Contacts of the strand formed by residues 415 - 422 (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 VAL 415 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406H  ILE*     4.5     8.3    -      -       +      -
    407H  LEU      3.8     4.7    -      -       -      +
    414H  ARG*     1.3    84.8    -      -       -      +
    416H  LEU*     1.3    60.7    +      -       -      +
    417H  GLY      3.9    18.6    -      -       -      +
    418H  ALA*     4.9     5.8    -      -       +      +
    432H  ALA*     6.3     0.2    -      -       +      -
    435H  ALA*     5.1     1.6    -      -       +      -
    436H  LEU*     3.7    36.1    -      -       +      +
    439H  GLY*     5.9     0.2    -      -       -      -
    440H  ALA      3.0    20.0    +      -       -      +
    441H  SER      3.6    20.4    -      -       -      +
    442H  CYS*     3.6     8.1    -      -       -      +
    445H  ILE*     3.8    13.5    -      -       +      -
    459H  PHE*     5.9     1.3    -      -       +      -
    463H  ASN*     3.7    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 416 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352H  ASN*     4.9     2.6    +      -       -      -
    368H  GLY*     3.5     5.5    -      -       -      -
    369H  LYS*     2.8    26.0    +      -       +      +
    374H  LEU*     4.0    28.0    -      -       +      -
    379H  ILE*     3.8    24.7    -      -       +      -
    381H  TYR*     4.4     1.1    -      -       +      -
    407H  LEU*     2.7    15.3    +      -       -      +
    408H  GLY      4.0     4.0    -      -       -      +
    409H  GLN*     3.6    45.8    -      -       +      +
    414H  ARG*     3.6    23.1    -      -       -      +
    415H  VAL*     1.3    77.3    -      -       -      +
    417H  GLY*     1.3    55.6    +      -       -      +
    436H  LEU*     4.5     4.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 417 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367H  VAL      3.4    10.8    -      -       -      -
    369H  LYS      3.5    18.2    -      -       -      -
    406H  ILE*     3.6     2.8    -      -       -      -
    407H  LEU*     2.9    31.4    +      -       -      +
    415H  VAL*     3.7     9.1    -      -       -      +
    416H  LEU*     1.3    79.2    -      -       -      +
    418H  ALA*     1.3    61.3    +      -       -      +
    419H  HIS*     4.0     6.3    -      -       -      -
    436H  LEU*     5.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 418 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365H  ALA      4.1     0.2    -      -       -      +
    366H  TRP*     3.1     6.8    -      -       -      +
    367H  VAL*     2.9    35.5    +      -       +      +
    405H  LYS      3.6     4.7    -      -       -      -
    406H  ILE*     3.7    19.3    -      -       +      -
    415H  VAL*     4.9     5.2    -      -       +      -
    417H  GLY*     1.3    72.8    -      -       -      -
    419H  HIS*     1.3    63.2    +      -       -      +
    420H  ILE*     5.0     5.2    -      -       +      -
    429H  VAL*     5.0     0.7    -      -       +      +
    432H  ALA*     3.7    30.3    -      -       +      -
    436H  LEU*     5.7     0.2    -      -       +      -
    459H  PHE*     3.9     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 419 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219H  ASP*     3.6    22.8    +      -       +      +
    222H  ILE*     3.6    25.6    -      -       +      +
    365H  ALA      3.7     2.9    -      -       -      -
    366H  TRP*     3.3    34.4    -      +       +      +
    367H  VAL      4.8     2.5    -      -       -      -
    368H  GLY      4.9     0.2    -      -       -      -
    369H  LYS      2.7    30.1    +      -       -      -
    370H  SER*     3.6    18.9    -      -       -      -
    403H  MET      4.0     0.9    -      -       -      +
    404H  VAL*     3.6     1.9    -      -       -      -
    405H  LYS*     2.8    51.8    +      -       +      +
    406H  ILE*     5.0     0.4    -      -       -      +
    407H  LEU*     3.6    17.0    -      -       +      +
    417H  GLY      4.0     0.2    -      -       -      -
    418H  ALA*     1.3    83.0    +      -       -      +
    420H  ILE*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 420 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222H  ILE*     4.6     2.3    -      -       -      +
    364H  VAL*     3.2     9.6    -      -       -      +
    365H  ALA      2.7    44.3    +      -       -      +
    388H  PHE*     4.0    18.6    -      -       +      -
    403H  MET      3.8     1.3    -      -       -      -
    404H  VAL*     4.1    13.7    -      -       +      -
    418H  ALA*     5.1     3.1    -      -       +      +
    419H  HIS*     1.3    82.9    -      -       -      +
    421H  LEU*     1.3    62.4    +      -       -      +
    425H  ALA*     3.6    26.8    -      -       +      +
    428H  MET*     4.0    29.6    -      -       +      +
    429H  VAL*     3.9    36.8    -      -       +      +
    459H  PHE*     4.8     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 421 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222H  ILE*     4.1    20.1    -      -       +      +
    225H  ASN*     3.6    32.5    -      -       +      +
    226H  PHE*     3.7    27.6    -      -       +      +
    229H  ILE*     3.8    16.6    -      -       +      -
    362H  PRO*     4.0    10.1    -      -       +      -
    363H  GLU      3.6     4.5    -      -       -      +
    364H  VAL*     3.7    27.6    -      -       +      -
    388H  PHE*     3.4     4.8    -      -       -      -
    402H  GLY*     3.1    14.4    -      -       -      -
    403H  MET*     2.8    42.2    +      -       +      +
    420H  ILE*     1.3    74.3    -      -       -      +
    422H  GLY*     1.3    58.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 422 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362H  PRO*     3.7    12.5    -      -       -      +
    363H  GLU*     2.8    30.7    +      -       -      +
    388H  PHE*     3.9     3.1    -      -       -      -
    401H  ASP      3.6     6.5    -      -       -      -
    420H  ILE      4.0     0.8    -      -       -      -
    421H  LEU*     1.3    77.2    -      -       -      +
    423H  PRO*     1.3    77.3    -      -       -      +
    424H  GLY      3.5     0.3    +      -       -      -
    425H  ALA*     3.5    11.3    +      -       -      +
----------------------------------------------------------
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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