Contacts of the strand formed by residues 169 - 178 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     3.9    18.7    -      -       +      +
     28A  ASN*     4.4    12.5    +      -       -      -
     29A  VAL      3.0    24.9    +      -       -      -
     30A  LYS      3.8     8.5    +      -       -      -
     32A  LYS*     3.5    34.6    +      -       +      -
    165A  ASN*     2.9    21.1    +      -       -      -
    167A  SER*     3.3     4.6    -      -       -      -
    168A  GLY*     1.3    82.8    -      -       -      +
    170A  ALA*     1.3    60.5    +      -       -      +
     58B  ASP*     3.4    16.9    +      -       -      +
     79B  ARG*     4.5    18.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     3.7     4.1    -      -       -      +
     32A  LYS      2.8    11.2    +      -       -      +
     33A  ILE*     3.4    20.8    -      -       +      -
     34A  ALA      2.9    26.2    +      -       -      -
    106A  VAL*     3.8    21.5    -      -       +      -
    115A  ASN*     4.2     8.1    -      -       -      +
    164A  MET*     4.1     9.2    -      -       +      -
    165A  ASN*     3.2    10.1    -      -       -      +
    167A  SER      4.3     1.3    -      -       -      +
    169A  HIS*     1.3    73.3    -      -       -      +
    171A  ILE*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PHE*     4.7     4.0    -      -       +      +
     19A  LEU*     3.6    32.3    -      -       +      +
     20A  LYS*     4.1    34.8    -      -       +      +
     23A  LEU*     4.2    15.3    -      -       +      -
     34A  ALA*     3.7     4.0    -      -       +      -
    163A  PHE*     3.5     2.3    -      -       -      +
    164A  MET*     3.3    24.9    -      -       -      +
    165A  ASN*     2.8    13.8    +      -       +      +
    169A  HIS      5.1     0.7    -      -       -      +
    170A  ALA*     1.3    80.9    -      -       -      +
    172A  LEU*     1.3    63.3    +      -       -      +
     58B  ASP*     3.3    28.3    -      -       +      +
     60B  VAL*     3.8    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LEU*     3.9     3.7    -      -       -      +
     33A  ILE*     4.3    11.9    -      -       +      -
     34A  ALA      3.1    11.6    +      -       -      +
     35A  VAL*     3.5    17.4    -      -       +      -
     36A  GLY      3.0    25.1    +      -       -      +
    102A  VAL*     4.4     6.5    -      -       +      -
    104A  PHE*     4.2    20.0    -      -       +      -
    117A  TRP*     3.7    44.9    -      -       +      -
    163A  PHE      3.3    15.3    -      -       -      +
    164A  MET*     4.0     8.1    -      -       +      -
    170A  ALA      4.2     0.4    -      -       -      -
    171A  ILE*     1.3    71.5    -      -       -      +
    173A  GLU*     1.3    59.8    +      -       -      +
    174A  ILE*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     4.1    19.7    -      -       +      +
     15A  GLY*     4.2    12.4    -      -       -      -
     16A  PHE      4.1     9.4    +      -       -      -
     19A  LEU*     3.7    11.4    -      -       +      +
     36A  GLY      3.7     3.1    -      -       -      -
    149A  TRP*     3.8    17.9    -      -       +      -
    161A  ARG*     3.9     0.3    +      -       -      +
    162A  GLY*     3.0     3.8    -      -       -      -
    163A  PHE      2.8    38.6    +      -       -      +
    171A  ILE      4.1     0.8    -      -       -      -
    172A  LEU*     1.3    72.8    -      -       -      +
    174A  ILE*     1.3    61.9    +      -       -      +
    175A  HIS*     2.9    31.3    +      -       +      +
     60B  VAL*     3.3    34.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     4.2     1.2    -      -       -      +
     36A  GLY      3.0    10.3    +      -       -      +
     37A  ILE*     3.4    17.0    -      -       +      -
     38A  ASP*     2.9    23.2    +      -       -      +
    102A  VAL*     3.5    33.9    -      -       +      -
    117A  TRP*     4.2    11.2    -      -       +      -
    119A  VAL*     3.9    24.7    -      -       +      -
    160A  SER*     4.7     2.7    -      -       -      -
    161A  ARG      3.2    10.3    -      -       -      +
    162A  GLY*     4.3     0.7    -      -       -      -
    172A  LEU*     3.7    29.2    -      -       +      -
    173A  GLU*     1.3    80.3    -      -       -      +
    175A  HIS*     1.3    77.8    +      -       -      +
    176A  VAL*     4.4    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLY      5.0     1.6    -      -       -      -
     14A  LEU*     4.4    15.0    -      -       +      +
     38A  ASP*     3.1    37.4    +      -       +      +
     40A  GLU*     5.7     0.2    -      -       -      +
    149A  TRP*     4.4     2.7    -      +       -      -
    159A  LYS      3.8     0.5    -      -       -      +
    160A  SER*     3.6     1.7    -      -       -      -
    161A  ARG*     2.6    78.2    +      -       +      +
    173A  GLU*     2.9    35.5    +      -       +      +
    174A  ILE*     1.3    77.2    +      -       -      +
    176A  VAL*     1.3    63.7    +      -       -      +
    177A  THR*     3.8    13.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ILE*     4.6     2.5    -      -       +      -
     38A  ASP      3.1     7.4    +      -       -      +
     40A  GLU*     2.8    33.6    +      -       -      +
     41A  SER*     3.9    14.1    -      -       -      -
     45A  TRP*     3.7    38.8    -      -       +      -
    100A  LEU*     4.1    17.3    -      -       +      -
    102A  VAL*     6.3     0.2    -      -       +      -
    119A  VAL*     4.7     2.2    -      -       +      -
    154A  LEU*     4.3    13.2    -      -       +      -
    158A  LEU*     4.3    10.5    -      -       +      -
    159A  LYS      3.6     8.5    -      -       -      +
    160A  SER*     4.6     9.2    -      -       -      -
    174A  ILE*     4.1    15.0    -      -       +      -
    175A  HIS*     1.3    73.7    -      -       -      +
    177A  THR*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLU*     3.6    24.2    -      -       +      -
     41A  SER*     4.4     4.9    -      -       -      -
    158A  LEU*     3.5     5.0    -      -       -      +
    159A  LYS*     2.9    49.9    +      -       -      +
    161A  ARG*     5.9     3.7    -      -       +      +
    175A  HIS*     4.2    18.3    +      -       +      +
    176A  VAL*     1.3    80.5    -      -       -      +
    178A  LYS*     1.3    71.4    +      -       -      +
    179A  ALA      3.3     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLU      3.3    24.2    +      -       -      -
     41A  SER*     3.6    15.7    -      -       -      +
     42A  GLY*     4.3    10.9    -      -       -      -
     67A  HIS*     3.6    25.0    +      -       -      -
    157A  GLY      3.7     7.9    -      -       -      +
    158A  LEU*     4.5     3.1    -      -       +      -
    159A  LYS*     3.9     5.4    +      -       -      -
    177A  THR*     1.3    81.2    +      -       -      +
    179A  ALA*     1.3    65.5    +      -       -      +
----------------------------------------------------------
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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