Contacts of the strand formed by residues 21 - 26 (chain M) in PDB entry 2DFS


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 21 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16M  PRO*     3.4     8.3    -      -       -      +
     17M  ASP*     3.0    34.2    +      -       -      +
     18M  PRO      4.6     0.6    -      -       -      -
     19M  GLU      3.7     0.8    -      -       -      -
     20M  GLU*     1.4    78.4    -      -       -      +
     22M  TRP*     1.3    80.2    +      -       +      +
     82M  GLU*     4.6     4.7    -      -       -      +
     86M  LEU*     4.6     3.4    -      -       +      -
    675M  GLU*     3.7     9.0    -      -       +      +
    676M  LYS*     3.6    42.6    -      -       +      +
    679M  VAL*     4.2    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 22 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14M  TRP*     3.6    50.0    -      -       +      -
     15M  ILE      3.4    22.4    -      -       -      -
     16M  PRO*     3.8    21.5    -      -       +      -
     17M  ASP*     4.2     2.2    -      -       -      -
     20M  GLU*     2.9    26.8    +      -       -      +
     21M  VAL*     1.3    92.6    -      -       +      +
     23M  LYS*     1.3    60.9    +      -       -      +
     60M  PRO*     5.8     0.2    -      -       +      -
     61M  PRO*     3.8    21.3    -      -       +      -
     82M  GLU*     2.9    33.6    +      -       +      +
     83M  PRO*     3.7    31.2    -      -       +      +
     86M  LEU*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 23 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14M  TRP*     3.3     7.7    -      -       -      -
     15M  ILE*     2.8    43.4    +      -       +      +
     17M  ASP*     3.0    46.0    +      -       +      +
     19M  GLU*     4.8     8.5    -      -       -      +
     20M  GLU*     5.2     6.3    -      -       +      +
     22M  TRP*     1.3    73.8    -      -       -      +
     24M  SER*     1.3    70.7    +      -       -      +
     42M  LEU*     5.2    17.3    -      -       +      -
     43M  GLU*     2.6    39.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 24 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  ARG*     4.6     3.8    -      -       -      +
     13M  VAL      3.6     5.8    +      -       -      -
     14M  TRP*     4.0    11.7    -      -       -      -
     23M  LYS*     1.3    80.5    -      -       -      +
     25M  ALA*     1.3    65.3    +      -       -      +
     41M  ARG      3.8     6.9    -      -       -      +
     42M  LEU*     4.2    15.0    -      -       -      +
     43M  GLU      5.1     0.2    +      -       -      -
     63M  ARG*     2.8    39.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 25 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  ARG*     3.2     7.7    -      -       -      +
     13M  VAL*     2.9    42.5    +      -       +      +
     15M  ILE*     4.4     7.9    -      -       +      -
     24M  SER*     1.3    77.4    +      -       -      +
     26M  GLU*     1.3    60.3    +      -       -      +
     40M  LEU*     3.7    32.5    -      -       +      -
     41M  ARG      3.2    12.1    -      -       -      +
     42M  LEU*     4.4     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 26 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10M  TYR*     3.5    39.1    -      -       -      +
     11M  ALA      3.4    16.2    -      -       -      +
     12M  ARG*     4.3    14.5    -      -       +      +
     25M  ALA*     1.3    75.3    -      -       -      +
     27M  LEU*     1.3    66.3    +      -       -      +
     28M  LEU*     3.3     4.5    +      -       -      +
     40M  LEU*     3.3    21.6    -      -       -      -
     41M  ARG*     2.6    60.0    +      -       +      +
----------------------------------------------------------
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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