Contacts of the strand formed by residues 396 - 399 (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 LEU 396 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312D  GLU*     4.6    14.4    -      -       +      +
    313D  PHE*     4.1    17.3    -      -       +      -
    317D  MET*     3.9    31.0    -      -       +      -
    318D  TYR      3.2     1.6    +      -       -      -
    319D  ALA*     3.1     8.0    -      -       +      +
    320D  ASN      2.9    23.7    +      -       -      -
    394D  VAL*     3.2     6.7    -      -       -      +
    395D  ASP*     1.3    80.4    -      -       -      +
    397D  THR*     1.3    67.7    +      -       -      +
    398D  MET*     3.9    25.4    -      -       +      -
    435D  THR*     4.4     1.1    -      -       -      -
    436D  LYS*     3.3    27.1    -      -       +      +
    438D  VAL*     3.5    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 397 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320D  ASN*     3.4     8.0    +      -       -      -
    394D  VAL*     5.3     0.7    -      -       -      -
    396D  LEU*     1.3    77.8    -      -       -      +
    398D  MET*     1.3    62.4    +      -       -      +
    399D  LEU*     3.7    14.1    -      -       +      +
    429D  LEU*     3.5    49.4    -      -       +      +
    435D  THR*     4.1     5.8    -      -       +      +
    436D  LYS      2.8    11.7    +      -       -      +
    437D  VAL*     3.4    35.2    -      -       +      -
    438D  VAL*     2.9    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 398 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309D  ALA*     3.6    29.6    -      -       +      +
    312D  GLU*     3.5    36.6    -      -       +      -
    313D  PHE*     4.4    15.3    -      -       +      -
    320D  ASN      2.9     9.3    +      -       -      -
    321D  LEU*     4.0    17.5    -      -       +      -
    322D  GLY*     2.6    33.8    +      -       -      -
    326D  PRO*     3.3    10.4    -      -       +      +
    329D  ALA*     4.6     8.1    -      -       -      -
    396D  LEU*     3.9    17.9    -      -       +      +
    397D  THR*     1.3    74.0    +      -       -      +
    399D  LEU*     1.3    59.1    +      -       -      +
    438D  VAL*     3.3    22.9    -      -       +      +
    440D  THR*     3.7    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 399 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322D  GLY*     3.8    16.6    -      -       -      -
    326D  PRO*     3.6     8.9    -      -       -      +
    397D  THR*     3.7    20.2    -      -       +      +
    398D  MET*     1.3    83.9    -      -       -      +
    400D  GLY*     1.3    69.6    +      -       -      +
    410D  LEU*     4.0    13.7    -      -       +      -
    412D  ASN*     4.4     3.1    -      -       -      +
    426D  ALA*     4.4    18.2    -      -       +      +
    429D  LEU*     3.9    16.8    -      -       +      -
    430D  VAL*     3.5    33.0    -      -       +      -
    437D  VAL*     4.5     7.6    -      -       +      -
    438D  VAL      3.0    10.2    +      -       -      +
    439D  VAL*     3.2    10.3    -      -       +      +
    440D  THR      3.0    22.5    +      -       -      -
----------------------------------------------------------
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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