Contacts of the strand formed by residues 371 - 374 (chain D) in PDB entry 2DB3


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 371 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300D  LEU*     5.7     1.6    -      -       +      -
    303D  ILE*     5.8     0.4    -      -       +      -
    304D  LEU*     4.1    10.8    -      -       +      -
    307D  LEU*     3.9    22.0    -      -       +      -
    321D  VAL*     3.6    27.1    -      -       +      +
    323D  ILE*     4.1     5.4    -      -       +      -
    338D  ALA*     5.6     2.7    -      -       +      -
    348D  LYS      3.3     2.4    +      -       -      -
    349D  ILE*     3.8    29.2    -      -       +      -
    350D  GLY*     2.7    33.8    +      -       -      +
    369D  CYS*     3.9     1.6    -      -       -      -
    370D  HIS*     1.3    84.4    -      -       +      +
    372D  VAL*     1.3    64.6    +      -       -      +
    373D  ILE*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 372 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319D  PRO*     3.4    32.5    -      -       +      -
    321D  VAL      3.0    10.5    +      -       -      +
    322D  VAL*     3.5     8.0    -      -       +      +
    323D  ILE      2.9    25.5    +      -       -      +
    350D  GLY*     3.7     4.9    -      -       -      +
    352D  VAL*     3.8    28.3    -      -       +      +
    365D  ILE*     4.7    10.5    -      -       +      -
    369D  CYS*     3.4    26.0    -      -       -      -
    371D  VAL*     1.3    72.9    -      -       -      +
    373D  ILE*     1.3    66.6    +      -       -      +
    374D  ALA*     4.0     3.8    +      -       +      -
    379D  LEU*     4.7     5.6    -      -       +      -
    388D  ILE*     4.6     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 373 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323D  ILE*     3.3    44.4    -      -       +      +
    325D  SER*     5.3     1.6    -      -       -      -
    331D  ALA*     3.4    35.7    -      -       +      +
    334D  ILE*     4.1    20.6    -      -       +      +
    335D  PHE*     3.9    20.2    -      -       +      -
    338D  ALA*     5.1     2.5    -      -       +      -
    349D  ILE*     4.7     5.4    -      -       +      -
    350D  GLY      3.1    15.3    +      -       -      +
    351D  ILE*     3.2     7.7    -      -       +      +
    352D  VAL*     2.9    24.1    +      -       -      +
    371D  VAL*     3.8    11.0    -      -       +      -
    372D  VAL*     1.3    73.0    -      -       -      +
    374D  ALA*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 374 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322D  VAL*     5.6     0.7    -      -       +      -
    323D  ILE      2.8    12.5    +      -       -      +
    324D  VAL*     3.2     7.2    -      -       -      +
    325D  SER*     2.9    26.2    +      -       -      -
    331D  ALA*     4.7     4.7    -      -       -      -
    352D  VAL*     3.2    32.1    -      -       +      -
    372D  VAL*     4.3     3.6    -      -       +      +
    373D  ILE*     1.3    77.0    -      -       -      +
    375D  THR*     1.3    62.6    +      -       -      +
    379D  LEU*     4.0    29.4    -      -       +      -
----------------------------------------------------------
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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