Contacts of the strand formed by residues 45 - 54 (chain E) in PDB entry 3ZWG


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 TRP 45 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  ILE*     3.4    25.4    -      -       +      -
     38E  ASP      3.8     4.9    -      -       -      -
     39E  ASN*     3.0    37.4    +      -       +      -
     41E  SER*     2.9    18.2    +      -       -      -
     43E  LYS      3.5    11.0    -      -       -      -
     44E  THR*     1.3    72.6    -      -       -      +
     46E  THR*     1.3    64.7    +      -       -      +
     63E  HIS      3.8     0.2    -      -       -      +
     64E  LYS*     3.6     6.4    -      -       -      +
     65E  VAL*     2.9    44.4    +      -       +      +
     71E  LEU*     4.5    15.5    -      -       +      -
     92E  TYR*     3.9    21.1    -      +       +      -
     93E  SER      3.3     5.6    -      -       -      +
     94E  MET*     3.8    26.3    -      -       +      +
    100E  LEU*     3.5    28.5    -      -       +      -
    176E  VAL*     3.6    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 46 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  THR*     4.3     4.9    +      -       -      +
     45E  TRP*     1.3    76.1    -      -       -      +
     47E  ALA*     1.3    66.4    +      -       -      +
     48E  MET*     4.4     0.2    -      -       -      +
     63E  HIS*     3.2    33.0    -      -       +      +
     64E  LYS*     2.9    33.0    +      -       -      +
     92E  TYR*     3.4     4.0    -      -       -      -
     93E  SER*     2.7    52.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 47 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149D  TRP*     3.6    23.5    -      -       +      +
     46E  THR*     1.3    76.0    -      -       -      +
     48E  MET*     1.3    62.9    +      -       -      +
     61E  LEU*     3.6    23.8    -      -       +      +
     62E  PRO      3.5    11.2    -      -       -      +
     63E  HIS*     2.9    22.3    +      -       -      +
     92E  TYR*     3.2    27.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 48 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149D  TRP*     2.7    38.4    +      -       -      +
     47E  ALA*     1.3    76.5    -      -       -      +
     49E  ASN*     1.3    65.5    +      -       -      +
     61E  LEU*     4.5     1.3    -      -       -      -
     91E  ALA*     2.9    15.9    +      -       +      +
     92E  TYR      3.6     5.8    -      -       -      -
     93E  SER*     3.5    37.5    -      -       -      +
     99E  THR*     3.5    19.5    -      -       +      +
    125E  GLN*     4.3    15.9    -      -       -      +
    126E  LYS      3.5    32.1    -      -       -      +
    127E  ARG*     3.8    23.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 49 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146D  ASP*     5.0     5.3    +      -       -      -
    147D  ASN      3.9     0.4    -      -       -      +
    148D  GLY*     3.3    22.0    -      -       -      -
     48E  MET*     1.3    84.6    -      -       -      +
     50E  THR*     1.3    77.0    +      -       -      +
     51E  TYR*     3.9     1.8    -      -       -      +
     61E  LEU*     3.7    12.0    -      -       -      +
     89E  VAL      3.8     0.9    -      -       -      +
     90E  ILE*     3.6     1.6    -      -       -      -
     91E  ALA*     2.8    30.4    +      -       -      +
    127E  ARG*     3.6    25.4    -      -       -      +
    128E  ALA*     3.0    43.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 50 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146D  ASP      3.6    17.0    -      -       -      +
    147D  ASN*     3.3    12.1    +      -       -      +
     49E  ASN*     1.3    84.5    +      -       -      +
     51E  TYR*     1.3    66.6    +      -       -      +
     52E  PHE*     3.4    37.1    +      -       +      -
     61E  LEU*     3.8    11.6    -      -       -      +
     73E  TYR*     3.1    33.8    +      -       +      +
     89E  VAL      3.2    16.8    -      -       -      +
     90E  ILE*     3.9     7.2    -      -       +      +
    104E  PHE*     4.5     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 51 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49E  ASN*     3.9     3.4    -      -       -      +
     50E  THR*     1.3    73.8    -      -       -      +
     52E  PHE*     1.3    70.6    +      -       -      +
     53E  ARG*     4.0    20.7    -      -       +      -
     88E  GLY*     3.1     5.9    -      -       -      -
     89E  VAL*     2.8    33.4    +      -       +      +
    128E  ALA*     3.6    27.1    -      -       +      +
    129E  ASP*     3.7    17.5    -      -       +      -
    130E  GLN*     2.7    57.8    +      -       +      +
    133E  TYR*     4.1    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 52 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147D  ASN*     4.2    16.6    -      -       +      -
     50E  THR*     3.4    29.3    +      -       +      -
     51E  TYR*     1.3    83.0    -      -       -      +
     53E  ARG*     1.3    62.7    +      -       -      +
     54E  SER*     3.7    13.4    -      -       -      +
     55E  GLY      3.2    28.9    -      -       -      +
     56E  THR*     3.8    13.2    -      -       -      -
     57E  SER*     3.6    31.6    -      -       -      -
     73E  TYR*     3.9    17.5    -      +       -      -
     75E  GLY*     4.5     3.8    -      -       -      -
     86E  VAL*     4.1    10.1    -      -       +      -
     87E  VAL      3.7     4.0    -      -       -      -
    104E  PHE*     3.9    20.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 53 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51E  TYR*     3.5    22.1    +      -       +      -
     52E  PHE*     1.3    74.0    -      -       -      +
     54E  SER*     1.3    70.0    +      -       -      +
     87E  VAL*     2.7    28.6    +      -       +      +
     88E  GLY      4.9     0.2    -      -       -      +
    130E  GLN*     3.5    31.0    +      -       -      +
    133E  TYR*     3.8    31.6    +      -       +      +
    138E  TYR*     5.5     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 54 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52E  PHE*     3.7     5.1    -      -       -      -
     53E  ARG*     1.3    95.4    +      -       -      +
     55E  GLY*     1.3    62.7    +      -       -      +
     78E  ASN*     4.5     2.2    -      -       -      -
     84E  THR*     4.4    16.1    -      -       -      +
     85E  GLY      3.5    22.8    +      -       -      -
     86E  VAL*     3.2     2.9    -      -       -      -
     87E  VAL*     2.9    36.3    +      -       -      +
----------------------------------------------------------
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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