Contacts of the strand formed by residues 19 - 25 (chain A) in PDB entry 2CD0


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 19 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     3.7    35.4    -      -       +      -
     13A  GLU*     4.8     4.7    -      -       +      -
     18A  THR*     1.3    75.0    -      -       -      +
     20A  THR*     1.3    72.6    +      -       -      +
     21A  ILE*     4.1    11.4    -      -       +      -
     73A  LEU      3.8     0.3    -      -       -      +
     74A  THR*     3.3     5.5    -      -       -      +
     75A  ILE*     2.9    54.9    +      -       +      -
     78A  LEU*     3.8    24.9    -      -       +      -
    104A  LEU*     4.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PRO*     5.5     2.1    -      -       -      +
     11A  VAL*     5.9     1.4    -      -       -      +
     18A  THR*     4.9     2.8    -      -       -      +
     19A  VAL*     1.3    79.9    +      -       -      +
     21A  ILE*     1.3    63.0    +      -       -      +
     22A  SER*     3.5     7.1    +      -       -      +
     72A  SER*     4.0    23.1    -      -       -      +
     73A  LEU      3.7     2.2    -      -       -      -
     74A  THR*     3.8    22.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  GLN*     4.1     2.2    -      -       -      +
      7A  PRO*     4.3     6.3    -      -       +      -
     11A  VAL*     5.0     2.0    -      -       +      -
     19A  VAL*     4.4    13.7    -      -       +      -
     20A  THR*     1.3    71.9    -      -       -      +
     22A  SER*     1.3    69.0    +      -       -      +
     35A  TRP*     3.5    16.4    -      -       +      -
     72A  SER*     3.4     3.1    -      -       -      -
     73A  LEU*     2.9    51.1    +      -       +      +
     75A  ILE*     5.2     4.3    -      -       +      -
     86A  TYR*     3.8    38.4    -      -       +      -
    102A  THR*     3.3    42.2    -      -       +      +
    104A  LEU*     4.8    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  THR      4.0     2.6    +      -       -      -
      6A  GLN*     3.4    28.4    -      -       -      +
      7A  PRO*     3.8    15.1    -      -       -      +
     20A  THR*     3.5     8.5    +      -       -      -
     21A  ILE*     1.3    76.3    -      -       -      +
     23A  CYS*     1.3    62.1    +      -       -      +
     24A  THR*     4.0     9.6    -      -       -      -
     35A  TRP*     4.1     0.4    -      -       -      -
     70A  SER*     5.6     2.7    -      -       -      -
     71A  ALA      3.7     4.9    -      -       -      -
     72A  SER*     4.1     9.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     3.8    23.3    -      -       -      -
      5A  THR      3.4     5.4    -      -       -      -
     22A  SER*     1.3    75.6    -      -       -      +
     24A  THR*     1.3    60.4    +      -       -      +
     25A  ARG      3.7     0.9    +      -       -      -
     28A  ILE*     3.9     4.1    -      -       -      +
     33A  VAL*     4.9     2.9    -      -       -      -
     35A  TRP*     3.4    18.2    -      -       +      -
     70A  SER*     3.4     1.7    -      -       -      -
     71A  ALA*     2.8    38.5    +      -       +      +
     88A  CYS*     2.0    48.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  LEU      3.4     1.6    -      -       -      +
      4A  LEU*     3.4     3.8    -      -       -      -
      5A  THR*     2.8    45.0    +      -       -      -
     22A  SER*     4.0     6.4    -      -       -      -
     23A  CYS*     1.3    73.8    +      -       -      +
     25A  ARG*     1.3    73.2    +      -       -      +
     26A  SER*     3.8     1.6    +      -       -      +
     68A  SER      4.3    10.7    +      -       -      +
     69A  ASN*     4.3     5.6    -      -       +      +
     70A  SER*     3.2    17.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  PHE*     3.2    55.4    -      -       +      -
      3A  LEU      3.3     5.2    -      -       -      -
      4A  LEU*     3.6    11.4    -      -       +      -
     23A  CYS      3.7     1.4    +      -       -      -
     24A  THR*     1.3    79.9    -      -       -      +
     26A  SER*     1.3    63.0    +      -       -      +
     27A  SER*     2.6    64.8    +      -       -      +
     28A  ILE*     3.9    21.2    -      -       +      +
     30A  ASN*     5.9     0.6    -      -       -      +
     31A  ASN*     4.1    10.9    -      -       -      +
     69A  ASN*     2.8    41.1    +      -       -      +
     90A  SER*     4.0    10.7    +      -       -      -
     91A  TYR      3.7     9.5    +      -       -      -
     92A  ASP*     4.7     5.3    +      -       -      -
----------------------------------------------------------
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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