Contacts of the strand formed by residues 363 - 368 (chain F) 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 GLU 363 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393E  ARG*     2.8    34.1    +      -       -      -
    357F  VAL*     5.1     0.2    -      -       +      -
    358F  ILE      3.3    12.8    -      -       -      +
    359F  TYR*     4.3    10.8    -      -       -      +
    360F  THR      3.2    15.9    -      -       -      +
    361F  HIS*     5.1     6.1    -      -       +      -
    362F  PRO*     1.3    74.7    -      -       +      +
    364F  VAL*     1.3    68.3    +      -       -      +
    421F  LEU*     3.5     1.7    -      -       -      +
    422F  GLY      2.9    36.4    +      -       -      +
    423F  PRO*     5.1     0.6    -      -       +      +
    424F  GLY*     3.7    11.1    -      -       -      +
    425F  ALA*     3.4    13.3    +      -       +      -
    426F  GLY*     2.8    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 364 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218F  ILE*     4.2     5.4    -      -       +      -
    222F  ILE*     3.6    30.5    -      -       +      -
    226F  PHE*     3.4    46.2    -      -       +      -
    357F  VAL*     3.3     1.9    -      -       -      +
    358F  ILE*     2.7    43.1    +      -       +      +
    363F  GLU*     1.3    81.2    -      -       -      +
    365F  ALA*     1.3    67.9    +      -       -      +
    366F  TRP*     4.0    18.6    -      -       +      -
    420F  ILE      3.2     7.9    -      -       -      +
    421F  LEU*     3.8     5.4    -      -       +      -
    425F  ALA*     4.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 365 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356F  SER      3.1    13.5    -      -       -      +
    357F  VAL*     3.9     8.3    -      -       +      -
    364F  VAL*     1.3    79.3    -      -       -      +
    366F  TRP*     1.3    65.4    +      -       -      +
    419F  HIS*     3.6     0.2    -      -       -      -
    420F  ILE*     2.7    42.4    +      -       +      +
    425F  ALA*     3.4    32.9    -      -       +      +
    429F  VAL*     3.7    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 366 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188F  VAL*     5.8     2.5    -      -       +      -
    214F  GLY      4.5     6.1    -      -       -      -
    216F  VAL      3.9     9.4    -      -       -      -
    217F  GLY*     3.7    17.6    +      -       -      -
    218F  ILE*     3.6    50.9    -      -       +      -
    222F  ILE*     5.7     0.9    -      -       +      -
    354F  VAL      4.5     0.3    -      -       -      +
    355F  PRO*     3.4     1.4    -      -       -      +
    356F  SER*     2.9    60.6    +      -       -      +
    358F  ILE*     4.1    20.9    -      -       +      -
    364F  VAL*     4.0    18.8    -      -       +      -
    365F  ALA*     1.3    85.6    -      -       -      +
    367F  VAL*     1.3    68.4    +      -       -      +
    368F  GLY      4.7     7.6    -      -       -      -
    418F  ALA      3.2    13.2    -      -       -      +
    419F  HIS*     3.3    27.4    -      +       +      +
    429F  VAL*     3.6     5.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 367 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352F  ASN      3.8     0.9    -      -       -      +
    353F  CYS*     3.6    37.5    -      -       -      +
    354F  VAL      4.0     2.7    -      -       -      -
    355F  PRO*     4.0    13.0    -      -       +      -
    366F  TRP*     1.3    78.7    -      -       -      +
    368F  GLY*     1.3    66.8    +      -       -      +
    417F  GLY*     3.5     0.7    -      -       -      -
    418F  ALA*     3.0    34.4    +      -       +      +
    419F  HIS*     4.7     1.4    +      -       -      -
    429F  VAL*     3.9    11.2    -      -       +      -
    432F  ALA*     3.7    35.7    -      -       +      -
    433F  ALA*     4.0     6.5    -      -       +      +
    436F  LEU*     3.9    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 368 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352F  ASN*     3.0    39.6    +      -       -      +
    366F  TRP*     4.7     8.8    -      -       -      -
    367F  VAL*     1.3    76.5    -      -       -      +
    369F  LYS*     1.3    62.1    +      -       -      -
    373F  GLN*     3.9     5.9    +      -       -      +
    416F  LEU      3.4    10.3    -      -       -      -
    419F  HIS*     5.1     0.2    -      -       -      -
    436F  LEU*     3.6     9.9    -      -       -      -
----------------------------------------------------------
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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