Contacts of the strand formed by residues 204 - 210 (chain L) 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 PRO 204 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195L  ALA*     6.0     2.2    -      -       +      -
    196L  ALA      3.4     2.5    -      -       -      +
    197L  THR*     3.6    20.9    -      -       +      +
    202L  THR      3.6     9.0    -      -       -      +
    203L  SER*     1.3    84.4    -      -       -      +
    205L  ILE*     1.3    65.4    +      -       -      +
    206L  VAL*     3.1    20.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 205 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112L  ALA*     5.7     2.7    -      -       +      -
    113L  PRO*     5.1     9.9    -      -       +      +
    115L  VAL*     4.1    24.8    -      -       +      +
    194L  CYS      3.8     0.5    -      -       -      +
    196L  ALA*     2.7    57.2    +      -       +      +
    198L  HIS*     4.0    10.8    -      -       +      +
    200L  THR*     3.4    25.8    -      -       +      +
    203L  SER*     3.1    26.9    -      -       -      +
    204L  PRO*     1.3    66.8    -      -       -      +
    206L  VAL*     1.3    62.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 206 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115L  VAL*     6.1     0.7    -      -       -      -
    193L  THR*     3.2    27.4    -      -       +      -
    194L  CYS      3.2     8.1    -      -       -      +
    195L  ALA*     3.7    17.9    -      -       +      -
    204L  PRO*     3.1    22.9    +      -       +      +
    205L  ILE*     1.3    83.4    -      -       -      +
    207L  LYS*     1.3    67.2    +      -       -      +
    208L  SER*     3.5     7.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 207 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139H  ALA*     4.6    18.4    -      -       -      +
    115L  VAL*     3.5    36.5    -      -       +      +
    116L  SER*     4.8     2.2    -      -       -      +
    117L  ILE*     3.5    36.9    +      -       +      +
    193L  THR*     3.1     1.2    -      -       -      +
    194L  CYS*     2.8    31.9    +      -       +      +
    206L  VAL*     1.3    75.8    -      -       -      +
    208L  SER*     1.3    67.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 208 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117L  ILE*     4.3     8.0    -      -       -      +
    191L  SER*     4.1     5.6    -      -       -      -
    192L  TYR      3.3     6.1    -      -       -      -
    193L  THR*     2.9    38.1    +      -       -      +
    206L  VAL*     3.5     7.4    -      -       -      +
    207L  LYS*     1.3    78.3    -      -       -      +
    209L  PHE*     1.3    66.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 209 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138H  SER*     4.7    16.6    -      -       -      +
    117L  ILE*     4.4    15.3    -      -       +      -
    119L  PRO*     3.9    29.4    -      -       +      -
    120L  PRO*     3.6    20.4    -      -       +      -
    132L  VAL*     4.0    18.4    -      -       +      -
    186L  TYR*     4.0    18.6    -      +       -      -
    191L  SER*     2.8    19.3    +      -       -      -
    192L  TYR*     2.8    65.9    +      +       +      -
    208L  SER*     1.3    78.7    -      -       -      +
    210L  ASN*     1.3    62.5    +      -       -      +
    211L  ALA*     4.1    15.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 210 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138H  SER*     6.1     0.9    -      -       -      -
    190L  ASN*     2.7    40.7    +      -       -      +
    191L  SER*     2.9    30.6    +      -       -      +
    209L  PHE*     1.3    76.5    -      -       -      +
    211L  ALA*     1.3    67.7    +      -       -      +
    212L  ASN*     4.2     4.4    +      -       -      +
----------------------------------------------------------
 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