Contacts of the strand formed by residues 111 - 115 (chain D) 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 VAL 111 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  SER*     3.7    21.5    -      -       -      +
    374A  ASP*     3.7    20.9    -      -       -      +
    378A  CYS*     4.3     5.4    -      -       +      -
    379A  PHE      3.3    12.3    -      -       -      +
    380A  VAL*     3.9    17.5    -      -       +      -
    102D  ILE      3.5     0.9    -      -       -      +
    103D  GLN*     3.1     7.3    +      -       -      +
    104D  ILE*     3.0    50.1    +      -       +      +
    105D  GLY*     3.8    16.6    -      -       -      -
    106D  ARG*     5.2     0.4    -      -       -      +
    109D  MET*     4.4    12.6    -      -       +      -
    110D  ASN*     1.3    78.5    -      -       -      +
    112D  TYR*     1.3    59.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 112 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369A  ILE*     6.3     0.4    -      -       +      -
    377A  THR      4.2     0.5    -      -       -      +
    378A  CYS*     3.5     2.3    -      -       -      -
    379A  PHE*     2.7    41.3    +      -       -      +
    380A  VAL*     6.3     0.2    -      -       -      -
    381A  SER*     6.2     1.1    -      -       -      -
     54D  ILE*     3.7    38.9    -      -       +      +
     55D  LEU*     3.7    35.4    -      -       +      -
    101D  GLU*     4.5    19.1    -      -       +      -
    102D  ILE      3.7     1.1    -      -       -      -
    103D  GLN*     3.6    37.5    +      -       +      -
    110D  ASN*     3.1    29.5    +      -       -      -
    111D  VAL*     1.3    75.7    -      -       -      +
    113D  TYR*     1.3    58.8    +      -       -      +
    114D  LEU*     3.8     3.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 113 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  CYS*     3.3    25.1    -      -       +      -
    377A  THR*     3.6     8.1    -      -       -      -
    378A  CYS*     3.7    14.8    -      -       -      -
     32B  ALA*     5.6     0.3    -      -       -      +
     50B  ASN*     5.4     0.5    +      -       -      -
     91B  PHE*     3.3    35.2    +      -       -      -
     92B  ASP      5.7     0.7    -      -       -      -
    100D  TYR      3.3     3.3    -      -       -      +
    101D  GLU*     3.4     1.4    -      -       -      -
    102D  ILE*     2.9    47.9    +      -       +      +
    104D  ILE*     3.8    25.4    -      -       +      -
    111D  VAL      3.7     1.2    +      -       -      -
    112D  TYR*     1.3    70.5    -      -       -      +
    114D  LEU*     1.3    78.7    +      -       -      +
    115D  MET*     3.4    31.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 114 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377A  THR*     2.8    41.3    +      -       -      +
    379A  PHE*     3.8    19.7    -      -       +      -
     91B  PHE      5.2     0.9    -      -       -      +
     52D  ASN*     3.2    36.3    -      -       +      +
     55D  LEU*     4.2    11.0    -      -       +      -
     59D  ASN*     3.4    31.0    -      -       -      +
     99D  HIS*     4.6     1.1    -      -       +      -
    100D  TYR      3.3     4.0    -      -       -      +
    101D  GLU*     4.0    22.4    -      -       +      -
    112D  TYR*     4.7     4.3    -      -       +      +
    113D  TYR*     1.3    74.3    -      -       -      +
    115D  MET*     1.3    61.6    +      -       -      +
    116D  TYR*     3.8    28.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 115 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ASN*     5.5     2.0    -      -       -      -
     91B  PHE*     4.2    12.6    -      -       +      -
     99D  HIS*     3.4     2.2    -      -       -      +
    100D  TYR*     3.0    62.2    +      -       +      +
    102D  ILE*     4.6    14.6    -      -       +      -
    113D  TYR*     3.4    42.8    +      -       +      +
    114D  LEU*     1.3    71.3    -      -       -      +
    116D  TYR*     1.3    59.5    +      -       -      +
    117D  ARG*     3.0    58.0    +      -       +      +
----------------------------------------------------------
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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