Contacts of the strand formed by residues 118 - 123 (chain G) in PDB entry 1ZMC


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 TYR 118 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37G  LYS*     3.6    32.7    -      -       +      +
    117G  GLY*     1.3    71.2    -      -       -      -
    119G  GLY*     1.3    69.1    +      -       -      +
    120G  LYS*     3.8     2.4    +      -       +      +
    128G  THR      3.4     2.1    -      -       -      +
    129G  ALA*     3.3     1.4    -      -       -      -
    130G  THR*     3.0    37.9    +      -       -      +
    283G  PHE*     3.3    22.9    -      +       -      -
    285G  LYS*     2.7    31.9    +      -       -      +
    286G  ASN*     3.9    20.1    +      -       +      -
    480G  FAD      3.2    27.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 119 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12G  ILE*     4.4     6.7    -      -       -      -
     35G  ILE*     4.3    13.9    -      -       -      -
    117G  GLY      3.6     2.4    +      -       -      -
    118G  TYR*     1.3    78.5    -      -       -      +
    120G  LYS*     1.3    61.2    +      -       -      -
    127G  VAL*     4.5     1.6    -      -       -      -
    128G  THR      3.4     6.1    -      -       -      -
    129G  ALA*     4.2     4.5    -      -       -      -
    286G  ASN      3.9     2.1    -      -       -      +
    287G  LEU*     3.7    10.6    -      -       -      +
    480G  FAD      2.8    38.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 120 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118G  TYR*     5.0     2.9    -      -       +      +
    119G  GLY*     1.3    73.6    -      -       -      -
    121G  ILE*     1.3    72.9    +      -       -      +
    122G  THR*     3.1    13.2    +      -       +      +
    127G  VAL*     3.5     3.0    -      -       -      +
    128G  THR*     2.8    36.0    +      -       -      +
    286G  ASN*     3.4    32.5    +      -       +      +
    287G  LEU      3.6     8.1    -      -       -      +
    288G  GLY*     4.2     6.1    -      -       -      +
    291G  GLU*     3.6    23.5    +      -       -      -
   2027G  SO4      4.6     5.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 121 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12G  ILE*     3.9    18.4    -      -       +      -
    120G  LYS*     1.3    77.2    -      -       -      +
    122G  THR*     1.3    58.9    +      -       -      +
    123G  GLY      3.3    26.2    +      -       -      +
    126G  GLN      3.6     6.7    -      -       -      +
    127G  VAL*     4.3     1.3    -      -       -      +
    144G  ILE*     3.7    25.1    -      -       +      -
    146G  ILE*     4.0    28.5    -      -       +      -
    287G  LEU*     2.7    27.0    +      -       +      +
    288G  GLY*     4.2     9.0    -      -       -      +
    289G  LEU*     4.6     1.6    -      -       +      -
    291G  GLU*     5.5     1.9    -      -       -      +
    292G  LEU*     3.7    33.9    -      -       +      +
    315G  ILE*     4.2     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 122 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120G  LYS*     3.1    18.5    +      -       +      +
    121G  ILE*     1.3    75.0    -      -       -      +
    123G  GLY*     1.3    56.1    +      -       -      +
    126G  GLN*     2.9    38.4    +      -       -      +
    128G  THR*     2.7    39.1    +      -       +      +
    292G  LEU*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 123 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121G  ILE*     3.3    15.3    -      -       -      +
    122G  THR*     1.3    77.6    -      -       -      +
    124G  LYS*     1.3    66.8    +      -       -      -
    125G  ASN      2.9     6.1    +      -       -      -
    126G  GLN*     2.9    24.0    +      -       -      +
    144G  ILE*     4.1     0.2    -      -       -      +
    292G  LEU*     4.5     6.2    -      -       -      +
----------------------------------------------------------
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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