Contacts of the strand formed by residues 247 - 251 (chain A) in PDB entry 2XTJ


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 247 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  GLU*     4.6     1.0    -      -       -      +
    182A  VAL*     3.2    25.4    -      -       +      +
    184A  LEU*     3.5    44.0    -      -       +      -
    199A  ARG      3.3     7.7    +      -       -      +
    200A  VAL*     3.5    20.6    -      -       +      -
    201A  MET*     2.8    28.2    +      -       -      +
    230A  LEU      5.2     0.4    -      -       -      +
    231A  ALA*     3.8    19.5    -      -       +      +
    234A  VAL*     3.7    22.7    -      -       +      -
    235A  SER*     3.3    28.7    -      -       -      +
    245A  ALA      4.9     0.2    -      -       -      -
    246A  SER*     1.3    80.7    +      -       -      +
    248A  ARG*     1.3    70.3    +      -       -      +
    249A  SER*     6.5     0.2    -      -       -      -
    286A  LEU*     5.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  GLU*     3.1    37.8    +      -       -      +
    182A  VAL      2.8    10.4    +      -       -      +
    183A  TYR*     3.4    48.2    +      -       +      +
    184A  LEU*     2.8    29.9    +      -       -      +
    200A  VAL*     5.4     0.7    -      -       -      -
    201A  MET*     3.0    46.4    -      -       +      +
    203A  THR*     3.8     8.3    -      -       +      -
    246A  SER*     5.4     0.2    +      -       -      -
    247A  MET*     1.3    80.3    -      -       -      +
    249A  SER*     1.3    61.4    +      -       -      +
    250A  LEU*     3.9     0.6    +      -       -      -
    274A  SER*     6.2     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  LEU*     3.7    10.2    +      -       -      +
    187A  THR      4.6     3.1    +      -       -      -
    188A  SER*     5.3     1.2    -      -       -      -
    189A  ILE*     3.7    44.3    +      -       -      +
    200A  VAL*     4.7     2.2    -      -       -      +
    201A  MET      3.0    13.4    +      -       -      -
    202A  VAL*     4.2    12.9    -      -       -      +
    203A  THR*     2.7    35.7    +      -       -      +
    247A  MET*     4.3     0.4    -      -       -      -
    248A  ARG*     1.3    72.0    -      -       -      +
    250A  LEU*     1.3    61.3    +      -       -      +
    251A  ARG*     4.5     1.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  TYR*     3.7    30.1    -      -       +      -
    184A  LEU      2.8    11.2    +      -       -      +
    185A  LEU*     3.5    16.8    -      -       +      -
    186A  ASP      3.2    24.6    +      -       -      +
    187A  THR      4.6     0.5    -      -       -      +
    203A  THR*     3.7    19.3    -      -       +      +
    205A  PHE*     3.8    23.8    -      -       +      -
    248A  ARG      4.3     2.7    -      -       -      +
    249A  SER*     1.3    81.3    +      -       -      +
    251A  ARG*     1.3    61.4    +      -       -      +
    252A  VAL*     3.8     0.4    -      -       +      -
    267A  GLY*     3.5    31.6    -      -       -      +
    270A  PHE*     3.6    23.3    -      -       +      -
    271A  ILE*     4.3     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  ASP      3.3     7.0    -      -       -      +
    187A  THR      4.7     1.3    -      -       -      +
    188A  SER*     3.8    34.5    +      -       -      +
    205A  PHE*     3.0    20.2    +      -       -      +
    206A  GLU*     2.6    47.0    +      -       +      -
    207A  ASN      3.0    25.1    +      -       -      -
    208A  VAL*     3.9    13.9    -      -       +      +
    211A  GLU*     4.5     1.8    +      -       -      -
    223A  CYS*     4.1    15.6    +      -       -      -
    249A  SER*     5.7     1.3    -      -       -      +
    250A  LEU*     1.3    71.8    -      -       -      +
    252A  VAL*     1.3    63.4    +      -       -      +
    253A  LEU      3.2    17.5    +      -       -      +
    254A  ASN*     3.6    24.7    -      -       -      +
    255A  CYS*     3.7    11.3    -      -       -      +
----------------------------------------------------------
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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