Contacts of the strand formed by residues 295 - 301 (chain B) in PDB entry 1S0O


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 295 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  ILE*     6.5     0.7    -      -       +      -
    287B  VAL*     3.9    27.1    -      -       +      -
    288B  ALA      3.4     2.7    -      -       -      +
    289B  VAL*     4.2    17.0    -      -       +      -
    293B  LEU      4.5     5.6    -      -       -      +
    294B  ASP*     1.3    95.7    +      -       -      +
    296B  VAL*     1.3    69.4    +      -       -      +
    297B  SER*     5.3     2.5    -      -       -      -
   1808E    G      4.1    14.4    +      -       -      +
   1809E    G      4.8     5.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 296 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287B  VAL*     3.6     1.7    -      -       -      +
    288B  ALA*     2.7    36.9    +      -       +      +
    290B  THR*     4.6     8.1    -      -       +      -
    294B  ASP*     5.2     0.4    -      -       -      +
    295B  ILE*     1.3    80.4    -      -       -      +
    297B  SER*     1.3    69.5    +      -       -      +
    298B  ARG*     3.4    25.8    -      -       -      +
    322B  ILE*     4.1    26.2    -      -       +      +
    326B  ASP*     3.5    28.9    -      -       +      +
    328B  ARG*     3.6    14.4    -      -       -      +
   1808E    G      3.6    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 297 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285B  HIS*     5.1    10.6    -      -       -      -
    286B  VAL      3.2    13.7    -      -       -      -
    287B  VAL*     4.1    16.8    -      -       -      -
    295B  ILE*     5.3     2.7    -      -       -      -
    296B  VAL*     1.3    78.7    -      -       -      +
    298B  ARG*     1.3    82.2    +      -       -      +
    299B  GLY      4.3     0.2    -      -       -      -
    322B  ILE*     4.2     1.3    -      -       -      -
   1807E    A      3.4    22.3    +      -       -      +
   1808E    G      2.9    15.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 298 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285B  HIS*     4.3     2.0    -      -       -      -
    286B  VAL      2.8    28.5    +      -       -      +
    296B  VAL*     3.4    14.9    -      -       -      +
    297B  SER*     1.3    89.7    +      -       -      +
    299B  GLY*     1.3    59.6    +      -       -      +
    318B  LEU*     3.3    36.1    -      -       +      +
    321B  LYS*     4.0    17.2    +      -       +      +
    322B  ILE*     3.5    20.1    -      -       +      +
    325B  GLU*     2.6    49.0    +      -       -      +
    326B  ASP*     6.1     0.6    -      -       -      +
   1807E    A      3.2    31.2    +      -       -      +
   1808E    G      3.3    23.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284B  ILE      3.1    13.0    -      -       -      -
    285B  HIS*     3.6    15.3    -      -       -      -
    298B  ARG*     1.3    75.5    -      -       -      +
    300B  ARG*     1.3    63.0    +      -       -      +
    318B  LEU*     3.6     9.2    -      -       -      +
    321B  LYS*     5.0     3.8    +      -       -      -
   1806E    A      4.9     4.5    -      -       -      +
   1807E    A      2.8    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282B  LYS      4.0     0.9    -      -       -      +
    283B  ALA*     3.4     2.4    -      -       -      -
    284B  ILE*     2.9    34.6    +      -       +      +
    285B  HIS*     5.0     1.6    +      -       -      -
    299B  GLY*     1.3    75.4    -      -       -      +
    301B  THR*     1.3    74.0    +      -       -      +
    302B  PHE*     3.4    36.2    -      -       +      -
    314B  GLU*     2.9    50.7    +      -       +      +
    317B  LYS*     4.7     8.7    -      -       -      +
    318B  LEU*     4.2     4.9    -      -       +      +
   1806E    A      5.5     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282B  LYS*     3.5    12.3    -      -       +      +
    283B  ALA*     3.8     7.3    -      -       +      +
    285B  HIS*     5.5     1.9    -      -       -      -
    300B  ARG*     1.3    85.5    +      -       -      +
    302B  PHE*     1.3    74.7    +      -       -      +
    303B  PRO*     4.5     1.4    -      -       -      +
    339B  LYS*     3.1    43.4    +      -       +      +
   1806E    A      3.2    18.0    +      -       -      -
----------------------------------------------------------
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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