Contacts of the strand formed by residues 363 - 368 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  VAL*     5.0     0.7    -      -       +      -
    358A  ILE      3.3    13.7    -      -       -      +
    359A  TYR*     4.3    10.4    -      -       -      +
    360A  THR      3.2    15.4    -      -       -      +
    361A  HIS*     5.1     4.3    -      -       -      +
    362A  PRO*     1.3    74.7    -      -       -      +
    364A  VAL*     1.3    63.2    +      -       -      +
    421A  LEU*     3.6     2.9    -      -       -      +
    422A  GLY      2.9    32.9    +      -       -      +
    423A  PRO*     5.5     0.7    -      -       +      -
    424A  GLY*     3.6    10.6    -      -       -      +
    425A  ALA*     3.2    20.7    +      -       +      +
    426A  GLY*     2.9    28.3    +      -       -      +
    427A  GLU      4.5     0.5    +      -       -      -
    393B  ARG*     2.8    33.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 364 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  ILE*     4.1     5.8    -      -       +      -
    222A  ILE*     3.7    29.6    -      -       +      -
    226A  PHE*     3.5    50.0    -      -       +      -
    357A  VAL*     3.2     4.7    -      -       -      +
    358A  ILE*     2.7    46.4    +      -       +      -
    360A  THR*     4.4     0.2    -      -       -      +
    363A  GLU*     1.3    77.4    -      -       -      +
    365A  ALA*     1.3    67.4    +      -       -      +
    366A  TRP*     3.8    19.7    -      -       +      -
    420A  ILE      3.3     5.2    -      -       -      +
    421A  LEU*     4.0     4.0    -      -       +      +
    425A  ALA*     4.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 365 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  SER      3.2     9.0    -      -       -      +
    357A  VAL*     3.8     6.3    -      -       +      -
    364A  VAL*     1.3    79.0    -      -       -      +
    366A  TRP*     1.3    66.6    +      -       -      +
    418A  ALA      3.9     0.2    -      -       -      +
    419A  HIS*     3.6     0.7    -      -       -      -
    420A  ILE*     2.8    42.5    +      -       +      +
    425A  ALA*     3.3    35.2    -      -       +      +
    429A  VAL*     3.6    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 366 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  VAL*     5.6     3.1    -      -       +      -
    214A  GLY      4.3     5.8    -      -       -      -
    216A  VAL      4.0     9.9    -      -       -      -
    217A  GLY*     3.7    18.5    +      -       -      -
    218A  ILE*     3.7    42.4    -      -       +      -
    219A  ASP      5.5     0.2    -      -       -      -
    222A  ILE*     5.7     1.1    -      -       +      -
    354A  VAL      4.5     0.2    -      -       -      +
    355A  PRO*     3.2     3.6    -      -       -      +
    356A  SER*     2.8    67.6    +      -       -      +
    358A  ILE*     4.1    22.9    -      -       +      -
    364A  VAL*     3.8    27.1    -      -       +      -
    365A  ALA*     1.3    82.9    -      -       -      +
    367A  VAL*     1.3    64.7    +      -       -      +
    368A  GLY      4.7     8.1    -      -       -      -
    418A  ALA      3.1    14.1    -      -       -      +
    419A  HIS*     3.4    25.4    -      +       +      +
    429A  VAL*     3.7     6.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 367 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352A  ASN      3.8     0.2    -      -       -      +
    353A  CYS*     3.4    39.7    -      -       -      +
    354A  VAL      4.0     2.2    -      -       -      -
    355A  PRO*     3.8    18.2    -      -       +      -
    366A  TRP*     1.3    79.6    -      -       -      +
    368A  GLY*     1.3    68.8    +      -       -      +
    417A  GLY*     3.5     0.5    -      -       -      -
    418A  ALA*     3.0    30.9    +      -       +      +
    419A  HIS*     4.8     1.0    +      -       -      -
    429A  VAL*     4.2     4.3    -      -       +      -
    432A  ALA*     3.9    29.2    -      -       +      -
    433A  ALA*     4.1    12.8    -      -       +      +
    436A  LEU*     3.8    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 368 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352A  ASN*     2.9    39.4    +      -       -      +
    354A  VAL      5.4     0.2    +      -       -      -
    366A  TRP*     4.7    10.0    -      -       -      -
    367A  VAL*     1.3    78.5    -      -       -      +
    369A  LYS*     1.3    62.2    +      -       -      +
    373A  GLN*     4.0     5.7    +      -       -      +
    416A  LEU      3.5    10.3    -      -       -      -
    436A  LEU*     3.5     9.0    -      -       -      -
----------------------------------------------------------
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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