Contacts of the strand formed by residues 268 - 271 (chain D) in PDB entry 3DLX


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 ARG 268 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  LYS*     3.2     6.7    -      -       +      -
     43D  TYR*     3.6    36.6    +      -       +      +
     48D  GLU      4.9     1.8    +      -       -      -
     49D  ALA      2.6    38.5    +      -       -      -
     52D  ASP*     3.0    40.6    +      -       -      -
    207D  PHE*     4.0    10.3    -      -       -      -
    240D  THR*     3.6    29.1    +      -       +      +
    241D  THR      3.1     6.4    +      -       -      +
    242D  VAL*     3.3    15.8    -      -       +      +
    243D  VAL*     2.8    33.1    +      -       -      +
    266D  VAL*     3.7     3.1    -      -       -      +
    267D  HIS*     1.3    86.0    -      -       +      +
    269D  LEU*     1.3    59.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 269 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  THR*     3.8    13.5    -      -       +      -
     41D  LYS      2.8     6.5    +      -       -      +
     42D  PHE*     3.2    40.9    -      -       +      +
     43D  TYR*     2.8    26.2    +      -       -      -
    215D  ALA*     3.4    25.1    -      -       +      -
    216D  ASP      4.2     1.6    -      -       -      +
    219D  GLY*     4.4     8.5    -      -       -      -
    221D  VAL*     4.6     2.7    -      -       +      -
    243D  VAL*     3.3    27.4    -      -       +      +
    245D  VAL*     3.8    28.0    -      -       +      -
    248D  ILE*     4.8     4.7    -      -       +      -
    266D  VAL*     4.4     2.7    -      -       +      -
    268D  ARG*     1.3    76.3    -      -       -      +
    270D  ILE*     1.3    71.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 270 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  TYR*     3.5    33.9    -      -       +      +
     44D  THR      5.7     0.9    -      -       -      -
     46D  PRO*     3.6    37.0    -      -       +      -
     49D  ALA*     3.9    17.5    -      -       +      -
     72D  ASN*     4.4    11.9    -      -       +      -
     73D  LEU*     4.1    13.9    -      -       +      -
    242D  VAL*     5.0     1.6    -      -       +      -
    243D  VAL      3.0     7.1    +      -       -      +
    244D  GLU*     3.3    21.9    -      -       +      -
    245D  VAL*     3.0    29.2    +      -       -      +
    248D  ILE*     4.8     1.8    -      -       -      -
    269D  LEU*     1.3    83.3    -      -       -      +
    271D  LYS*     1.3    68.0    +      -       -      +
    272D  GLY*     4.5     2.2    -      -       -      -
    273D  GLU      5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 271 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  TYR      4.5     3.0    +      -       -      -
    245D  VAL*     3.4     8.3    -      -       -      +
    246D  GLU      3.4    30.2    +      -       -      +
    247D  GLU*     4.1    22.1    -      -       -      +
    248D  ILE*     3.8    25.9    -      -       +      +
    270D  ILE*     1.3    75.5    -      -       -      +
    272D  GLY*     1.3    72.5    +      -       -      +
    273D  GLU*     3.4     4.9    +      -       -      +
----------------------------------------------------------
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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