Contacts of the strand formed by residues 283 - 287 (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 LEU 283 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  GLU*     3.7    18.2    -      -       +      -
    183A  TYR*     3.7    31.4    -      -       +      +
    271A  ILE*     4.4    13.7    -      -       +      +
    275A  GLN*     3.6    42.6    -      -       +      +
    280A  VAL*     5.8     7.6    -      -       +      -
    281A  GLY      3.5    11.1    +      -       -      +
    282A  PRO*     1.3    75.1    -      -       -      +
    284A  VAL*     1.3    63.6    +      -       -      +
    285A  VAL*     5.4     0.9    -      -       +      -
    308A  GLY      5.1     4.8    +      -       -      +
    309A  VAL*     3.8    24.5    -      -       +      +
    310A  VAL*     2.9    30.6    +      -       -      +
    400A  LEU*     4.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  VAL*     4.3    10.5    -      -       +      -
    181A  GLU      3.0    12.5    +      -       -      +
    182A  VAL*     4.4    12.8    -      -       +      -
    183A  TYR*     2.7    32.9    +      -       -      +
    283A  LEU*     1.3    77.5    -      -       -      +
    285A  VAL*     1.3    64.3    +      -       -      +
    310A  VAL*     3.4    17.7    -      -       +      +
    312A  VAL*     4.0    24.9    -      -       +      -
    393A  ALA*     4.2    21.1    -      -       +      +
    396A  ALA*     4.5     8.3    -      -       +      -
    397A  ALA*     4.5     5.8    -      -       -      +
    400A  LEU*     4.0    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  TYR*     3.4     8.1    -      -       +      +
    185A  LEU*     4.0    13.5    -      -       +      -
    268A  LEU*     4.6     3.4    -      -       +      -
    271A  ILE*     3.8    41.3    -      -       +      -
    283A  LEU*     5.2     1.3    -      -       +      -
    284A  VAL*     1.3    79.3    -      -       -      +
    286A  LEU*     1.3    62.5    +      -       -      +
    287A  LEU*     4.3    11.7    -      -       +      +
    304A  LEU*     4.7     1.3    -      -       +      -
    309A  VAL*     3.5    26.5    -      -       +      -
    310A  VAL      2.8    11.4    +      -       -      +
    311A  LEU*     3.6    18.8    -      -       +      +
    312A  VAL*     2.9    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  VAL*     4.9     6.3    -      -       +      +
    183A  TYR      2.7    15.4    +      -       -      +
    184A  LEU*     3.9    20.6    -      -       +      -
    185A  LEU*     3.2    20.8    +      -       -      +
    230A  LEU*     4.9     5.4    -      -       +      +
    234A  VAL*     3.9    18.2    -      -       +      -
    247A  MET*     5.4     1.3    -      -       +      -
    284A  VAL      4.3     0.2    -      -       -      -
    285A  VAL*     1.3    73.3    -      -       -      +
    287A  LEU*     1.3    61.6    +      -       -      +
    288A  PRO*     3.2    21.9    -      -       +      +
    312A  VAL*     3.5    12.3    -      -       +      +
    386A  SER      4.9     1.1    -      -       -      +
    389A  ALA*     3.7    36.6    -      -       +      +
    390A  ALA*     3.7    21.8    -      -       +      +
    393A  ALA*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  LEU*     4.0    31.6    -      -       +      -
    264A  THR*     4.3    16.8    -      -       +      -
    268A  LEU*     4.3    11.4    -      -       +      -
    285A  VAL*     4.3     5.2    -      -       +      +
    286A  LEU*     1.3    75.4    -      -       -      +
    288A  PRO*     1.3    57.5    -      -       -      +
    289A  LEU*     2.8    19.7    +      -       +      -
    297A  LEU*     6.1     0.2    -      -       +      -
    301A  CYS*     4.6     7.4    -      -       -      -
    311A  LEU*     3.8    34.1    -      -       +      -
    312A  VAL      2.7    16.3    +      -       -      +
    313A  THR*     2.6    43.0    +      -       -      +
    314A  ALA      3.3     0.9    +      -       -      -
    327A  PRO*     4.4    17.9    -      -       +      -
    333A  VAL*     5.1     0.7    -      -       +      -
----------------------------------------------------------
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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