Contacts of the strand formed by residues 243 - 249 (chain A) in PDB entry 6KSF


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 LEU 243 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  ASP*     4.4     4.9    -      -       -      +
    242A  PRO*     1.3    74.0    -      -       -      +
    244A  LEU*     1.3    75.0    +      -       -      +
    245A  SER*     4.4     6.5    -      -       -      -
    276A  MET      3.6     0.7    -      -       -      +
    277A  VAL*     3.3     5.2    -      -       -      -
    278A  MET*     2.8    55.3    +      -       +      +
    283A  ARG*     3.7    31.4    -      -       -      +
    342A  THR*     4.1    13.2    -      -       +      -
    343A  VAL      3.4    10.1    -      -       -      +
    344A  ARG*     3.4    44.2    -      -       +      +
    401A   CL      4.2     0.4    -      -       +      -
    403A  SIN      4.6     7.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  SER*     3.3    41.3    -      -       -      +
    203A  VAL*     3.8    21.1    -      -       +      -
    204A  ALA*     4.3     3.8    -      -       +      +
    212A  PHE*     3.7    29.6    -      -       +      -
    242A  PRO*     4.0    18.8    -      -       +      +
    243A  LEU*     1.3    80.1    -      -       -      +
    245A  SER*     1.3    61.6    +      -       -      +
    246A  PHE*     3.9    17.3    -      -       +      -
    275A  ILE*     5.2     1.1    -      -       +      -
    276A  MET      3.5     3.8    -      -       -      +
    277A  VAL*     4.5    12.3    -      -       +      -
    341A  MET      3.5     1.0    -      -       -      +
    342A  THR*     3.2     7.4    -      -       -      +
    343A  VAL*     2.9    38.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  LEU*     4.4    11.7    -      -       -      -
    244A  LEU*     1.3    75.6    -      -       -      +
    246A  PHE*     1.3    60.7    +      -       -      +
    247A  SER      4.3     0.2    +      -       -      -
    270A  MET*     5.6     3.1    -      -       -      -
    274A  ASP      3.9     0.9    -      -       -      +
    275A  ILE*     3.4     4.7    -      -       -      +
    276A  MET*     2.9    55.5    +      -       -      +
    278A  MET*     5.3     4.9    -      -       -      -
    340A  ASN*     3.2    27.1    +      -       -      -
    341A  MET      3.1     4.3    -      -       -      -
    342A  THR*     4.1     3.4    +      -       -      -
    403A  SIN      5.7     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  PHE*     4.2    11.2    -      +       -      -
    196A  LEU*     4.9     0.4    -      -       +      -
    199A  LEU*     3.8    28.0    -      -       +      -
    200A  SER*     4.2    11.4    -      -       -      -
    203A  VAL*     4.1     9.6    -      -       +      -
    244A  LEU*     3.9    38.4    -      -       +      -
    245A  SER*     1.3    75.1    -      -       -      +
    247A  SER*     1.3    60.6    +      -       -      +
    248A  PHE*     4.1     9.2    -      -       +      -
    273A  GLY      6.3     0.2    -      -       -      -
    274A  ASP      3.8     4.5    -      -       -      +
    275A  ILE*     3.5    35.9    -      -       +      -
    339A  VAL      3.8     0.2    -      -       -      +
    340A  ASN*     3.1    10.0    -      -       -      +
    341A  MET*     2.8    71.3    +      -       +      +
    343A  VAL*     4.6     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  SER      4.3     0.4    +      -       -      -
    246A  PHE*     1.3    74.6    -      -       -      +
    248A  PHE*     1.3    63.3    +      -       -      +
    250A  GLN      4.7     1.6    +      -       -      -
    270A  MET*     4.5    17.8    +      -       -      +
    271A  HIS      4.3    10.2    +      -       -      -
    272A  SER*     4.5     1.5    -      -       -      -
    273A  GLY*     2.7    32.6    +      -       -      -
    274A  ASP*     3.3    13.0    +      -       -      -
    338A  ARG*     2.7    40.3    +      -       -      +
    339A  VAL      3.4     3.6    -      -       -      -
    340A  ASN*     4.0     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  PHE*     4.0    34.5    -      +       -      -
    111A  GLN*     3.8    34.1    -      -       +      -
    114A  TRP*     3.8    22.7    -      -       +      -
    115A  VAL*     3.5    29.6    -      -       +      -
    118A  CYS*     5.1     0.9    -      -       -      -
    246A  PHE*     4.1     9.9    -      -       +      -
    247A  SER*     1.3    83.2    +      -       -      +
    249A  GLY*     1.3    60.3    +      -       -      +
    272A  SER*     3.7     4.5    -      -       -      +
    273A  GLY*     4.1     0.9    -      -       -      -
    334A  LEU*     4.9     1.1    -      -       -      -
    338A  ARG*     3.5     7.2    -      -       -      +
    339A  VAL*     2.9    49.4    +      -       +      +
    341A  MET*     3.6    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  PHE*     1.3    72.1    -      -       -      +
    250A  GLN*     1.3    69.1    +      -       -      +
    251A  SER      3.7     0.3    +      -       -      -
    272A  SER*     3.0    21.3    +      -       -      -
    302A  PRO*     3.3    23.9    -      -       -      +
    305A  LEU*     4.1    16.3    -      -       -      +
    334A  LEU*     4.3    13.7    -      -       -      +
    337A  ALA      4.0     5.2    -      -       -      -
----------------------------------------------------------
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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