Contacts of the strand formed by residues 38 - 43 (chain K) in PDB entry 2J28


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 ILE 38 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25K  LEU*     4.1    26.9    +      -       +      +
     36K  GLY      4.9     0.9    -      -       -      +
     37K  ASP*     1.3    75.8    +      -       -      +
     39K  ILE*     1.3    77.6    +      -       -      +
     59K  LYS*     4.0    21.5    -      -       +      -
     60K  ALA      3.5     2.7    -      -       -      -
     61K  VAL*     3.8     0.9    -      -       +      -
     87K  LEU*     3.5    28.7    -      -       +      -
     92K  GLU*     3.8    22.4    -      -       -      +
    112K  PHE*     3.3    39.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 39 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2K  ILE      4.9     2.0    -      -       -      +
      8K  LEU*     6.1     2.0    -      -       +      -
     21K  CYS*     3.2    35.0    -      -       +      -
     23K  LYS      3.4     0.9    -      -       -      +
     24K  VAL*     3.3    35.0    -      -       +      -
     25K  LEU*     3.7     9.9    -      -       -      +
     33K  ALA*     3.3    31.6    -      -       +      -
     37K  ASP*     5.0     0.4    -      -       +      -
     38K  ILE*     1.3    94.1    -      -       -      +
     40K  LYS*     1.3    69.3    +      -       -      +
     41K  ILE*     3.5     8.9    +      -       +      -
     59K  LYS*     3.0     3.8    -      -       -      -
     60K  ALA*     2.5    45.8    +      -       -      +
     62K  VAL*     4.1    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 40 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2561B    U      3.3    18.4    -      -       -      +
   2562B    U      2.9    20.9    +      -       -      +
     21K  CYS*     3.4     4.0    -      -       -      -
     22K  ILE*     2.9    54.8    +      -       +      +
     23K  LYS*     3.2    19.2    +      -       +      +
     25K  LEU*     4.0     7.4    -      -       +      +
     39K  ILE*     1.3    76.9    -      -       -      +
     41K  ILE*     1.3    60.4    +      -       -      +
     57K  VAL*     4.1    15.0    -      -       +      -
     58K  LEU      3.4    15.5    -      -       -      +
     59K  LYS*     2.7    33.4    -      -       +      +
     89K  ASN*     2.9    22.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 41 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8K  LEU*     4.3     6.3    -      -       +      -
     19K  VAL*     3.5    33.7    -      -       +      +
     20K  MET      3.2     8.7    -      -       -      +
     21K  CYS*     3.4    32.1    -      -       +      +
     22K  ILE*     4.7     0.6    -      -       -      +
     39K  ILE*     3.5    12.9    +      -       +      -
     40K  LYS*     1.3    73.3    -      -       -      +
     42K  THR*     1.3    68.4    +      -       -      +
     43K  ILE*     4.3     5.6    -      -       +      +
     57K  VAL*     3.4     9.7    -      -       -      +
     58K  LEU*     3.0    33.1    +      -       +      +
     60K  ALA*     4.3    11.9    -      -       +      -
     84K  CYS*     3.9    19.3    -      -       -      -
     86K  LEU*     4.0    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 42 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1952B    A      3.4    55.1    +      -       +      +
     19K  VAL*     3.5     0.9    -      -       -      -
     20K  MET*     2.9    26.9    +      -       -      -
     22K  ILE*     3.0    32.8    -      -       -      +
     41K  ILE*     1.3    78.0    +      -       -      +
     43K  ILE*     1.3    68.0    +      -       -      +
     44K  LYS*     3.0     8.1    +      -       -      +
     55K  GLY*     3.7     5.6    -      -       -      +
     56K  ASP      3.2    11.2    -      -       -      +
     57K  VAL*     3.8     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 43 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1952B    A      5.0     0.9    +      -       -      -
     15K  GLY      5.0     0.2    -      -       -      +
     16K  ALA      4.8     1.3    -      -       -      +
     19K  VAL*     3.5    16.6    -      -       +      -
     41K  ILE*     4.5     5.8    -      -       +      -
     42K  THR*     1.3    70.0    -      -       -      +
     44K  LYS*     1.3    60.2    +      -       -      +
     45K  GLU      4.1     0.2    -      -       -      +
     46K  ALA*     3.8    18.4    -      -       +      +
     52K  VAL*     3.3    30.7    -      -       +      -
     53K  LYS      3.6    10.1    -      -       -      +
     54K  LYS*     3.3    21.6    -      -       -      +
     55K  GLY*     2.7    29.3    +      -       -      -
     56K  ASP*     2.7    29.9    +      -       +      +
     58K  LEU*     3.3    38.8    -      -       +      -
     86K  LEU*     4.5     3.1    -      -       +      -
----------------------------------------------------------
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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