Contacts of the strand formed by residues 162 - 165 (chain G) in PDB entry 1XBT


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 162 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141E  PRO      3.4    26.5    -      -       -      -
    142E  LEU      2.7    28.7    +      -       -      -
    143E  ALA      3.8     8.9    -      -       -      -
    144E  GLU*     2.8    24.9    +      -       -      -
     27G  PRO*     3.6     6.0    -      -       -      +
    130G  ARG*     3.4    34.1    -      -       +      -
    161G  ALA*     1.3    94.9    -      -       +      +
    163G  THR*     1.3    64.4    +      -       -      +
    183G  SER*     3.4     5.5    -      -       -      -
    184G  VAL*     2.8    39.3    +      -       +      +
    185G  CYS      3.9     3.8    -      -       -      -
    186G  ARG*     3.1    36.3    +      -       +      -
    189G  TYR*     4.3    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 163 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27G  PRO*     3.5     4.5    -      -       -      +
     28G  MET*     3.1    58.0    +      -       +      +
    124G  LEU*     4.6     2.3    -      -       -      +
    126G  GLY      5.1     2.7    +      -       -      -
    127G  THR      4.2     5.4    +      -       -      +
    128G  PHE*     3.5    24.3    -      -       -      +
    130G  ARG*     5.5     0.2    -      -       -      +
    162G  TYR*     1.3    77.2    -      -       -      +
    164G  LYS*     1.3    61.4    +      -       -      +
    181G  TYR*     3.7    23.3    -      -       +      -
    182G  HIS      3.5     6.7    -      -       -      +
    183G  SER*     5.0     0.4    -      -       -      +
    189G  TYR*     3.8     7.5    -      -       -      -
   7195G  TTP      3.9    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 164 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128G  PHE      5.0     0.4    -      -       -      -
    155G  GLU*     2.8    32.1    +      -       -      -
    162G  TYR      4.2     0.6    -      -       -      -
    163G  THR*     1.3    72.8    -      -       -      +
    165G  ARG*     1.3    72.9    +      -       -      +
    166G  LEU*     4.6    11.2    -      -       +      +
    181G  TYR*     3.2     8.3    -      -       -      -
    182G  HIS*     2.8    40.7    +      -       +      +
    184G  VAL*     4.4    13.2    -      -       +      +
    188G  CYS      2.8    25.9    +      -       -      +
    189G  TYR*     4.0    31.5    +      -       +      +
    191G  LYS*     4.5    11.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 165 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128G  PHE*     3.3    50.6    +      -       +      +
    164G  LYS*     1.3    84.0    -      -       -      +
    166G  LEU*     1.3    65.2    +      -       -      +
    167G  GLY      3.9    18.2    -      -       -      +
    169G  GLU*     2.9    47.6    +      -       -      +
    171G  GLU      2.7    21.6    +      -       -      -
    172G  VAL      2.9    25.1    +      -       -      -
    174G  VAL*     3.5    14.6    -      -       -      +
    180G  LYS*     3.7    11.2    -      -       +      +
    181G  TYR*     2.9    33.3    +      -       +      -
   7195G  TTP      3.6     3.0    +      -       -      -
----------------------------------------------------------
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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