Contacts of the strand formed by residues 363 - 368 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393A  ARG*     2.6    34.7    +      -       -      -
    357B  VAL*     5.1     0.7    -      -       +      -
    358B  ILE      3.3    14.1    -      -       -      +
    359B  TYR*     4.2     9.4    -      -       -      +
    360B  THR      3.2    15.7    -      -       -      +
    361B  HIS*     5.2     4.2    +      -       -      +
    362B  PRO*     1.3    76.6    -      -       -      +
    364B  VAL*     1.3    64.3    +      -       -      +
    421B  LEU*     3.7     0.7    -      -       -      +
    422B  GLY      3.0    36.2    +      -       -      +
    423B  PRO*     5.2     0.8    -      -       +      +
    424B  GLY*     3.6    10.0    -      -       -      +
    425B  ALA*     3.2    14.5    +      -       +      -
    426B  GLY*     2.9    28.0    +      -       -      +
    427B  GLU      4.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 364 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  ILE*     4.2     6.1    -      -       +      -
    222B  ILE*     3.7    26.2    -      -       +      -
    226B  PHE*     3.4    47.3    -      -       +      -
    357B  VAL*     3.3     1.9    -      -       -      +
    358B  ILE*     2.7    43.2    +      -       +      +
    362B  PRO      4.2     0.2    -      -       -      +
    363B  GLU*     1.3    80.5    -      -       -      +
    365B  ALA*     1.3    66.9    +      -       -      +
    366B  TRP*     4.0    19.3    -      -       +      -
    420B  ILE      3.2    11.7    -      -       -      +
    421B  LEU*     3.7     5.8    -      -       +      -
    425B  ALA*     4.0     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 365 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356B  SER      3.2    13.5    -      -       -      +
    357B  VAL*     4.0     5.4    -      -       +      -
    364B  VAL*     1.3    78.4    -      -       -      +
    366B  TRP*     1.3    67.4    +      -       -      +
    419B  HIS*     3.6     0.2    -      -       -      -
    420B  ILE*     2.8    37.1    +      -       +      +
    425B  ALA*     3.3    34.3    -      -       +      +
    429B  VAL*     3.7    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 366 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  VAL*     5.6     2.5    -      -       +      -
    214B  GLY      4.1    11.0    -      -       -      -
    216B  VAL      4.0    10.8    -      -       -      -
    217B  GLY*     3.3    20.2    +      -       -      -
    218B  ILE*     3.7    52.5    -      -       +      -
    222B  ILE*     5.7     1.1    -      -       +      -
    354B  VAL      4.5     0.3    -      -       -      +
    355B  PRO*     3.3     3.8    -      -       -      +
    356B  SER*     2.9    63.9    +      -       -      -
    358B  ILE*     4.0    16.4    -      -       +      -
    364B  VAL*     4.0    15.5    -      -       +      -
    365B  ALA*     1.3    85.0    -      -       -      +
    367B  VAL*     1.3    65.9    +      -       -      +
    368B  GLY      4.7     7.4    -      -       -      -
    418B  ALA      3.1    13.7    -      -       -      +
    419B  HIS*     3.3    25.6    -      +       +      +
    429B  VAL*     3.7     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 367 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352B  ASN      3.9     2.5    -      -       -      +
    353B  CYS*     3.6    35.4    -      -       -      +
    354B  VAL      3.9     3.1    -      -       -      -
    355B  PRO*     3.9    19.1    -      -       +      -
    366B  TRP*     1.3    80.8    -      -       -      +
    368B  GLY*     1.3    66.1    +      -       -      +
    417B  GLY*     3.5     0.3    -      -       -      -
    418B  ALA*     2.9    34.2    +      -       +      +
    419B  HIS*     4.8     1.4    +      -       -      -
    429B  VAL*     4.0     3.1    -      -       +      -
    432B  ALA*     3.8    29.8    -      -       +      -
    433B  ALA*     4.1    11.7    -      -       -      +
    436B  LEU*     3.9    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 368 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217B  GLY      5.7     0.7    -      -       -      +
    352B  ASN*     3.2    38.7    +      -       -      +
    354B  VAL      5.3     0.4    +      -       -      -
    366B  TRP*     4.7     9.4    -      -       -      -
    367B  VAL*     1.3    76.4    -      -       -      +
    369B  LYS*     1.3    59.7    +      -       -      +
    373B  GLN*     3.9     6.4    +      -       -      +
    416B  LEU      3.5     9.2    -      -       -      -
    419B  HIS*     5.0     0.4    -      -       -      -
    436B  LEU*     3.7     9.4    -      -       -      -
----------------------------------------------------------
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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