Contacts of the strand formed by residues 415 - 422 (chain C) 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 VAL 415 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406C  ILE*     4.3     9.0    -      -       +      -
    407C  LEU      3.8     5.6    -      -       -      +
    413C  ASP      3.4     0.4    +      -       -      -
    414C  ARG*     1.3    81.8    +      -       -      +
    416C  LEU*     1.3    62.2    +      -       -      +
    417C  GLY      3.9    19.7    -      -       -      +
    418C  ALA*     4.8     6.1    -      -       +      +
    435C  ALA*     5.1     3.4    -      -       +      -
    436C  LEU*     3.6    34.1    -      -       +      +
    439C  GLY*     6.0     0.3    -      -       -      -
    440C  ALA      3.0    21.5    +      -       -      +
    441C  SER      3.6    17.7    -      -       -      -
    442C  CYS*     3.6     7.9    -      -       -      +
    445C  ILE*     3.7    24.5    -      -       +      -
    459C  PHE*     6.1     0.4    -      -       +      -
    463C  ASN*     3.7     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 416 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352C  ASN*     5.0     2.8    +      -       -      -
    368C  GLY*     3.4     7.9    -      -       -      -
    369C  LYS*     2.9    26.9    +      -       +      +
    374C  LEU*     3.8    25.6    -      -       +      -
    379C  ILE*     3.7    27.6    -      -       +      -
    381C  TYR*     4.5     0.9    -      -       +      -
    407C  LEU*     2.7    10.7    +      -       -      +
    408C  GLY      4.1     3.8    -      -       -      +
    409C  GLN*     3.7    43.5    -      -       +      +
    414C  ARG*     3.6    21.1    -      -       +      +
    415C  VAL*     1.3    77.9    -      -       -      +
    417C  GLY*     1.3    58.6    +      -       -      +
    436C  LEU*     4.5     5.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 417 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367C  VAL      3.6     6.3    -      -       -      -
    369C  LYS      3.6    19.3    -      -       -      -
    405C  LYS      4.0     0.3    -      -       -      +
    406C  ILE*     3.5     5.9    -      -       -      +
    407C  LEU*     2.8    36.8    +      -       -      +
    415C  VAL*     3.6     4.8    -      -       -      +
    416C  LEU*     1.3    82.0    -      -       -      +
    418C  ALA*     1.3    61.2    +      -       -      +
    419C  HIS*     4.0     4.9    -      -       -      -
    436C  LEU*     5.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 418 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366C  TRP*     3.1     7.2    -      -       -      +
    367C  VAL*     3.0    38.1    +      -       +      +
    405C  LYS      3.8     3.6    -      -       -      -
    406C  ILE*     3.9    16.4    -      -       +      -
    415C  VAL*     4.8     6.7    -      -       +      -
    417C  GLY*     1.3    74.1    -      -       -      +
    419C  HIS*     1.3    61.5    +      -       -      +
    420C  ILE*     5.1     4.0    -      -       +      -
    429C  VAL*     5.2     0.4    -      -       +      +
    432C  ALA*     3.6    31.0    -      -       +      -
    436C  LEU*     5.5     1.1    -      -       +      +
    459C  PHE*     4.0     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 419 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219C  ASP*     3.6    21.1    +      -       +      +
    222C  ILE*     3.7    24.4    -      -       +      +
    365C  ALA      3.6     3.8    -      -       -      +
    366C  TRP*     3.2    34.1    -      +       +      +
    367C  VAL      4.9     2.0    -      -       -      -
    368C  GLY      4.9     0.2    -      -       -      -
    369C  LYS      2.6    32.5    +      -       -      -
    370C  SER*     3.5    18.4    -      -       -      -
    403C  MET      3.9     0.9    -      -       -      +
    404C  VAL*     3.5     2.8    -      -       -      +
    405C  LYS*     2.8    55.6    +      -       +      +
    406C  ILE*     4.9     0.8    -      -       -      +
    407C  LEU*     3.9    12.3    -      -       +      +
    417C  GLY*     4.0     3.1    -      -       -      -
    418C  ALA*     1.3    82.6    +      -       -      +
    420C  ILE*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 420 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222C  ILE*     4.8     2.6    -      -       -      +
    364C  VAL*     3.1     9.2    -      -       -      +
    365C  ALA      2.7    45.6    +      -       -      +
    388C  PHE*     4.0    25.8    -      -       +      -
    403C  MET      3.7     1.8    -      -       -      -
    404C  VAL*     4.0    21.3    -      -       +      -
    418C  ALA      5.2     2.0    -      -       -      -
    419C  HIS*     1.3    83.8    -      -       -      +
    421C  LEU*     1.3    61.8    +      -       -      +
    422C  GLY      4.0     0.4    -      -       -      -
    425C  ALA*     3.5    28.9    -      -       +      +
    428C  MET*     4.0    16.4    -      -       +      +
    429C  VAL*     3.9    34.5    -      -       +      +
    432C  ALA*     5.2     0.9    -      -       +      -
    459C  PHE*     4.8     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 421 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222C  ILE*     4.0    20.6    -      -       +      +
    225C  ASN*     3.3    36.6    -      -       +      +
    226C  PHE*     3.6    42.0    -      -       +      +
    229C  ILE*     4.0    11.7    -      -       +      -
    362C  PRO*     3.9    15.7    -      -       +      -
    363C  GLU      3.6     6.5    -      -       -      +
    364C  VAL*     3.9     6.1    -      -       +      -
    388C  PHE*     3.4     3.8    -      -       -      -
    402C  GLY*     3.2    14.7    -      -       -      -
    403C  MET*     2.8    41.7    +      -       +      +
    419C  HIS      4.3     0.2    -      -       -      -
    420C  ILE*     1.3    72.3    -      -       -      +
    422C  GLY*     1.3    57.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 422 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362C  PRO*     3.6    16.4    -      -       -      +
    363C  GLU      2.9    26.1    +      -       -      +
    388C  PHE*     3.7     4.9    -      -       -      -
    401C  ASP      3.6     7.9    -      -       -      -
    420C  ILE      4.0     1.2    -      -       -      -
    421C  LEU*     1.3    75.5    -      -       -      +
    423C  PRO*     1.3    78.2    -      -       -      +
    424C  GLY      3.6     0.2    +      -       -      -
    425C  ALA*     3.5    10.3    +      -       -      -
----------------------------------------------------------
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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