Contacts of the strand formed by residues 153 - 158 (chain A) in PDB entry 4Z1H


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 THR 153 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  GLN*     5.1     2.3    +      -       -      -
    147A  THR*     3.7     1.7    -      -       -      -
    148A  ASN*     2.9    51.7    +      -       -      +
    151A  LYS*     3.3    20.3    -      -       +      +
    152A  GLY*     1.3    73.2    -      -       -      +
    154A  ILE*     1.3    63.4    +      -       -      +
    155A  THR*     4.4     5.7    +      -       -      -
    254A  ILE*     4.3    12.0    -      -       +      +
    255A  ILE      3.1     9.6    -      -       -      +
    256A  HIS*     3.2    37.9    -      -       +      +
    257A  LEU*     4.5     4.5    -      -       -      -
    265A  SER*     3.9     5.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  PHE*     4.0    16.2    -      -       +      -
    113A  ILE*     4.1    24.2    -      -       +      -
    145A  LEU*     4.7     8.7    -      -       +      -
    146A  GLN      3.4    13.7    -      -       -      +
    147A  THR*     4.6     2.5    -      -       +      -
    153A  THR*     1.3    72.4    -      -       -      +
    155A  THR*     1.3    69.4    +      -       -      +
    156A  ILE*     6.1     1.3    -      -       +      -
    253A  ILE      3.8     1.2    -      -       -      +
    255A  ILE*     2.9    55.5    +      -       +      +
    257A  LEU*     4.2     7.4    -      -       +      -
    264A  PHE      3.5    25.1    -      -       -      +
    270A  VAL*     4.0    21.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  ILE*     4.2    15.4    -      -       +      +
    144A  HIS      3.8     0.3    -      -       -      +
    145A  LEU*     3.3     7.1    -      -       -      +
    146A  GLN*     2.9    52.8    +      -       -      +
    153A  THR*     4.4     5.2    +      -       -      -
    154A  ILE*     1.3    77.9    -      -       -      +
    156A  ILE*     1.3    65.0    +      -       -      +
    252A  LYS*     3.9    25.3    -      -       +      -
    253A  ILE      3.2    10.1    -      -       -      +
    254A  ILE*     3.7    32.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  ILE*     4.9     0.7    -      -       -      +
    116A  LEU*     3.7    37.7    -      -       +      +
    117A  ILE*     3.6    36.3    -      -       +      +
    120A  ALA*     4.5     4.5    -      -       +      -
    143A  ILE*     4.1    10.3    -      -       +      -
    144A  HIS      3.3     3.6    -      -       -      +
    145A  LEU*     3.7    29.4    -      -       +      -
    154A  ILE*     6.1     1.6    -      -       +      -
    155A  THR*     1.3    75.7    -      -       -      +
    157A  GLN*     1.3    63.6    +      -       -      +
    158A  ASP*     5.0     2.4    -      -       -      +
    251A  THR      3.8     1.9    -      -       -      +
    252A  LYS*     3.7     0.9    -      -       -      -
    253A  ILE*     2.9    50.1    +      -       +      +
    255A  ILE*     5.1     2.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ILE*     3.5    29.4    +      -       +      +
     75A  ILE*     3.4    35.3    -      -       +      +
     76A  SER      4.9     0.3    +      -       -      -
     79A  GLU*     5.8     0.8    +      -       -      -
    142A  GLU      4.0     0.3    -      -       -      +
    143A  ILE*     3.6     3.5    -      -       -      +
    144A  HIS*     2.9    34.1    +      -       +      +
    155A  THR      4.2     0.4    -      -       -      -
    156A  ILE*     1.3    75.4    -      -       -      +
    158A  ASP*     1.3    71.8    +      -       -      +
    159A  THR*     5.4     2.0    -      -       +      +
    248A  ARG*     4.0    28.3    +      -       -      +
    249A  THR      5.6     1.2    +      -       -      -
    251A  THR      3.2    11.0    -      -       -      +
    252A  LYS*     3.8    30.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ALA*     3.6    35.4    -      -       +      +
    123A  ALA*     3.9     8.7    -      -       -      +
    124A  LEU*     4.5     2.9    -      -       +      -
    142A  GLU      3.6    10.1    -      -       -      +
    143A  ILE*     4.6     0.9    -      -       +      -
    156A  ILE*     5.0     2.6    -      -       -      +
    157A  GLN*     1.3    81.4    -      -       -      +
    159A  THR*     1.3    60.9    +      -       -      +
    160A  GLY*     3.3    16.1    +      -       -      +
    161A  ILE      4.2     0.7    -      -       -      +
    249A  THR      3.9     0.9    -      -       -      +
    250A  GLY*     3.1     4.3    -      -       -      -
    251A  THR*     2.9    43.1    +      -       -      +
    253A  ILE*     6.0     0.7    -      -       -      +
    601A  4KP      3.2    22.6    +      -       -      -
----------------------------------------------------------
 Back to top of page


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