Contacts of the strand formed by residues 403 - 409 (chain H) in PDB entry 1ZMD


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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221H  GLU*     3.7    30.3    -      -       +      +
    222H  ILE*     4.0    21.0    -      -       +      +
    225H  ASN*     3.3    29.6    -      -       -      +
    385H  LYS*     4.2    28.0    -      -       -      -
    386H  PHE      3.3    15.3    -      -       -      +
    387H  PRO*     3.9     7.2    -      -       +      -
    388H  PHE*     3.6     6.0    -      -       -      -
    402H  GLY*     1.3    78.5    -      -       -      +
    404H  VAL*     1.3    68.1    +      -       -      +
    405H  LYS*     4.5     5.8    -      -       +      -
    419H  HIS      4.0     0.9    -      -       -      +
    420H  ILE*     3.8     0.9    -      -       -      -
    421H  LEU*     2.8    34.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 404 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385H  LYS*     3.2     5.5    -      -       -      +
    386H  PHE      2.9    32.9    +      -       -      +
    388H  PHE*     3.8    13.7    -      -       +      -
    403H  MET*     1.3    78.7    -      -       -      +
    405H  LYS*     1.3    62.5    +      -       -      +
    406H  ILE*     4.2     7.9    -      -       +      -
    419H  HIS      3.6     7.4    -      -       -      +
    420H  ILE*     4.1    13.2    -      -       +      -
    428H  MET*     4.1     4.3    -      -       -      -
    458H  ALA*     3.7    31.9    -      -       +      +
    459H  PHE*     3.9    26.2    -      -       +      +
    462H  ALA*     3.4    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 405 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219H  ASP*     2.9    37.4    +      -       -      -
    221H  GLU*     2.7    33.0    +      -       -      +
    222H  ILE*     4.6     6.3    -      -       +      -
    371H  GLU*     2.7    26.5    +      -       -      +
    383H  VAL*     4.0    16.8    -      -       +      -
    384H  GLY      3.3     3.6    -      -       -      +
    385H  LYS*     3.9    17.3    -      -       +      +
    403H  MET*     4.2     8.7    -      -       +      -
    404H  VAL*     1.3    75.0    -      -       -      +
    406H  ILE*     1.3    68.0    +      -       -      +
    407H  LEU*     4.2    11.9    -      -       +      -
    418H  ALA*     3.6     2.3    -      -       -      -
    419H  HIS*     2.8    53.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 406 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382H  LYS      3.7     0.3    -      -       -      +
    383H  VAL*     3.4     7.1    -      -       -      +
    384H  GLY      2.8    35.1    +      -       -      +
    404H  VAL*     4.2     2.2    -      -       +      -
    405H  LYS*     1.3    78.1    -      -       -      +
    407H  LEU*     1.3    71.2    +      -       -      +
    408H  GLY      4.1     0.2    +      -       -      -
    415H  VAL*     4.5     6.1    -      -       +      -
    417H  GLY      3.6     2.9    -      -       -      +
    418H  ALA*     3.7    17.9    -      -       +      -
    442H  CYS*     3.7    21.5    -      -       -      -
    459H  PHE*     3.6    22.7    -      -       +      -
    462H  ALA*     3.6    30.1    -      -       +      +
    463H  ASN*     3.5    38.6    -      -       -      +
    466H  ALA*     3.9     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 407 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219H  ASP*     4.7     0.9    -      -       -      +
    369H  LYS      3.2    26.5    -      -       -      +
    370H  SER      3.7     1.6    -      -       -      -
    371H  GLU*     3.5    46.7    -      -       +      +
    374H  LEU*     3.8    19.3    -      -       +      -
    381H  TYR*     4.1     4.5    -      -       +      -
    382H  LYS      3.3     3.1    -      -       -      +
    383H  VAL*     3.9    20.6    -      -       +      -
    405H  LYS*     4.2    10.1    -      -       -      -
    406H  ILE*     1.3    77.8    -      -       -      +
    408H  GLY*     1.3    53.8    +      -       -      +
    415H  VAL*     3.7     2.4    -      -       -      -
    416H  LEU*     2.7    32.3    +      -       -      -
    417H  GLY      2.9    17.0    +      -       -      +
    419H  HIS*     3.6    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 408 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381H  TYR*     3.2     4.5    -      -       -      +
    382H  LYS*     2.7    46.6    +      -       -      -
    406H  ILE*     4.1     2.4    -      -       -      +
    407H  LEU*     1.3    74.3    -      -       -      +
    409H  GLN*     1.3    64.8    +      -       -      -
    413H  ASP      4.9     0.2    -      -       -      -
    414H  ARG      3.3     8.5    -      -       -      -
    416H  LEU*     4.0     4.5    -      -       -      -
    442H  CYS*     3.9    18.2    -      -       -      -
    466H  ALA*     5.0     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 409 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379H  ILE*     4.2     9.1    -      -       +      +
    380H  GLU      3.9     3.8    -      -       -      +
    382H  LYS*     4.0     2.1    -      -       -      -
    408H  GLY*     1.3    70.7    -      -       -      -
    410H  LYS*     1.3    61.8    +      -       -      +
    411H  SER*     3.6    14.1    +      -       -      +
    412H  THR*     3.3    22.8    +      -       -      +
    413H  ASP*     2.8    28.8    +      -       -      -
    414H  ARG*     2.8    23.8    +      -       -      +
    416H  LEU*     3.6    32.1    -      -       +      +
   2029H  SO4      2.6    36.8    +      -       -      +
----------------------------------------------------------
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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