Contacts of the strand formed by residues 278 - 283 (chain A) in PDB entry 1DY7


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 PRO 278 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  MET*     3.4    37.7    -      -       +      +
    142A  MET*     4.1    20.0    -      -       +      -
    143A  ARG*     3.7    23.5    +      -       +      +
    146A  TRP*     4.2    11.4    -      -       +      -
    236A  ILE*     3.5    25.1    -      -       +      -
    269A  VAL*     4.1     7.2    -      -       +      -
    270A  ILE      4.1     4.5    -      -       -      +
    271A  MET*     4.2     5.2    -      -       +      -
    276A  LEU      3.1     6.9    -      -       -      +
    277A  GLU*     1.3    86.7    -      -       +      +
    279A  LYS*     1.3    60.4    +      -       -      +
    280A  LYS      3.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  MET*     4.4     0.4    -      -       -      -
    257A  TYR*     4.8     6.5    -      -       +      -
    270A  ILE      2.9    12.0    +      -       -      +
    271A  MET      4.4     0.9    -      -       -      -
    272A  ASP*     3.9    19.3    -      -       +      +
    277A  GLU*     3.4    40.5    +      -       +      +
    278A  PRO*     1.3    76.8    -      -       -      +
    280A  LYS*     1.3    64.6    +      -       -      +
    330A  LEU*     3.8    26.2    -      -       +      +
    292B  GLN*     3.0    21.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  MET*     4.8     0.2    -      -       -      +
    268A  TYR*     3.9     1.0    -      -       -      +
    269A  VAL*     3.3     3.3    -      -       -      -
    270A  ILE*     2.8    47.0    +      -       +      +
    278A  PRO      3.9     0.4    -      -       -      -
    279A  LYS*     1.3    83.8    -      -       -      +
    281A  ILE*     1.3    62.3    +      -       -      +
    282A  GLN*     3.4    35.0    +      -       +      +
    330A  LEU*     2.7    42.1    +      -       +      +
    331A  ASP*     4.2     5.5    +      -       -      +
    333A  LEU*     4.3    17.9    -      -       +      +
    289B  TYR*     5.4     3.4    +      -       -      +
    292B  GLN*     3.5    13.2    -      -       -      +
    321B  LYS*     5.1    10.4    -      -       -      +
    337B  GLU*     5.2     2.1    +      -       -      -
    339B  SER*     3.2    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  GLY*     3.8     2.9    -      -       -      -
    139A  MET*     3.4    46.0    -      -       +      +
    142A  MET*     3.6    22.0    -      -       +      -
    267A  GLN*     4.0    25.4    -      -       +      +
    268A  TYR      3.5     9.6    -      -       -      +
    269A  VAL*     3.8    19.7    -      -       +      -
    280A  LYS*     1.3    74.1    -      -       -      +
    282A  GLN*     1.3    71.1    +      -       -      +
    287B  MET*     3.3    37.8    -      -       +      +
    292B  GLN*     2.9    23.6    +      -       +      +
    321B  LYS*     5.0     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  GLN*     3.1     6.4    -      -       -      -
    268A  TYR*     2.9    77.9    +      -       +      +
    270A  ILE*     6.2     0.2    -      -       +      -
    280A  LYS*     3.4    36.4    -      -       +      +
    281A  ILE*     1.3    83.1    +      -       -      +
    283A  SER*     1.3    65.5    +      -       -      +
    333A  LEU*     3.5    20.0    -      -       +      +
    335A  THR*     5.3     1.6    -      -       -      +
    287B  MET*     4.4     1.6    -      -       -      -
    321B  LYS*     4.5     7.8    -      -       -      +
    337B  GLU*     3.1    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  PRO      3.5     8.1    +      -       -      -
    267A  GLN*     4.2     3.1    -      -       -      -
    268A  TYR*     5.3     0.7    -      -       -      -
    282A  GLN*     1.3    80.2    -      -       -      +
    284A  THR*     1.3    63.6    +      -       -      +
    285A  ARG*     3.1    35.3    +      -       -      +
    323A  LEU*     5.9     0.9    -      -       -      +
    285B  ARG      4.6     3.3    +      -       -      +
    286B  GLY*     4.0    25.7    -      -       -      -
    287B  MET*     4.0    12.3    -      -       -      +
    294B  TYR*     3.9    11.6    -      -       -      -
----------------------------------------------------------
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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