Contacts of the strand formed by residues 173 - 180 (chain H) in PDB entry 1J5O


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 VAL 173 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164H  TRP*     3.9    13.7    -      -       +      -
    169H  LEU*     4.3     8.5    -      -       +      +
    170H  SER*     4.1    32.2    +      -       -      +
    171H  SER      3.8     2.4    +      -       -      -
    172H  GLY*     1.3    78.3    -      -       -      +
    174H  HIS*     1.3    79.0    +      -       -      +
    175H  THR*     4.0     8.5    -      -       -      +
    189H  SER*     3.9    11.7    -      -       -      +
    190H  SER      3.3    12.3    -      -       -      +
    191H  VAL*     3.7    20.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 174 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172H  GLY      6.1     1.1    -      -       -      -
    173H  VAL*     1.3    82.9    +      -       -      +
    175H  THR*     1.3    55.5    -      -       -      +
    176H  PHE*     3.6    20.3    -      +       +      -
    189H  SER*     2.2    23.9    +      -       -      -
    190H  SER*     2.7    28.0    +      -       -      +
    137L  ASN*     3.6    16.8    -      -       +      -
    138L  ASN*     2.8    33.9    +      -       -      -
    164L  THR*     5.4     5.1    -      -       +      +
    167L  ASP*     5.0    18.6    -      -       +      -
    172L  THR*     5.5     2.0    -      -       -      -
    173L  TYR      5.7     0.2    -      -       -      -
    174L  SER*     3.2    26.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 175 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162H  VAL*     5.1    15.7    +      -       +      +
    173H  VAL*     4.0     9.7    -      -       -      +
    174H  HIS*     1.3    73.5    +      -       -      +
    176H  PHE*     1.3    68.9    +      -       -      +
    177H  PRO*     4.0     3.6    -      -       -      +
    187H  LEU*     4.4    14.6    -      -       +      -
    189H  SER*     2.9    23.7    +      -       -      +
    164L  THR*     3.9    13.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 176 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174H  HIS*     3.6    37.0    -      -       +      -
    175H  THR*     1.3    77.2    -      -       -      +
    177H  PRO*     1.3    73.0    -      -       +      +
    178H  ALA*     4.2     0.2    -      -       -      -
    187H  LEU*     3.1    24.7    -      -       -      +
    188H  SER*     2.9    25.2    +      -       -      +
    189H  SER*     3.8     1.6    -      -       -      -
    190H  SER*     4.0     2.2    -      -       -      -
    135L  PHE*     3.6    25.6    -      +       -      -
    137L  ASN*     4.3     5.8    -      -       -      -
    162L  SER*     3.9    16.6    -      -       -      +
    164L  THR*     3.5    22.7    -      -       +      -
    174L  SER*     3.9    25.1    -      -       -      -
    175L  MET      4.3     0.7    -      -       -      -
    176L  SER*     3.3    26.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 177 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158H  GLU*     5.8     0.7    -      -       -      +
    175H  THR      4.0     5.4    -      -       -      +
    176H  PHE*     1.3    85.1    -      -       +      +
    178H  ALA*     1.3    66.0    +      -       -      +
    179H  VAL*     4.3     1.2    -      -       -      +
    187H  LEU*     4.6     3.4    -      -       +      -
    162L  SER*     3.2    33.0    +      -       -      +
    163L  TRP      4.7     9.0    -      -       -      +
    164L  THR*     5.0     9.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 178 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155H  TYR*     3.5    24.7    -      -       -      +
    158H  GLU*     4.6    13.0    +      -       -      +
    176H  PHE      3.3     3.7    +      -       -      -
    177H  PRO*     1.3    77.7    -      -       -      +
    179H  VAL*     1.3    62.4    +      -       -      +
    185H  TYR*     3.9    10.2    -      -       +      -
    186H  THR      3.1    36.6    -      -       -      +
    187H  LEU*     3.6    10.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 179 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177H  PRO      4.3     7.4    -      -       -      +
    178H  ALA*     1.3    81.5    -      -       -      +
    180H  LEU*     1.3    66.5    +      -       +      +
    181H  GLN*     2.6    21.4    +      -       -      +
    184H  LEU      3.2     6.5    -      -       -      +
    185H  TYR*     4.3     3.4    -      -       -      -
    186H  THR*     3.5    16.8    +      -       -      +
    160L  LEU*     4.6    19.9    -      -       +      +
    161L  ASN      4.9    10.1    -      -       -      +
    162L  SER*     4.4    15.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 180 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43H  SER*     6.0     2.2    -      -       -      +
    178H  ALA      5.9     0.2    -      -       -      +
    179H  VAL*     1.3    78.6    -      -       +      +
    181H  GLN*     1.3    59.7    +      -       -      +
    182H  SER      3.4     3.3    +      -       -      -
    183H  ASP*     3.8    12.0    +      -       -      +
    184H  LEU      3.1    14.1    -      -       -      +
    185H  TYR*     3.2    35.0    -      -       +      +
    160L  LEU*     5.4     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page


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