Contacts of the strand formed by residues 123 - 126 (chain D) in PDB entry 1ZVM


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 LEU 123 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121D  LYS      4.9     0.4    -      -       -      +
    122D  ILE*     1.3    76.3    -      -       -      +
    124D  LEU*     1.3    93.3    +      -       -      +
    125D  TRP*     4.1     3.6    +      -       +      -
    132D  ALA*     4.0    21.3    -      -       +      +
    135D  PHE*     3.3    37.5    -      -       +      -
    136D  THR*     4.0     7.6    -      -       +      -
    142D  MET*     4.2    14.6    -      -       +      -
    143D  PHE      2.8    15.5    +      -       -      +
    144D  THR*     3.6    30.0    -      -       +      +
    145D  LEU      4.8     0.2    +      -       -      -
    196D  PHE*     4.7     0.2    -      -       -      -
    205D  HIS*     3.6    10.1    -      -       +      +
    206D  VAL      4.5     0.4    -      -       -      -
    207D  MET*     4.0    22.9    -      -       +      +
    241D  TRP*     4.5     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 124 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122D  ILE*     3.9    13.7    -      -       +      -
    123D  LEU*     1.3    82.2    -      -       -      +
    125D  TRP*     1.3    61.8    +      -       -      +
    196D  PHE*     3.9    28.5    -      -       +      -
    197D  ALA*     4.7     7.6    -      -       +      -
    204D  VAL*     4.2    15.9    -      -       +      -
    205D  HIS      2.7    15.3    +      -       -      +
    206D  VAL*     3.0    13.6    -      -       +      -
    207D  MET      2.9    20.3    +      -       -      -
    222D  PHE*     3.8    22.2    -      -       +      -
    226D  GLU*     3.9    32.3    -      -       +      +
    230D  LEU*     4.3    17.0    -      -       +      -
    238D  LEU*     5.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 125 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123D  LEU*     4.1     9.6    -      -       +      -
    124D  LEU*     1.3    82.4    -      -       -      +
    126D  SER*     1.3    63.1    +      -       -      +
    127D  ARG*     3.5    16.8    -      -       -      -
    128D  ILE*     3.5    18.4    -      -       +      -
    129D  LYS*     3.3    55.0    -      -       +      -
    132D  ALA*     3.7    26.2    -      -       +      -
    133D  HIS*     4.2     2.0    -      -       -      -
    144D  THR*     4.2     6.0    -      -       -      -
    145D  LEU*     5.1     2.1    -      -       -      +
    146D  GLU*     2.8    34.0    +      -       -      -
    206D  VAL*     4.1     3.6    -      -       -      -
    207D  MET*     3.4    17.3    -      -       +      +
    222D  PHE*     4.6     1.5    -      -       -      +
    226D  GLU*     4.3    11.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 126 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125D  TRP*     1.3    76.0    -      -       -      +
    127D  ARG*     1.3    83.0    +      -       -      +
    128D  ILE*     3.3     9.7    +      -       -      +
    207D  MET      3.1     9.9    +      -       -      +
    208D  LEU*     3.8    20.6    -      -       -      +
    209D  ASP      4.1     8.8    +      -       -      -
    215D  ILE      5.6     1.2    -      -       -      +
    217D  ASP*     5.7     1.4    +      -       -      +
    220D  SER*     3.6    20.3    +      -       -      -
    222D  PHE*     3.8    17.6    +      -       -      +
    307D  SO4      4.6     2.1    +      -       -      -
----------------------------------------------------------
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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