Contacts of the strand formed by residues 403 - 409 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221F  GLU*     3.9    25.4    -      -       +      +
    222F  ILE*     3.7    27.5    -      -       +      +
    225F  ASN*     3.8    24.5    -      -       -      +
    385F  LYS*     4.0    28.7    -      -       -      -
    386F  PHE      3.2    17.0    -      -       -      +
    387F  PRO*     3.9     7.0    -      -       +      -
    388F  PHE*     3.7     5.4    -      -       -      -
    402F  GLY*     1.3    78.5    -      -       -      +
    404F  VAL*     1.3    64.3    +      -       -      +
    405F  LYS*     4.5    10.1    -      -       +      -
    419F  HIS      3.9     1.0    -      -       -      +
    420F  ILE*     3.6     1.2    -      -       -      -
    421F  LEU*     2.7    44.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 404 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385F  LYS*     3.4     5.0    -      -       -      +
    386F  PHE      3.0    28.4    +      -       -      +
    388F  PHE*     3.6    26.9    -      -       +      -
    403F  MET*     1.3    76.9    -      -       -      +
    405F  LYS*     1.3    60.6    +      -       -      +
    406F  ILE*     4.3     6.7    -      -       +      -
    418F  ALA*     6.3     0.2    -      -       +      -
    419F  HIS      3.6     6.5    -      -       -      +
    420F  ILE*     3.7    15.9    -      -       +      -
    428F  MET*     4.2     5.4    -      -       -      -
    458F  ALA*     3.9    26.0    -      -       +      +
    459F  PHE*     3.9    26.0    -      -       +      +
    462F  ALA*     3.6    19.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 405 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219F  ASP*     2.7    36.7    +      -       -      -
    221F  GLU*     2.7    27.6    +      -       -      +
    222F  ILE*     4.4     9.0    -      -       +      -
    371F  GLU*     2.6    31.5    +      -       -      +
    383F  VAL*     4.1    16.2    -      -       +      -
    384F  GLY      3.5     5.2    -      -       -      +
    385F  LYS*     4.3     7.9    -      -       +      +
    403F  MET*     4.1    12.9    +      -       +      -
    404F  VAL*     1.3    73.7    -      -       -      +
    406F  ILE*     1.3    78.0    +      -       -      +
    407F  LEU*     4.4     7.2    -      -       +      -
    417F  GLY      3.9     0.5    -      -       -      +
    418F  ALA*     3.7     1.6    -      -       -      -
    419F  HIS*     2.8    50.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 406 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382F  LYS      3.7     0.9    -      -       -      +
    383F  VAL*     3.5     5.9    -      -       -      -
    384F  GLY      2.8    36.7    +      -       -      +
    404F  VAL*     4.3     2.9    -      -       +      -
    405F  LYS*     1.3    81.5    -      -       -      +
    407F  LEU*     1.3    69.2    +      -       -      +
    415F  VAL*     4.3     9.0    -      -       +      -
    417F  GLY      3.7     1.1    -      -       -      +
    418F  ALA*     4.1    13.5    -      -       +      -
    442F  CYS*     4.0    20.9    -      -       -      -
    459F  PHE*     3.8    20.6    -      -       +      -
    462F  ALA*     3.5    29.4    -      -       +      +
    463F  ASN*     3.6    37.5    -      -       -      +
    466F  ALA*     4.0     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 407 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219F  ASP*     5.2     0.2    -      -       -      +
    369F  LYS      3.2    25.8    -      -       -      +
    370F  SER      3.8     0.2    -      -       -      -
    371F  GLU*     3.7    35.9    -      -       +      +
    374F  LEU*     3.8    23.1    -      -       +      -
    381F  TYR*     3.9     7.4    -      -       +      -
    382F  LYS      3.5     1.3    -      -       -      -
    383F  VAL*     3.6    26.5    -      -       +      -
    405F  LYS*     4.4     8.7    -      -       +      -
    406F  ILE*     1.3    84.3    -      -       -      +
    408F  GLY*     1.3    52.8    +      -       -      +
    415F  VAL*     3.5     2.4    -      -       -      -
    416F  LEU*     2.6    34.3    +      -       -      -
    417F  GLY      3.0    16.7    +      -       -      +
    419F  HIS*     3.9    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 408 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381F  TYR*     3.1     4.2    -      -       -      +
    382F  LYS*     2.7    44.6    +      -       -      +
    406F  ILE*     4.1     2.6    -      -       -      +
    407F  LEU*     1.3    75.1    -      -       -      +
    409F  GLN*     1.3    65.5    +      -       -      -
    413F  ASP      4.9     0.7    -      -       -      -
    414F  ARG      3.1     9.6    -      -       -      -
    416F  LEU*     3.8     3.6    -      -       -      -
    442F  CYS*     4.0    18.6    -      -       -      -
    466F  ALA*     5.2     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 409 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379F  ILE*     4.7     4.6    -      -       -      +
    380F  GLU      3.1     6.4    -      -       -      +
    382F  LYS*     4.0     2.0    -      -       -      -
    408F  GLY*     1.3    70.0    -      -       -      -
    410F  LYS*     1.3    73.8    +      -       -      +
    411F  SER*     3.1    20.1    +      -       -      -
    412F  THR*     2.9    34.6    -      -       +      +
    413F  ASP*     2.8    30.7    +      -       -      -
    414F  ARG*     2.7    13.8    +      -       +      +
    416F  LEU*     3.3    29.9    -      -       +      +
   2024F  SO4      2.8    41.4    +      -       -      -
----------------------------------------------------------
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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