Contacts of the strand formed by residues 57 - 63 (chain J) in PDB entry 4CDC


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 SER 57 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334B  ALA*     5.4     4.7    -      -       -      -
    335B  LEU*     6.4     1.3    -      -       -      -
    338B  LEU*     5.4    10.7    -      -       -      +
     49J  THR*     4.6    11.4    -      -       -      -
     50J  ALA      3.2     7.4    -      -       -      -
     51J  TYR*     4.4     6.3    -      -       -      -
     55J  GLY      4.2     1.7    +      -       -      -
     56J  ASN*     1.3    76.6    -      -       -      +
     58J  GLY*     1.3    59.4    +      -       -      +
     59J  HIS*     6.1     0.2    -      -       -      -
     72J  LEU*     3.6     7.0    -      -       -      +
     73J  ASN      5.3     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 58 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49J  THR*     3.6     4.9    -      -       -      +
     50J  ALA*     2.6    31.6    +      -       -      -
     57J  SER*     1.3    74.8    -      -       -      +
     59J  HIS*     1.3    79.9    +      -       -      -
     71J  VAL      3.3    13.2    -      -       -      -
     72J  LEU*     3.5     7.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 59 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48J  ASP*     3.2    37.7    -      -       -      +
     49J  THR*     4.9     2.7    -      -       -      -
     50J  ALA*     4.0     2.7    -      -       -      +
     58J  GLY*     1.3    85.7    +      -       -      -
     60J  PHE*     1.3    63.6    +      -       -      +
     70J  ILE*     3.5     4.0    -      -       -      +
     71J  VAL*     2.9    39.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 60 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8J  TYR*     3.9    22.7    -      +       -      -
     11J  LEU*     3.8    30.3    -      -       +      -
     12J  LEU*     3.7    19.7    -      -       +      -
     44J  LEU*     3.7    23.6    -      -       +      -
     45J  GLN      3.1    27.4    -      -       -      -
     47J  LEU      3.9     4.2    -      -       -      +
     48J  ASP*     3.1    31.8    +      -       -      +
     49J  THR      3.2    24.2    -      -       -      -
     59J  HIS*     1.3    77.6    -      -       -      +
     61J  THR*     1.3    69.3    +      -       -      +
     68J  PHE*     5.9     0.4    -      -       +      -
     69J  GLU      3.2    13.5    -      -       -      +
     70J  ILE*     3.9    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 61 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8J  TYR*     6.3     0.2    -      -       -      -
     60J  PHE*     1.3    85.1    -      -       -      +
     62J  ILE*     1.3    78.1    +      -       -      +
     63J  ILE*     4.5     4.7    -      -       +      -
     68J  PHE*     3.2     4.9    -      -       -      +
     69J  GLU      3.0    37.9    +      -       -      +
    280K  TYR*     3.6    36.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 62 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  CYS      4.0     7.6    -      -       -      +
      7J  THR      3.7    24.9    -      -       -      +
      8J  TYR*     3.7    33.2    -      -       +      +
     11J  LEU*     3.8    23.5    -      -       +      +
     60J  PHE*     4.4     2.4    -      -       -      -
     61J  THR*     1.3    89.7    +      -       -      +
     63J  ILE*     1.3    59.7    +      -       -      +
     64J  TYR      3.7    26.4    +      -       -      +
     67J  GLY      3.2    20.0    -      -       -      +
     81J  PHE*     4.2    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 63 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61J  THR*     4.4     5.2    -      -       +      +
     62J  ILE*     1.3    74.9    -      -       -      +
     64J  TYR*     1.3    66.9    +      -       -      +
     65J  ASN      2.9     4.7    +      -       -      -
     66J  GLN*     3.0    20.5    +      -       +      +
     67J  GLY      2.8    12.8    +      -       -      +
     68J  PHE*     3.4    35.0    -      -       -      +
     69J  GLU*     3.6    10.1    -      -       +      +
     78J  PHE*     4.0    18.8    -      -       +      -
    278K  PHE*     4.4    19.3    -      -       +      -
    280K  TYR*     4.0    29.8    -      -       +      -
    281K  LEU*     4.1    25.4    -      -       +      -
----------------------------------------------------------
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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