Contacts of the strand formed by residues 286 - 292 (chain A) in PDB entry 3SN6


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 SER 286 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  THR      4.4     4.4    +      -       -      -
    243A  ALA*     3.4     6.3    -      -       -      +
    244A  ILE      2.9    24.1    +      -       -      -
    277A  TRP*     4.5     0.2    -      -       -      -
    284A  THR      3.9     2.2    +      -       -      -
    285A  ILE*     1.3    74.2    -      -       -      +
    287A  VAL*     1.3    59.0    +      -       -      +
    288A  ILE      4.0     0.2    -      -       -      -
    356A  ARG      4.8     0.9    +      -       -      -
    357A  HIS*     3.5     9.6    -      -       -      -
    358A  TYR*     3.0    34.5    +      -       -      +
    360A  TYR*     4.2     1.7    +      -       -      -
    382A  ILE*     3.6    41.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  ILE*     3.3    24.9    -      -       +      +
    246A  PHE*     3.7    23.1    -      -       +      -
    273A  PHE*     3.4    29.6    -      -       +      -
    276A  ILE*     4.4    17.7    -      -       +      -
    277A  TRP*     3.7    24.5    -      -       +      -
    285A  ILE      4.4     3.4    -      -       -      +
    286A  SER*     1.3    73.2    -      -       -      +
    288A  ILE*     1.3    64.8    +      -       -      +
    289A  LEU*     3.5     2.9    +      -       +      +
    358A  TYR      3.1     6.8    +      -       -      -
    359A  CYS*     3.1     8.0    -      -       -      -
    360A  TYR*     3.1    22.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  ALA*     3.9    26.2    -      -       +      -
    244A  ILE      2.9     9.8    +      -       -      +
    245A  ILE*     3.4    12.0    -      -       +      +
    246A  PHE      2.9    26.1    +      -       -      -
    286A  SER      3.9     0.2    +      -       -      -
    287A  VAL*     1.3    70.9    -      -       -      +
    289A  LEU*     1.3    62.0    +      -       -      +
    290A  PHE*     3.8    18.6    +      -       +      -
    360A  TYR*     3.5    17.9    -      -       +      +
    362A  HIS*     4.4     6.3    -      -       +      -
    375A  VAL*     3.8    22.9    -      -       +      +
    378A  ASP*     3.5    44.2    -      -       +      +
    379A  CYS*     4.1     8.5    -      -       -      +
    382A  ILE*     4.2     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  PHE*     3.3    33.4    -      -       +      +
    248A  VAL*     3.9    12.8    -      -       +      -
    273A  PHE*     5.4     0.4    -      -       +      -
    287A  VAL*     3.5     4.2    +      -       +      +
    288A  ILE*     1.3    71.8    -      -       -      +
    290A  PHE*     1.3    56.7    +      -       -      +
    291A  LEU*     3.5    30.7    -      -       +      -
    342A  ARG      5.2     0.7    -      -       -      +
    345A  PHE*     3.4    38.6    -      -       +      -
    346A  LEU*     6.5     0.2    -      -       +      -
    359A  CYS*     3.9    16.4    -      -       -      -
    360A  TYR      2.6    15.1    +      -       -      +
    361A  PRO*     3.2    18.4    -      -       +      -
    362A  HIS*     2.7    35.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ILE*     4.4    20.2    -      -       +      -
    245A  ILE*     3.7    26.2    -      -       +      -
    246A  PHE      2.9     8.1    +      -       -      +
    247A  VAL*     3.2    18.2    -      -       +      +
    248A  VAL      2.9    27.4    +      -       -      +
    288A  ILE*     3.8     7.8    +      -       +      -
    289A  LEU*     1.3    73.3    -      -       -      +
    291A  LEU*     1.3    63.4    +      -       -      +
    292A  ASN*     3.5     1.5    +      -       -      +
    362A  HIS*     3.5    38.4    -      +       +      -
    364A  THR*     3.9    15.0    -      -       -      +
    371A  ASN*     3.7    33.7    -      -       +      -
    374A  ARG*     4.4     5.8    -      -       +      -
    375A  VAL*     3.6    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  VAL*     3.4    30.1    -      -       +      +
    250A  SER*     3.1    13.2    -      -       -      +
    289A  LEU*     3.5    26.9    -      -       +      -
    290A  PHE*     1.3    70.5    -      -       -      +
    292A  ASN*     1.3    57.3    +      -       -      +
    294A  GLN*     2.6    27.7    +      -       -      +
    341A  ILE*     3.9    23.8    -      -       +      -
    342A  ARG*     3.9    19.1    -      -       +      +
    345A  PHE*     4.0     7.2    -      -       +      -
    362A  HIS      2.8    20.2    +      -       -      +
    363A  PHE*     3.3    24.2    -      -       +      -
    364A  THR*     2.9    17.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  SER*     3.5    25.8    +      -       -      +
     56A  ILE*     4.8     6.9    -      -       -      +
    247A  VAL*     4.0    20.4    -      -       +      +
    248A  VAL      2.9    15.3    +      -       -      +
    249A  ALA*     4.1     7.9    -      -       +      -
    250A  SER*     2.9    24.2    +      -       -      -
    290A  PHE*     3.5     1.5    +      -       -      +
    291A  LEU*     1.3    72.4    -      -       -      +
    293A  LYS*     1.3    77.6    +      -       +      +
    294A  GLN      3.2     3.3    +      -       -      -
    364A  THR*     3.3    14.8    -      -       -      +
    365A  CYS*     3.1    37.1    +      -       -      +
----------------------------------------------------------
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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