Contacts of the strand formed by residues 403 - 409 (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 MET 403 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221G  GLU*     3.9    22.0    -      -       +      +
    222G  ILE*     3.7    27.5    -      -       +      +
    225G  ASN*     3.9    26.2    -      -       -      +
    385G  LYS*     4.2    21.5    -      -       +      -
    386G  PHE      3.1    17.3    -      -       -      +
    387G  PRO*     3.8     6.7    -      -       +      -
    388G  PHE*     3.4     7.3    -      -       -      -
    402G  GLY*     1.3    77.7    -      -       -      +
    404G  VAL*     1.3    69.7    +      -       -      +
    405G  LYS*     4.0    14.6    -      -       +      -
    419G  HIS      4.0     0.5    -      -       -      +
    420G  ILE*     3.6     1.6    -      -       -      -
    421G  LEU*     2.7    37.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 404 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384G  GLY      3.8     0.2    -      -       -      +
    385G  LYS*     3.3     5.7    -      -       -      +
    386G  PHE      2.8    31.0    +      -       -      +
    388G  PHE*     3.6    18.6    -      -       +      -
    403G  MET*     1.3    75.9    -      -       -      +
    405G  LYS*     1.3    64.1    +      -       -      +
    406G  ILE*     4.3     5.2    -      -       +      -
    419G  HIS      3.6     8.1    -      -       -      +
    420G  ILE*     3.9    13.5    -      -       +      -
    428G  MET*     4.2     4.0    -      -       -      -
    458G  ALA*     3.6    37.0    -      -       +      +
    459G  PHE*     3.8    28.0    -      -       +      +
    462G  ALA*     3.6    18.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 405 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219G  ASP*     2.6    37.2    +      -       -      +
    221G  GLU*     2.7    29.9    +      -       -      +
    222G  ILE*     4.6     3.1    -      -       +      -
    371G  GLU*     2.8    34.4    +      -       -      +
    383G  VAL*     4.3    14.1    -      -       +      -
    384G  GLY      3.3     8.7    -      -       -      +
    385G  LYS*     4.4     4.9    -      -       +      -
    403G  MET*     4.0    20.0    -      -       +      -
    404G  VAL*     1.3    76.9    -      -       -      +
    406G  ILE*     1.3    65.3    +      -       -      +
    407G  LEU*     4.0    11.9    -      -       +      -
    417G  GLY      4.0     0.3    -      -       -      +
    418G  ALA*     3.7     3.5    -      -       -      -
    419G  HIS*     2.7    48.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 406 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382G  LYS      3.7     0.3    -      -       -      +
    383G  VAL*     3.4     6.4    -      -       -      +
    384G  GLY      2.7    36.6    +      -       -      +
    404G  VAL*     4.3     3.1    -      -       +      -
    405G  LYS*     1.3    81.3    -      -       -      +
    407G  LEU*     1.3    69.0    +      -       -      +
    415G  VAL*     4.2     9.9    -      -       +      -
    417G  GLY      3.8     0.4    -      -       -      -
    418G  ALA*     4.0    11.7    -      -       +      -
    442G  CYS*     3.9    20.4    -      -       -      -
    459G  PHE*     3.6    23.8    -      -       +      -
    462G  ALA*     3.5    35.0    -      -       +      +
    463G  ASN*     3.5    39.3    -      -       -      +
    466G  ALA*     4.1     6.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 407 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369G  LYS      3.4    24.2    -      -       -      +
    370G  SER      3.8     2.0    -      -       -      -
    371G  GLU*     3.6    42.4    -      -       +      +
    374G  LEU*     3.9    20.2    -      -       +      -
    381G  TYR*     4.0     6.3    -      -       +      -
    382G  LYS      3.4     2.7    -      -       -      +
    383G  VAL*     3.9    21.3    -      -       +      -
    405G  LYS*     4.0    11.2    -      -       -      -
    406G  ILE*     1.3    83.5    -      -       -      +
    408G  GLY*     1.3    52.9    +      -       -      +
    415G  VAL*     3.6     2.8    -      -       -      +
    416G  LEU*     2.7    33.5    +      -       -      -
    417G  GLY      3.0    18.0    +      -       -      +
    419G  HIS*     4.1    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 408 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381G  TYR*     3.2     5.4    -      -       -      +
    382G  LYS*     2.8    40.9    +      -       -      +
    406G  ILE      4.1     1.0    -      -       -      -
    407G  LEU*     1.3    74.8    -      -       -      +
    409G  GLN*     1.3    64.3    +      -       -      -
    413G  ASP      4.8     0.2    -      -       -      -
    414G  ARG      3.3     9.4    -      -       -      -
    416G  LEU*     3.9     4.0    -      -       -      -
    442G  CYS*     4.0    21.1    -      -       -      -
    466G  ALA*     5.1     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 409 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379G  ILE*     4.3     7.4    -      -       +      -
    380G  GLU*     3.4    14.4    +      -       -      +
    382G  LYS*     3.9     2.1    -      -       -      -
    408G  GLY*     1.3    72.5    -      -       -      -
    410G  LYS*     1.3    63.1    +      -       -      +
    411G  SER*     2.4    52.3    +      -       -      +
    412G  THR*     2.5    35.2    +      -       +      +
    413G  ASP*     2.7    30.8    +      -       -      -
    414G  ARG*     2.8    16.2    +      -       +      +
    416G  LEU*     3.6    19.3    -      -       +      +
   2028G  SO4      2.5    37.8    +      -       -      +
----------------------------------------------------------
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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