Contacts of the strand formed by residues 29 - 38 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  GLN*     1.3    76.7    -      -       -      +
     30A  LYS*     1.3    62.3    +      -       -      -
     31A  TRP*     3.8     4.9    +      -       -      -
     54A  THR      3.8     1.2    -      -       -      +
     55A  ILE*     3.4     9.1    -      -       -      -
     56A  TYR      2.8    35.6    +      -       -      -
    140A  ARG*     3.5     4.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  GLY*     1.3    72.3    -      -       -      -
     31A  TRP*     1.3    66.1    +      -       -      +
     32A  TYR*     4.0    20.5    +      -       +      +
     53A  ALA*     4.1    17.0    -      -       +      -
     54A  THR      3.8     3.4    -      -       -      -
     55A  ILE*     4.1    30.4    -      -       +      +
     69A  VAL*     6.0     1.1    -      -       -      -
    140A  ARG*     2.9    27.8    +      -       -      +
    175A  CYS      5.2     0.4    +      -       -      -
    176A  ILE*     2.8    30.1    +      -       -      +
    177A  ASP*     3.6     2.8    -      -       -      +
    178A  GLY      3.2    33.9    -      -       -      +
     21C  ASN*     3.6    23.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  PHE*     3.0    48.1    +      +       -      -
     29A  GLY      4.0     1.6    -      -       -      -
     30A  LYS*     1.3    74.8    -      -       -      +
     32A  TYR*     1.3    63.6    +      -       -      +
     33A  VAL*     4.0     0.5    +      -       -      +
     53A  ALA*     3.3     2.9    -      -       -      +
     54A  THR*     2.8    37.2    +      -       -      +
     56A  TYR*     3.9    24.0    -      +       -      -
    113A  THR*     3.7     4.9    -      -       -      -
    115A  TYR*     3.5    12.6    -      -       -      -
    117A  GLN      3.6    13.7    -      -       -      -
    118A  HIS      3.6    36.1    -      -       -      -
    119A  ALA*     4.0     0.4    -      -       +      -
    138A  TYR*     3.4    40.8    -      +       +      -
    139A  GLY      3.6    17.0    -      -       -      -
    140A  ARG*     3.4    42.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  LYS*     4.0    15.5    +      -       +      +
     31A  TRP*     1.3    74.6    -      -       -      +
     33A  VAL*     1.3    61.4    +      -       -      +
     34A  VAL*     3.2     5.1    +      -       +      -
     51A  MET*     4.1    13.7    -      -       +      -
     52A  TYR      3.8     1.6    -      -       -      -
     53A  ALA*     4.1    10.1    -      -       +      -
    138A  TYR*     3.3     5.8    -      -       -      -
    139A  GLY      2.7    36.1    +      -       -      +
    140A  ARG      3.4    26.5    -      -       -      -
    141A  THR*     3.5    26.0    -      -       -      +
    142A  LYS*     3.9    19.2    -      -       +      -
    176A  ILE*     3.4    49.1    +      -       +      -
    177A  ASP*     3.1    21.1    +      -       -      -
     20C  GLN*     5.2     3.1    +      -       -      -
     21C  ASN*     4.5     9.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  TRP      5.0     1.3    -      -       -      +
     32A  TYR*     1.3    70.3    -      -       -      +
     34A  VAL*     1.3    58.6    +      -       -      +
     35A  GLY      3.6    20.9    -      -       -      +
     36A  LEU*     4.0    17.9    -      -       +      -
     51A  MET*     3.6    16.6    -      -       -      +
     52A  TYR*     3.0    57.0    +      -       +      +
     54A  THR*     4.3     4.0    -      -       -      +
    136A  THR*     3.9     9.6    -      -       +      -
    137A  LEU      3.7     3.4    -      -       -      -
    138A  TYR*     3.9    23.1    -      -       +      -
    169A  PRO*     3.6    14.2    -      -       +      +
    203A  SO4      4.2     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  TYR*     3.8    11.9    -      -       +      +
     33A  VAL*     1.3    75.2    -      -       -      +
     35A  GLY*     1.3    57.6    +      -       -      +
     51A  MET*     4.1    10.7    -      -       +      +
    137A  LEU*     2.8    17.3    +      -       +      +
    139A  GLY*     3.9     7.9    -      -       -      +
    141A  THR      3.8    17.5    -      -       -      +
    142A  LYS      3.8    25.1    -      -       -      +
    144A  LEU*     4.1    32.1    -      -       +      +
    149A  LYS*     4.5    12.3    -      -       +      +
    168A  PHE*     3.4    16.9    -      -       +      +
    169A  PRO*     3.4    13.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  VAL*     3.6     9.1    -      -       -      +
     34A  VAL*     1.3    80.1    -      -       -      +
     36A  LEU*     1.3    61.0    +      -       -      -
    136A  THR*     3.5     4.0    -      -       -      -
    137A  LEU*     2.8    38.1    +      -       -      +
    152A  PHE*     3.7    13.2    -      -       -      -
    167A  VAL      3.6     9.0    -      -       -      -
    168A  PHE*     4.0     5.2    -      -       -      -
    169A  PRO*     4.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  VAL*     4.0    11.4    -      -       +      -
     35A  GLY*     1.3    74.7    -      -       -      +
     37A  ALA*     1.3    63.6    +      -       -      +
     41A  ILE*     3.9    24.1    -      -       +      +
     49A  GLN*     3.8    31.0    -      -       -      +
     52A  TYR*     4.2    19.5    -      -       +      +
    134A  LYS*     4.0    21.1    -      -       +      +
    135A  ILE      3.6     3.1    -      -       -      +
    136A  THR*     3.9    21.5    -      -       -      +
    152A  PHE*     3.7     3.0    -      -       -      -
    166A  ILE*     3.5     1.0    -      -       -      +
    167A  VAL*     2.8    50.8    +      -       +      +
    169A  PRO*     4.8     3.4    -      -       +      -
    202A  4OL      5.7     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     1.3    76.7    -      -       -      +
     38A  GLY*     1.3    57.8    +      -       -      +
     41A  ILE*     3.9     5.4    -      -       -      -
    134A  LYS*     3.0     5.0    -      -       -      +
    135A  ILE*     2.6    40.4    +      -       +      +
    152A  PHE*     3.8     8.1    -      -       +      -
    156A  SER*     3.3    26.2    -      -       -      +
    161A  LEU*     3.9     9.0    -      -       +      -
    165A  HIS      3.3    12.1    -      -       -      +
    166A  ILE*     3.8    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ALA*     1.3    75.9    -      -       -      +
     39A  ASN*     1.3    58.0    +      -       -      -
     40A  ALA      3.1     6.3    -      -       -      -
     41A  ILE*     3.1    17.9    +      -       -      +
    133A  PHE*     3.2    13.9    -      -       -      -
    134A  LYS*     3.9     2.0    -      -       -      -
    161A  LEU*     3.5    17.0    -      -       -      +
    165A  HIS*     3.0    28.6    +      -       -      +
    202A  4OL      5.8     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