Contacts of the strand formed by residues 161 - 164 (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 THR 161 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160H  VAL*     1.3    79.7    -      -       -      +
    162H  VAL*     1.3    62.0    +      -       -      +
    163H  THR*     5.9     3.1    -      -       -      -
    207H  VAL*     3.3     0.7    -      -       -      +
    208H  ALA*     2.3    66.7    +      -       -      +
    210H  PRO*     5.2     2.2    -      -       +      +
    215H  LYS*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 162 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150H  CYS*     5.4     3.1    -      -       +      -
    152H  VAL*     4.9     3.4    -      -       +      -
    160H  VAL*     4.4     6.7    -      -       +      +
    161H  THR*     1.3    80.8    -      -       -      +
    163H  THR*     1.3    76.6    +      -       -      +
    164H  TRP*     5.1     5.9    -      -       -      +
    175H  THR*     5.1    16.4    +      -       +      +
    187H  LEU*     4.9    18.4    -      -       +      -
    189H  SER*     5.5     5.8    -      -       -      -
    205H  CYS*     4.5     8.7    -      -       +      -
    206H  ASN*     2.7    30.5    -      -       -      +
    207H  VAL*     3.5    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 163 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161H  THR*     5.9     2.2    -      -       -      -
    162H  VAL*     1.3    82.2    -      -       -      +
    164H  TRP*     1.3    68.2    +      -       -      +
    166H  SER*     3.9     1.2    -      -       -      -
    167H  GLY*     3.0    30.2    +      -       -      -
    169H  LEU      5.0     2.9    -      -       -      -
    204H  THR      3.4     0.9    -      -       -      +
    205H  CYS*     3.4     3.6    -      -       -      -
    206H  ASN*     2.5    56.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 164 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148H  LEU*     4.4     4.7    -      -       +      -
    149H  GLY*     3.4    47.1    -      -       -      -
    150H  CYS*     3.9     1.3    -      -       +      -
    162H  VAL*     5.1     5.1    -      -       +      +
    163H  THR*     1.3    85.4    +      -       -      +
    165H  ASN*     1.3    69.1    +      -       -      +
    166H  SER      3.3     0.9    -      -       -      -
    167H  GLY      3.2     3.8    +      -       -      -
    169H  LEU*     3.0    50.8    +      -       +      +
    173H  VAL*     3.9    18.3    -      -       +      +
    189H  SER*     3.5    18.3    +      -       -      -
    191H  VAL*     3.2    35.9    -      -       +      +
    203H  VAL*     3.5    21.1    -      -       +      -
    204H  THR*     2.8    23.1    -      -       -      -
    205H  CYS*     3.4    27.8    -      -       +      +
    220H  ILE*     4.7    10.3    -      -       -      -
----------------------------------------------------------
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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