    80.6    -      -       -      +
    175F  HIS*     1.3    76.0    +      -       -      +
    176F  VAL*     4.3    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 175 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11F  GLY      5.0     1.3    -      -       -      -
     14F  LEU*     4.5    15.0    -      -       +      +
     38F  ASP*     3.1    38.5    +      -       +      +
     40F  GLU*     5.7     0.4    -      -       -      +
    149F  TRP*     4.5     1.8    -      +       -      -
    159F  LYS      3.8     0.5    -      -       -      +
    160F  SER*     3.7     1.4    -      -       -      -
    161F  ARG*     2.6    81.7    +      -       +      +
    173F  GLU*     2.9    35.9    +      -       +      +
    174F  ILE*     1.3    79.4    -      -       -      +
    176F  VAL*     1.3    64.0    +      -       -      +
    177F  THR*     3.7    13.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 176 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37F  ILE*     4.6     2.2    -      -       +      -
     38F  ASP      3.1     7.6    +      -       -      +
     40F  GLU*     2.8    31.4    +      -       -      +
     41F  SER*     3.2    14.4    +      -       -      -
     45F  TRP*     3.6    37.9    -      -       +      -
    100F  LEU*     4.1    19.5    -      -       +      -
    119F  VAL*     4.7     2.2    -      -       +      -
    154F  LEU*     4.2    19.1    -      -       +      -
    158F  LEU*     4.3    11.0    -      -       +      -
    159F  LYS      3.6     7.9    -      -       -      +
    160F  SER*     4.6     4.0    -      -       -      -
    174F  ILE*     4.3    14.8    -      -       +      -
    175F  HIS*     1.3    73.9    -      -       -      +
    177F  THR*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 177 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40F  GLU*     3.8    22.9    -      -       +      -
     41F  SER*     4.4     4.9    -      -       -      -
    158F  LEU*     3.5     5.1    -      -       -      +
    159F  LYS*     3.0    51.2    +      -       -      +
    161F  ARG*     5.8     3.8    -      -       +      +
    175F  HIS*     4.0    18.6    +      -       +      +
    176F  VAL*     1.3    81.7    -      -       -      +
    178F  LYS*     1.3    74.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 178 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40F  GLU      3.4    24.7    +      -       -      -
     41F  SER*     3.5    15.5    -      -       -      +
     42F  GLY*     4.2    11.0    -      -       -      -
     67F  HIS*     3.8    20.0    +      -       -      -
    157F  GLY      3.7     7.4    -      -       -      +
    158F  LEU*     4.5     2.9    -      -       +      -
    159F  LYS*     3.8     5.0    +      -       -      -
    177F  THR*     1.3    81.9    +      -       -      +
    179F  ALA*     1.3    65.4    +      -       -      +
     44G  THR*     5.7     0.6    -      -       -      +
     64G  LYS*     3.3    29.3    -      -       -      +
----------------------------------------------------------
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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