Contacts of the strand formed by residues 378 - 382 (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 CYS 378 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  HIS*     2.8    18.4    +      -       -      -
    372A  SER*     2.8    35.2    +      -       -      +
    374A  ASP*     4.3     1.6    -      -       +      -
    375A  CYS*     2.1    60.4    +      -       -      +
    376A  SER      3.6     0.2    -      -       -      -
    377A  THR*     1.3    78.3    -      -       -      +
    379A  PHE*     1.3    58.1    +      -       -      +
    104D  ILE*     3.8    15.3    -      -       -      -
    111D  VAL*     4.3     3.6    -      -       +      -
    112D  TYR      3.5     5.4    -      -       -      +
    113D  TYR*     3.6    24.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  HIS*     4.6     2.9    -      -       -      -
    194A  ARG*     4.5     2.0    -      -       -      -
    195A  GLU*     3.6    35.7    -      -       +      -
    239A  ALA*     3.8    18.6    -      -       +      -
    369A  ILE*     4.1    15.7    -      -       +      -
    370A  GLY      3.5    18.6    -      -       -      +
    371A  ALA*     4.1     2.0    -      -       -      -
    372A  SER*     3.7     2.5    -      -       -      +
    377A  THR      4.0    11.2    -      -       -      -
    378A  CYS*     1.3    80.3    -      -       -      +
    380A  VAL*     1.3    59.7    +      -       -      +
     55D  LEU*     3.7    34.1    -      -       +      -
     57D  ILE*     3.9     5.8    -      -       +      -
     59D  ASN*     3.6    34.3    -      -       -      -
    110D  ASN      4.0     0.2    -      -       -      +
    111D  VAL*     3.3     4.0    -      -       -      +
    112D  TYR*     2.7    38.8    +      -       -      +
    114D  LEU*     3.8     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  SER*     5.7     2.2    -      -       -      +
    229A  HIS*     3.1    44.9    +      -       +      -
    369A  ILE*     3.6     3.8    -      -       -      -
    370A  GLY      2.9    19.3    +      -       -      -
    371A  ALA      3.8     0.9    -      -       -      +
    372A  SER*     3.6    29.2    -      -       -      +
    379A  PHE*     1.3    75.6    -      -       -      +
    381A  SER*     1.3    74.6    +      -       -      +
    382A  GLN*     4.2    16.2    -      -       +      +
    109D  MET*     5.4     8.5    -      -       +      -
    110D  ASN      3.4    11.0    -      -       -      +
    111D  VAL*     3.9    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  ASP*     3.1    42.4    +      -       -      +
    368A  ILE      3.4     4.8    -      -       -      -
    369A  ILE*     4.5     9.6    -      -       -      +
    380A  VAL*     1.3    85.5    -      -       -      +
    382A  GLN*     1.3    61.9    +      -       -      +
    109D  MET*     5.3     5.0    -      -       -      +
    110D  ASN*     3.1    34.2    +      -       -      +
    112D  TYR*     6.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  SER*     5.8     3.6    -      -       -      -
    225A  SER*     5.4     9.5    +      -       -      +
    226A  HIS*     6.0     3.3    -      -       -      -
    229A  HIS*     3.4    39.4    -      -       +      +
    367A  ASP      3.4     1.9    +      -       -      -
    368A  ILE*     2.8    34.6    +      -       -      +
    380A  VAL*     4.2    14.3    -      -       +      +
    381A  SER*     1.3    80.9    +      -       -      +
    383A  SER*     1.3    71.1    +      -       -      +
    387A  GLN*     3.8    11.9    -      -       -      +
    109D  MET*     5.0    12.7    -      -       -      +
----------------------------------------------------------
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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