Contacts of the strand formed by residues 58 - 63 (chain A) in PDB entry 2XZF


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 TYR 58 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     4.3     0.9    -      -       -      -
     54A  ARG*     3.2     9.6    -      -       -      +
     55A  ARG      2.8    41.0    +      -       -      +
     56A  GLY*     5.1     0.4    -      -       -      -
     57A  LYS*     1.3    84.2    -      -       -      +
     59A  LEU*     1.3    59.4    +      -       -      +
     60A  ILE*     4.2     0.2    -      -       -      +
     70A  ILE*     3.6    23.3    -      -       +      -
     71A  SER      3.7     3.8    -      -       -      +
     72A  HIS*     3.6    31.8    -      +       +      -
    125A  TYR*     3.5    20.6    -      +       -      -
    126A  PHE*     3.5    29.6    -      +       +      -
    129A  LYS*     3.7    16.5    -      -       +      +
    131A  ILE*     4.3    21.8    -      -       +      +
    400A  GOL      2.6    29.9    +      -       -      -
      9B    T      4.3    12.5    +      -       -      -
     10B    T      4.1     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     3.7    22.2    -      -       +      +
      9A  VAL*     3.9    17.0    -      -       +      -
     10A  ARG*     3.6    38.1    -      -       +      +
     13A  LEU*     4.4     7.4    -      -       +      -
     52A  ILE*     4.1     7.2    -      -       +      -
     53A  SER      3.7     7.9    -      -       -      +
     54A  ARG*     4.9     0.7    -      -       +      -
     57A  LYS      3.9     1.2    +      -       -      -
     58A  TYR*     1.3    73.8    -      -       -      +
     60A  ILE*     1.3    60.8    +      -       -      +
     61A  PHE*     4.1     8.3    -      -       +      -
     69A  LEU      3.6     0.2    -      -       -      +
     70A  ILE*     3.4     4.5    -      -       -      +
     71A  SER*     2.8    43.7    +      -       -      +
     73A  LEU*     3.9    11.2    -      -       +      -
     79A  TYR*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  ILE*     3.4     4.6    -      -       -      -
     53A  SER*     2.7    50.7    +      -       -      +
     54A  ARG      4.2     7.0    -      -       -      +
     55A  ARG*     4.1    18.2    -      -       +      +
     58A  TYR      4.2     5.4    -      -       -      +
     59A  LEU*     1.3    78.5    -      -       -      +
     61A  PHE*     1.3    61.6    +      -       -      +
     62A  GLU*     3.6     6.0    +      -       +      +
     68A  ARG*     4.1    34.3    -      -       +      -
     69A  LEU      3.5     4.7    -      -       -      +
     70A  ILE*     4.5     9.0    -      -       +      -
    122A  VAL*     4.4    12.8    -      -       +      -
    126A  PHE*     3.8    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     3.8    31.2    -      -       +      -
     17A  ILE*     3.9    10.1    -      -       +      -
     49A  ILE*     5.0     2.9    -      -       +      -
     51A  GLY      3.8     4.0    -      -       -      -
     52A  ILE*     3.4    20.2    -      -       +      -
     59A  LEU*     4.5     8.3    -      -       +      -
     60A  ILE*     1.3    74.5    -      -       -      +
     62A  GLU*     1.3    59.2    +      -       -      +
     63A  ILE*     3.8    21.6    +      -       +      +
     68A  ARG*     3.3     6.9    -      -       -      -
     69A  LEU*     2.9    61.6    +      -       +      +
     71A  SER*     4.0    12.1    -      -       -      -
     79A  TYR*     3.6    31.9    -      +       -      -
     96A  MET*     5.0     9.9    -      -       +      -
    103A  LEU*     3.9    19.5    -      -       +      -
    114A  TRP*     5.4     1.1    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ILE*     3.7     0.9    -      -       -      +
     50A  GLN*     2.7    39.5    +      -       +      +
     51A  GLY*     2.8    39.5    +      -       -      +
     52A  ILE      4.1     0.7    +      -       -      -
     53A  SER*     2.7    31.1    +      -       -      -
     60A  ILE*     4.1     6.9    -      -       +      +
     61A  PHE*     1.3    72.0    -      -       -      +
     63A  ILE*     1.3    55.7    +      -       -      +
     68A  ARG*     3.6    42.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ILE*     4.0    17.3    -      -       +      -
     44A  LEU*     4.0    28.3    -      -       +      -
     47A  LYS*     3.7    21.8    -      -       +      -
     48A  THR      3.7     9.6    -      -       -      +
     49A  ILE*     4.1    11.2    -      -       +      -
     61A  PHE*     3.8    27.4    -      -       +      +
     62A  GLU*     1.3    79.1    -      -       -      +
     64A  GLY*     1.3    70.1    +      -       -      +
     67A  PHE*     3.1    36.4    +      -       +      +
     68A  ARG*     4.0     1.0    -      -       -      +
     69A  LEU*     4.3     7.0    -      -       +      +
     96A  MET*     3.9    25.1    -      -       +      -
----------------------------------------------------------
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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