Contacts of the strand formed by residues 56 - 60 (chain K) in PDB entry 3J7Y


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 HIS 56 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16K  ARG*     3.8    39.6    +      -       +      +
     17K  ILE      2.8     7.8    +      -       -      +
     18K  TRP*     3.5    55.1    +      +       +      -
     19K  TYR*     2.8    31.8    +      -       -      -
     55K  ASP*     1.3    73.7    -      -       -      +
     57K  VAL*     1.3    61.2    +      -       -      +
     58K  VAL      4.1     0.2    -      -       -      -
    124K  ARG*     3.5    26.7    +      -       +      +
    126K  HIS*     3.5     6.2    +      -       +      -
    117a  PHE*     3.5    40.8    -      +       +      -
    265c  THR*     4.8     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 57 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19K  TYR*     3.8     7.6    -      -       +      +
     21K  LEU*     3.8    19.3    -      -       +      -
     35K  ALA*     3.7    20.9    -      -       +      +
     38K  ARG*     3.5    32.8    -      -       +      -
     39K  LEU*     4.1    14.4    -      -       +      +
     55K  ASP      4.0     0.8    +      -       -      +
     56K  HIS*     1.3    76.4    -      -       -      +
     58K  VAL*     1.3    64.6    +      -       -      +
     59K  ILE*     3.7    22.9    -      -       +      -
    124K  ARG      3.2     8.3    +      -       -      +
    125K  LEU*     3.5    11.0    -      -       +      +
    126K  HIS*     2.8    26.5    +      -       -      -
    145K  LEU*     6.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 58 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18K  TRP*     3.9    14.6    -      -       +      -
     19K  TYR      2.8    14.4    +      -       -      +
     20K  LEU*     3.4    16.8    -      -       +      -
     21K  LEU*     2.8    30.8    +      -       -      +
     57K  VAL*     1.3    76.3    -      -       -      +
     59K  ILE*     1.3    60.5    +      -       -      +
    126K  HIS*     3.4    10.3    -      -       +      -
    128K  PHE*     3.6    29.6    -      -       +      -
    133K  ILE*     4.2     7.9    -      -       +      -
    137K  ILE*     3.4    26.9    -      -       +      -
    141K  LEU*     3.5    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 59 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21K  LEU*     3.3    21.8    -      -       +      +
     23K  GLY      4.9     0.2    -      -       -      +
     31K  LEU*     4.3    21.3    -      -       +      -
     35K  ALA*     4.0    15.3    -      -       +      -
     57K  VAL*     3.7    11.4    -      -       +      -
     58K  VAL*     1.3    80.8    -      -       -      +
     60K  MET*     1.3    65.4    +      -       -      +
     62K  THR*     4.0    18.8    -      -       +      -
    104K  VAL*     4.1     5.4    -      -       +      -
    108K  ILE*     3.6    31.6    -      -       +      -
    125K  LEU*     4.0     4.5    -      -       +      -
    126K  HIS      2.8     8.2    +      -       -      +
    127K  LEU*     3.6    18.8    -      -       +      -
    128K  PHE*     2.9    29.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 60 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20K  LEU*     4.0     8.7    -      -       +      -
     21K  LEU      2.8    19.4    +      -       -      +
     22K  ASP*     3.4    22.2    -      -       +      +
     23K  GLY*     2.8    27.7    +      -       -      -
     59K  ILE*     1.3    77.6    -      -       -      +
     61K  ASN*     1.3    62.1    +      -       -      +
     62K  THR*     3.3     4.2    +      -       -      +
    128K  PHE*     3.5     6.3    -      -       +      -
    130K  ASP      3.7    11.0    -      -       -      +
    131K  GLU*     3.2    37.5    -      -       -      +
    133K  ILE*     3.5    38.1    -      -       +      -
    146b  ARG*     3.3    37.2    -      -       +      +
----------------------------------------------------------
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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