Contacts of the strand formed by residues 46 - 53 (chain A) in PDB entry 3ZUU


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 LEU 46 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  VAL*     3.3    37.7    -      -       +      -
     37A  LEU*     5.0     3.4    -      -       +      -
     38A  MET      3.7    10.5    -      -       -      +
     39A  ARG*     4.1     9.9    -      -       +      -
     44A  ASN      3.7     1.3    +      -       -      +
     45A  GLU*     1.3    78.9    -      -       -      +
     47A  VAL*     1.3    69.2    +      -       -      +
     96A  TYR*     3.6    48.9    +      -       +      +
     98A  SER*     4.5    11.2    -      -       -      -
    109B  ALA*     4.0    19.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  TYR*     4.0    18.4    -      -       +      -
     36A  ARG      3.6     0.2    -      -       -      +
     37A  LEU*     3.3     7.6    -      -       -      +
     38A  MET*     2.9    59.4    +      -       +      +
     40A  ASP*     4.9     3.4    -      -       +      +
     45A  GLU*     3.5    29.2    -      -       +      +
     46A  LEU*     1.3    81.8    -      -       -      +
     48A  ALA*     1.3    62.4    +      -       -      +
     49A  VAL*     4.8     1.1    -      -       +      -
     81A  LYS*     4.5     6.5    -      -       +      -
     93A  VAL*     4.0    24.0    -      -       +      -
     94A  MET      3.3    14.4    -      -       -      +
     96A  TYR*     3.9     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  PHE*     4.1    23.6    -      -       +      -
     35A  ALA*     5.1     3.6    -      -       +      -
     36A  ARG      3.2     5.4    -      -       -      +
     37A  LEU*     4.1     6.7    -      -       +      -
     47A  VAL*     1.3    75.5    -      -       -      +
     49A  VAL*     1.3    63.3    +      -       -      +
     50A  LYS*     4.3     0.4    -      -       +      -
     92A  ILE      3.6     1.2    -      -       -      +
     93A  VAL*     3.5     2.6    -      -       -      -
     94A  MET*     2.9    40.0    +      -       +      +
     95A  GLU      4.7     0.2    -      -       -      +
     96A  TYR*     3.9    26.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  HIS*     4.8     2.5    -      -       +      +
     35A  ALA*     3.3     8.0    -      -       -      +
     36A  ARG*     2.9    37.5    +      -       +      +
     38A  MET*     3.9    31.6    -      -       +      -
     47A  VAL*     4.8     1.3    -      -       +      -
     48A  ALA*     1.3    81.4    -      -       -      +
     50A  LYS*     1.3    71.0    -      -       -      +
     51A  TYR*     3.5    38.3    -      -       +      +
     91A  ALA*     4.0    12.6    -      -       +      -
     92A  ILE      3.2    10.3    -      -       -      +
     93A  VAL*     4.0    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  PHE*     2.9    31.6    +      -       +      +
     33A  GLY*     3.2    18.6    -      -       -      -
     34A  VAL      3.3    21.1    +      -       -      +
     35A  ALA*     3.9     5.6    -      -       +      -
     48A  ALA*     6.5     0.2    -      -       +      -
     49A  VAL*     1.3    75.7    -      -       -      +
     51A  TYR*     1.3    64.5    +      -       -      +
     52A  ILE*     4.3     1.3    -      -       +      -
     90A  LEU      3.6     3.3    -      -       -      +
     91A  ALA*     3.7     2.8    -      -       -      -
     92A  ILE*     3.0    45.0    +      -       +      +
     94A  MET*     3.6    26.4    -      -       +      +
    162A  GLY      4.6    13.7    +      -       -      +
    163A  TYR*     4.6    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     3.9    30.7    -      -       +      -
     13A  PRO*     3.7    31.9    -      -       +      -
     16A  HIS*     2.9    36.0    +      +       -      -
     34A  VAL      5.6     1.7    +      -       -      -
     35A  ALA*     5.7     1.1    -      -       -      -
     36A  ARG*     3.6    26.2    +      -       +      -
     49A  VAL*     3.5    27.7    -      -       +      +
     50A  LYS*     1.3    79.5    -      -       -      +
     52A  ILE*     1.3    64.5    +      -       -      +
     53A  GLU*     5.7     0.3    -      -       -      +
     86A  THR*     4.9     1.6    -      -       +      -
     89A  HIS*     3.9    26.8    -      -       +      +
     90A  LEU      3.7     1.8    -      -       -      -
     91A  ALA*     3.9    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  LYS*     5.5     1.3    -      -       +      -
     51A  TYR*     1.3    76.6    -      -       -      +
     53A  GLU*     1.3    68.2    +      -       +      +
     57A  LYS*     4.0    31.9    -      -       +      +
     58A  ILE*     4.1    13.3    -      -       +      +
     62A  VAL*     4.3    31.2    -      -       +      -
     89A  HIS*     3.1     8.7    -      -       -      -
     90A  LEU*     3.0    34.8    +      -       +      +
     92A  ILE*     4.4    20.6    -      -       +      -
    163A  TYR*     4.8    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  TYR      5.7     0.4    -      -       -      +
     52A  ILE*     1.3    76.1    -      -       +      +
     54A  ARG*     1.3    72.2    +      -       -      +
     55A  GLY      3.6     0.5    +      -       -      -
     57A  LYS*     3.1    48.9    +      -       +      +
     58A  ILE*     3.7    11.1    -      -       -      +
     88A  THR      3.5     3.1    -      -       -      +
     89A  HIS*     3.3    24.0    +      -       +      +
----------------------------------------------------------
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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