Contacts of the strand formed by residues 29 - 38 (chain E) in PDB entry 4ZHF


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 GLY 29 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28E  GLN*     1.3    79.8    -      -       -      +
     30E  LYS*     1.3    62.4    +      -       -      -
     31E  TRP*     3.8     5.7    +      -       -      -
     54E  THR      3.8     0.7    -      -       -      +
     55E  ILE*     3.4     8.5    -      -       -      -
     56E  TYR      2.8    35.5    +      -       -      -
     57E  GLU*     6.2     0.2    -      -       -      -
    140E  ARG*     3.5     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 30 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29E  GLY*     1.3    72.1    -      -       -      -
     31E  TRP*     1.3    64.6    +      -       -      +
     32E  TYR*     3.8    21.2    +      -       +      +
     53E  ALA*     4.1    17.5    -      -       +      -
     54E  THR      3.8     3.4    -      -       -      -
     55E  ILE*     4.1    28.9    -      -       +      +
     69E  VAL*     5.4     1.5    -      -       -      +
    140E  ARG*     2.9    31.6    +      -       -      +
    175E  CYS      5.3     0.2    +      -       -      -
    176E  ILE      2.8    34.2    +      -       -      +
    177E  ASP*     3.6    18.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 31 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27E  PHE*     3.0    47.8    +      +       -      -
     29E  GLY      4.0     2.0    -      -       -      -
     30E  LYS*     1.3    74.8    -      -       -      +
     32E  TYR*     1.3    63.6    +      -       -      +
     33E  VAL*     5.0     0.2    -      -       -      +
     53E  ALA*     3.3     3.1    -      -       -      +
     54E  THR*     2.8    37.3    +      -       -      +
     56E  TYR*     3.9    24.5    -      +       -      -
    113E  THR*     3.8     4.9    -      -       -      -
    115E  TYR      3.4    20.0    -      -       -      -
    117E  GLN      3.6    14.1    -      -       -      -
    118E  HIS*     3.6    35.7    -      -       -      -
    119E  ALA*     3.9     0.7    -      -       +      -
    138E  TYR*     3.3    40.8    -      +       +      -
    139E  GLY      3.6    17.5    -      -       -      -
    140E  ARG*     3.4    36.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 32 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  LYS*     3.8    19.7    +      -       +      +
     31E  TRP*     1.3    76.0    -      -       -      +
     33E  VAL*     1.3    62.3    +      -       -      +
     34E  VAL*     3.1     4.4    +      -       +      -
     51E  MET*     4.0    12.8    -      -       -      -
     52E  TYR      3.8     2.2    -      -       -      -
     53E  ALA*     4.1     7.9    -      -       +      -
    138E  TYR*     3.3     5.7    -      -       -      -
    139E  GLY      2.7    34.6    +      -       -      +
    140E  ARG      3.4    26.5    -      -       -      -
    141E  THR*     3.5    24.2    -      -       -      +
    142E  LYS*     3.9    20.1    -      -       +      -
    176E  ILE*     3.4    41.6    +      -       +      -
    177E  ASP*     3.2    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 33 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  TRP      5.0     0.4    -      -       -      +
     32E  TYR*     1.3    70.9    -      -       -      +
     34E  VAL*     1.3    58.4    +      -       -      +
     35E  GLY      3.6    20.9    -      -       -      +
     36E  LEU*     3.9    18.6    -      -       +      -
     51E  MET*     3.6    17.0    -      -       -      +
     52E  TYR*     3.0    57.8    +      -       +      +
     54E  THR*     4.3     4.9    -      -       -      +
    136E  THR*     3.9     9.0    -      -       +      -
    137E  LEU      3.8     3.1    -      -       -      -
    138E  TYR*     3.9    23.8    -      -       +      -
    169E  PRO*     3.6    13.9    -      -       +      +
    203E  SO4      4.1     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 34 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32E  TYR*     3.8    12.1    -      -       +      +
     33E  VAL*     1.3    74.8    -      -       -      +
     35E  GLY*     1.3    58.9    +      -       -      +
     51E  MET*     4.1    10.5    -      -       +      -
    137E  LEU*     2.8    17.1    +      -       +      +
    139E  GLY*     3.9     8.3    -      -       -      +
    141E  THR      3.8    16.2    -      -       -      +
    142E  LYS      3.7    26.0    -      -       -      +
    143E  GLU*     5.2     0.2    -      -       -      -
    144E  LEU*     4.1    31.9    -      -       +      +
    149E  LYS*     4.5    13.0    -      -       +      +
    168E  PHE*     3.3    16.5    -      -       -      +
    169E  PRO*     3.4    13.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 35 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  VAL*     3.6    10.0    -      -       -      +
     34E  VAL*     1.3    80.9    -      -       -      +
     36E  LEU*     1.3    61.4    +      -       -      -
    136E  THR*     3.6     4.2    -      -       -      -
    137E  LEU*     2.8    39.8    +      -       -      +
    152E  PHE*     3.8    10.5    -      -       -      -
    167E  VAL      3.5     8.7    -      -       -      -
    168E  PHE*     4.0     4.9    -      -       -      -
    169E  PRO*     4.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 36 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  VAL*     3.9    12.1    -      -       +      -
     35E  GLY*     1.3    74.1    -      -       -      +
     37E  ALA*     1.3    63.6    +      -       -      +
     41E  ILE*     3.9    28.8    -      -       +      +
     49E  GLN*     3.9    25.4    -      -       -      +
     52E  TYR*     4.1    22.4    -      -       +      +
    134E  LYS*     4.0    20.4    -      -       +      +
    135E  ILE      3.6     2.7    -      -       -      +
    136E  THR*     3.9    21.5    -      -       -      +
    152E  PHE*     3.7     3.0    -      -       -      -
    166E  ILE*     3.5     1.2    -      -       -      +
    167E  VAL*     2.8    47.0    +      -       +      +
    169E  PRO*     4.8     6.1    -      -       +      -
    202E  4OL      6.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 37 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36E  LEU*     1.3    76.3    -      -       -      +
     38E  GLY*     1.3    56.8    +      -       -      +
     41E  ILE*     3.8     5.8    -      -       -      -
    134E  LYS*     3.0     5.2    -      -       -      +
    135E  ILE*     2.7    39.6    +      -       +      +
    152E  PHE*     3.8     7.9    -      -       +      -
    156E  SER*     3.3    26.7    -      -       -      +
    161E  LEU*     3.9     9.2    -      -       +      -
    165E  HIS      3.3    12.1    -      -       -      +
    166E  ILE*     3.8    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 38 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  ALA*     1.3    75.8    -      -       -      +
     39E  ASN*     1.3    58.4    +      -       -      -
     40E  ALA      3.2     5.8    -      -       -      -
     41E  ILE*     3.1    18.1    +      -       -      +
    133E  PHE      3.2    13.7    -      -       -      -
    134E  LYS*     3.9     1.6    -      -       -      -
    161E  LEU*     3.5    17.5    -      -       -      +
    165E  HIS*     3.0    28.8    +      -       -      +
    202E  4OL      4.8     0.2    -      -       -      -
----------------------------------------------------------
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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