Contacts of the strand formed by residues 34 - 39 (chain F) in PDB entry 2ZUQ


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 MET 34 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4F  LEU*     3.8    13.2    -      -       +      -
     22F  CYS*     4.9     0.2    -      -       -      -
     27F  PHE*     4.2    12.8    -      -       +      -
     29F  PHE*     5.2     3.6    -      -       +      -
     32F  TYR      5.2     0.2    -      -       -      +
     33F  ASP*     1.3    83.5    -      -       -      +
     35F  SER*     1.3    66.0    +      -       -      +
     50F  TYR*     3.2    10.2    -      -       -      -
     51F  ILE*     2.8    52.1    +      -       +      +
     72F  ARG*     3.7    24.2    -      -       -      +
     79F  LEU*     3.5    31.0    -      -       +      -
     96F  CYS*     3.6    16.8    -      -       -      -
     97F  ALA      3.4    20.6    -      -       -      +
     98F  ARG*     3.7    19.5    -      -       -      -
     99F  PRO*     4.1     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 35 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34F  MET*     1.3    82.1    -      -       -      +
     36F  TRP*     1.3    66.7    +      -       -      +
     37F  VAL*     4.6     0.3    -      -       -      +
     47F  TRP*     4.5     1.6    -      -       -      -
     49F  ALA      3.1    17.9    -      -       -      -
     50F  TYR*     3.7    15.3    -      -       -      +
     70F  ILE*     4.2     3.4    -      -       -      -
     79F  LEU*     4.0     4.5    -      -       -      +
     96F  CYS*     3.8     3.8    -      -       -      -
     97F  ALA      2.9    37.3    +      -       -      +
     99F  PRO*     4.8     1.7    -      -       -      +
    106F  MET*     3.1    30.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 36 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  GLU*     3.7    19.7    -      -       +      -
     20F  LEU*     4.1    10.1    -      -       +      -
     21F  SER      3.7    18.4    -      -       -      -
     22F  CYS*     3.6    27.1    -      -       +      -
     35F  SER*     1.3    73.9    -      -       -      +
     37F  VAL*     1.3    65.0    +      -       -      +
     47F  TRP*     3.8     4.0    -      -       -      -
     48F  VAL*     3.2    25.0    +      -       +      -
     49F  ALA*     3.2    18.2    +      -       +      +
     70F  ILE*     3.4    23.8    -      -       +      +
     79F  LEU*     3.8    10.7    -      -       +      +
     80F  TYR*     3.6    18.1    +      -       -      -
     81F  LEU*     3.4    53.8    -      -       +      +
     94F  TYR*     4.2    21.3    -      -       +      -
     95F  TYR      3.5     7.6    -      -       -      -
     96F  CYS*     3.7    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 37 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123E  PHE*     3.2    33.4    -      -       +      -
     36F  TRP*     1.3    79.4    -      -       -      +
     38F  ARG*     1.3    58.3    +      -       -      +
     45F  LEU*     4.3     3.6    -      -       +      -
     46F  GLU      3.1    24.0    -      -       -      +
     47F  TRP*     3.8     4.0    -      -       +      +
     48F  VAL*     5.2     0.2    -      -       -      -
     94F  TYR*     3.6     1.7    -      -       -      +
     95F  TYR*     2.6    42.7    +      -       -      +
     97F  ALA*     4.4     3.8    -      -       +      -
    106F  MET*     3.6    36.3    -      -       +      -
    109F  TRP*     3.8    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 38 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37F  VAL*     1.3    75.0    -      -       -      +
     39F  GLN*     1.3    61.2    +      -       -      +
     40F  THR*     5.5     2.2    -      -       +      +
     45F  LEU*     3.3     8.3    -      -       -      +
     46F  GLU*     2.7    75.2    +      -       +      +
     48F  VAL*     3.4    21.9    -      -       +      +
     63F  THR*     4.3    10.3    +      -       -      +
     64F  VAL*     4.0    18.0    -      -       -      +
     68F  PHE*     4.0     2.4    -      -       -      -
     89F  GLU*     4.5    10.9    +      -       -      +
     90F  ASP*     2.5    37.4    +      -       -      +
     91F  THR      5.2     0.4    -      -       -      -
     92F  ALA*     3.9    13.7    -      -       +      -
     93F  MET      3.5     8.1    -      -       -      +
     94F  TYR*     3.2    43.3    +      -       +      -
     95F  TYR*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 39 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64E  GLN*     3.1    33.1    +      -       -      +
    113E  TYR*     2.9    30.3    +      -       -      -
     38F  ARG*     1.3    76.4    -      -       -      +
     40F  THR*     1.3    72.3    +      -       -      +
     43F  LYS*     3.0    29.3    +      -       +      +
     44F  ARG      3.0    12.8    -      -       -      +
     45F  LEU*     3.7    17.5    -      -       +      +
     92F  ALA*     3.0     4.1    -      -       -      +
     93F  MET*     2.9    34.2    +      -       +      +
     95F  TYR*     3.7    20.8    +      -       +      -
----------------------------------------------------------
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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