Contacts of the strand formed by residues 31 - 38 (chain E) in PDB entry 1J8H


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 ASN 31 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  ALA*     4.5     2.4    -      -       -      +
     99D  ASN      3.2    20.0    +      -       -      -
    102D  GLU*     3.8     2.4    -      -       -      +
     29E  HIS*     3.4     0.9    -      -       -      +
     30E  GLU*     1.3    86.3    -      -       -      +
     32E  MET*     1.3    66.1    +      -       -      +
     33E  PHE*     3.8    11.9    -      -       +      -
     49E  SER      3.3     2.7    -      -       -      -
     50E  TYR*     3.5    34.0    -      -       +      +
     94E  SER*     3.0     5.5    -      -       -      -
     95E  SER*     2.7    52.3    +      -       -      +
     97E  THR*     3.2    29.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 32 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23E  CYS*     3.5    42.2    -      -       -      +
     25E  GLN*     3.9    18.6    -      -       +      +
     29E  HIS      4.9     0.4    -      -       -      +
     30E  GLU      4.0     0.2    +      -       -      -
     31E  ASN*     1.3    80.5    -      -       -      +
     33E  PHE*     1.3    65.1    +      -       -      +
     48E  PHE*     3.4     0.7    -      -       -      -
     49E  SER      2.9    32.2    +      -       -      +
     69E  ARG*     3.5    31.9    -      -       -      +
     72E  LYS      3.6    13.0    -      -       -      +
     73E  GLU      3.8    11.4    -      -       -      +
     75E  PHE*     3.4    33.4    -      -       +      -
     92E  CYS*     4.2     1.1    -      -       -      -
     93E  ALA      3.2     6.3    -      -       -      +
     94E  SER*     4.0    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 33 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99D  ASN      3.9     6.1    -      -       -      -
    102D  GLU      4.0     0.2    -      -       -      -
    103D  LYS*     3.3    36.1    -      -       +      -
     31E  ASN*     3.8    26.9    -      -       +      -
     32E  MET*     1.3    75.0    -      -       -      +
     34E  TRP*     1.3    62.2    +      -       -      +
     35E  TYR*     3.6    18.2    -      -       +      -
     45E  LEU*     4.0     7.9    -      -       +      -
     47E  TYR      3.7     4.9    -      -       -      -
     48E  PHE*     3.5    17.5    -      -       +      -
     50E  TYR*     3.8    13.0    -      +       -      -
     75E  PHE*     3.9     3.4    -      -       -      -
     91E  LEU      3.8     0.4    -      -       -      +
     92E  CYS*     3.4    10.6    -      -       -      -
     93E  ALA*     2.8    43.3    +      -       +      +
     95E  SER*     3.7    13.9    -      -       -      -
    106E  TYR*     3.4    37.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with TRP 34 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  GLN*     3.6    23.8    -      -       -      -
     21E  LEU*     3.8    29.2    -      -       +      -
     22E  GLU      3.8     7.0    -      -       -      -
     23E  CYS*     3.5    21.7    -      -       +      +
     33E  PHE*     1.3    74.2    -      -       -      +
     35E  TYR*     1.3    63.8    +      -       -      +
     45E  LEU*     3.6     4.3    -      -       -      +
     46E  ILE*     2.8    27.0    +      -       +      -
     47E  TYR*     2.9    19.1    +      -       +      +
     67E  VAL*     4.5     0.7    -      -       +      -
     75E  PHE*     3.0    49.2    +      +       -      -
     77E  LEU*     3.5    49.9    -      -       +      +
     90E  TYR*     3.6    25.6    -      -       +      -
     91E  LEU      3.4    23.8    -      -       -      -
     92E  CYS*     3.9     5.8    -      -       +      -
    112E  THR*     5.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 35 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103D  LYS*     4.4     0.3    -      -       -      -
    104D  LEU      2.9    25.6    +      -       -      -
    106D  PHE*     3.8    15.0    -      +       -      -
     33E  PHE*     3.6    20.4    -      -       +      -
     34E  TRP*     1.3    79.1    -      -       -      +
     36E  ARG*     1.3    58.2    +      -       -      +
     43E  LEU*     4.0    28.9    -      -       +      -
     44E  ARG      3.2     9.2    -      -       -      +
     45E  LEU*     3.5    40.0    -      -       +      +
     46E  ILE*     4.1     4.5    -      -       -      +
     90E  TYR*     3.4     6.1    -      -       -      +
     91E  LEU*     2.7    45.6    +      -       +      +
     93E  ALA*     4.7     5.4    -      -       +      -
    106E  TYR*     2.4    46.3    +      +       -      -
    108E  PHE*     5.2     6.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 36 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35E  TYR*     1.3    75.3    -      -       -      +
     37E  GLN*     1.3    60.6    +      -       -      +
     38E  ASP*     2.9    37.3    +      -       -      +
     42E  GLY      3.6     1.0    -      -       -      +
     43E  LEU*     3.6     2.7    -      -       -      -
     44E  ARG*     3.0    43.2    +      -       -      +
     46E  ILE*     3.7    12.7    -      -       +      +
     60E  ILE*     3.7    30.9    -      -       +      +
     65E  TYR*     2.8    37.0    +      -       -      -
     85E  ASN*     3.0    29.7    +      -       -      -
     86E  GLN*     3.7     5.4    -      -       -      +
     87E  THR      3.5     9.1    +      -       -      -
     88E  SER*     3.5    13.7    +      -       -      +
     89E  MET      3.2     5.8    -      -       -      +
     90E  TYR*     3.9     8.5    -      -       +      -
     91E  LEU*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 37 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  GLN*     3.0    34.6    +      -       -      +
     43D  LEU*     4.4     1.0    -      -       -      +
     87D  GLU*     4.2     5.3    +      -       -      -
     89D  PHE*     3.5    20.7    -      -       +      -
     36E  ARG*     1.3    74.8    -      -       -      +
     38E  ASP*     1.3    66.3    +      -       -      +
     39E  PRO*     4.6     0.3    -      -       -      +
     42E  GLY*     3.3     6.7    -      -       -      +
     43E  LEU*     3.4    24.2    -      -       +      -
     88E  SER*     3.0    12.5    +      -       -      -
     89E  MET*     2.6    41.6    +      -       +      +
     91E  LEU*     3.6    21.6    -      -       +      +
    113E  ARG*     4.4     4.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 38 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36E  ARG*     2.9    44.7    +      -       -      +
     37E  GLN*     1.3    77.6    +      -       -      +
     39E  PRO*     1.3    70.0    -      -       +      +
     40E  GLY      3.3     0.2    +      -       -      -
     41E  LEU*     2.9    40.5    +      -       +      +
     42E  GLY*     3.2    13.9    +      -       -      +
     44E  ARG*     3.3    11.6    +      -       -      -
     87E  THR      3.7     2.9    -      -       -      +
     88E  SER*     2.7    24.8    +      -       -      -
    113E  ARG*     5.8     0.2    +      -       -      -
----------------------------------------------------------
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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