Contacts of the strand formed by residues 165 - 171 (chain A) in PDB entry 2XRG


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 165 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  PRO      3.8     1.3    +      -       -      +
    164A  PRO*     1.3    73.3    -      -       -      +
    166A  ILE*     1.3    65.1    +      -       -      +
    167A  ILE*     3.9    31.4    -      -       +      -
    259A  LEU*     5.1     0.7    -      -       +      -
    301A  SER      3.2    10.3    +      -       -      +
    302A  VAL*     3.5    14.6    -      -       +      +
    303A  TYR*     3.0    27.4    +      -       -      +
    352A  ASN*     3.4    22.7    -      -       +      +
    354A  ILE*     3.9    15.7    -      -       +      -
    512A  MET*     4.2    19.1    -      -       +      +
    515A  LEU*     3.8    32.8    -      -       +      -
    516A  LEU*     4.4    19.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  PRO*     5.7     0.2    -      -       +      -
    165A  LEU*     1.3    77.7    -      -       -      +
    167A  ILE*     1.3    71.5    +      -       -      +
    168A  PHE*     3.8     4.5    +      -       +      +
    288A  ILE*     4.1    27.1    -      -       +      -
    292A  LEU*     4.4    14.6    -      -       +      -
    303A  TYR*     3.5    27.6    -      -       +      +
    305A  PHE*     5.4     5.6    -      -       +      -
    338A  LEU*     4.4    26.5    -      -       +      -
    342A  LEU*     4.7     9.0    -      -       +      -
    351A  VAL*     3.7    21.8    -      -       +      -
    352A  ASN      3.2     7.9    +      -       -      +
    353A  VAL*     3.7    15.0    -      -       +      +
    354A  ILE*     3.2    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  LEU*     3.9    22.7    -      -       +      -
    166A  ILE*     1.3    75.0    -      -       -      +
    168A  PHE*     1.3    56.8    +      -       -      +
    169A  SER*     4.6     4.0    -      -       -      +
    259A  LEU*     4.3    12.8    -      -       +      -
    273A  PHE*     4.3    17.0    -      -       +      -
    302A  VAL*     4.5     1.3    -      -       +      -
    303A  TYR      3.1    16.2    +      -       -      +
    304A  ALA*     3.6     5.0    -      -       +      +
    305A  PHE*     2.8    34.3    +      -       -      +
    354A  ILE*     4.0    13.7    -      -       +      +
    356A  VAL*     4.3    20.4    -      -       +      -
    512A  MET*     3.8    28.5    -      -       -      -
   1862A  SWH      4.2    20.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  ILE*     3.8     5.9    +      -       +      +
    167A  ILE*     1.3    70.3    -      -       -      +
    169A  SER*     1.3    59.8    +      -       -      +
    170A  VAL*     3.9    17.7    +      -       +      -
    285A  ILE*     4.2    14.4    -      -       +      -
    305A  PHE*     3.6    42.0    -      +       +      -
    307A  SER*     5.3     0.7    -      -       -      -
    331A  ILE*     4.7     5.2    -      -       +      -
    334A  THR*     4.4    11.7    -      -       +      -
    335A  VAL*     3.7    29.6    -      -       +      -
    338A  LEU*     4.3    19.7    -      -       +      -
    353A  VAL*     6.4     1.3    -      -       +      -
    354A  ILE      2.8    16.9    +      -       -      +
    355A  PHE*     3.6    35.7    -      +       +      -
    356A  VAL      3.1    25.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  ILE*     3.7     4.3    +      -       -      +
    168A  PHE*     1.3    73.2    -      -       -      +
    170A  VAL*     1.3    62.6    +      -       -      +
    213A  LEU*     4.3    18.5    -      -       -      +
    216A  LEU*     5.9     0.7    -      -       -      -
    305A  PHE*     2.9    21.3    +      -       -      +
    306A  TYR*     3.6    17.1    -      -       -      +
    307A  SER*     3.2    21.8    +      -       -      -
    356A  VAL*     3.3    18.4    -      -       -      -
    357A  GLY*     5.8     1.8    -      -       -      -
   1862A  SWH      4.3    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  PHE*     3.9    22.2    -      -       +      +
    169A  SER*     1.3    77.7    -      -       -      +
    171A  ASP*     1.3    61.3    +      -       -      +
    172A  GLY      3.7     1.9    +      -       -      -
    173A  PHE*     3.8    27.3    +      -       +      -
    306A  TYR*     5.7     0.9    -      -       -      -
    307A  SER*     3.8    20.0    -      -       -      -
    309A  GLN      4.1     7.4    -      -       -      +
    331A  ILE*     4.2    16.6    -      -       +      -
    355A  PHE*     3.8    25.1    -      -       +      -
    356A  VAL      2.9    20.1    +      -       -      +
    357A  GLY*     3.4    22.3    -      -       -      -
    358A  ASP*     3.8     4.0    +      -       -      +
    486A  VAL*     5.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  VAL*     1.3    70.4    -      -       -      +
    172A  GLY*     1.3    65.1    +      -       -      +
    209A  THR*     3.4     4.3    -      -       -      +
    306A  TYR*     2.7    27.7    +      -       +      +
    307A  SER      3.1    21.2    +      -       -      +
    308A  GLU      3.8    13.0    -      -       -      +
    309A  GLN      3.8     0.6    +      -       -      -
    310A  PRO*     3.2    10.2    -      -       -      +
    311A  ASP*     3.1    27.5    +      -       +      -
    358A  ASP*     3.1     7.3    -      -       -      +
    359A  HIS*     3.2     6.2    +      -       -      -
   1862A  SWH      3.3    14.8    +      -       -      -
   1864A   ZN      2.0    37.7    -      -       -      -
----------------------------------------------------------
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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