Contacts of the strand formed by residues 291 - 296 (chain D) in PDB entry 6B0Z


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 MET 291 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109D  ARG*     3.9    20.0    -      -       -      -
    110D  GLU      3.4    14.4    -      -       -      +
    111D  ALA*     4.4     3.6    -      -       +      -
    112D  ILE*     3.8     1.0    -      -       -      +
    278D  SER      3.5    23.1    -      -       -      +
    279D  ASP*     4.2     7.2    -      -       -      -
    282D  ALA*     3.9     5.8    -      -       +      -
    287D  SER      4.2     8.7    -      -       -      +
    288D  LEU*     3.5     5.3    +      -       -      +
    289D  GLY      3.6     0.8    -      -       -      -
    290D  MET*     1.3    80.9    -      -       -      +
    292D  THR*     1.3    74.7    +      -       -      +
    308D  ALA*     3.0    37.3    +      -       +      +
    331D  ALA*     3.4    11.3    -      -       -      +
    502D  C81      3.6    49.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 292 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108D  PHE      4.5     0.2    -      -       -      -
    109D  ARG*     3.3    26.9    -      -       -      +
    110D  GLU*     2.9    21.7    +      -       -      +
    112D  ILE*     4.2     3.8    -      -       +      -
    291D  MET*     1.3    78.5    -      -       -      +
    293D  SER*     1.3    63.3    +      -       -      +
    294D  VAL*     4.4    11.7    -      -       -      +
    306D  GLU      3.6     8.7    -      -       -      +
    307D  ALA*     4.4     0.2    -      -       -      +
    308D  ALA*     4.0     2.2    -      -       -      +
    331D  ALA      3.5    15.9    -      -       -      +
    334D  PHE*     3.5    34.8    -      -       +      +
    335D  ALA*     3.9     7.6    -      -       -      +
    338D  ARG*     3.3    19.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 293 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  VAL*     3.2    23.4    -      -       -      +
    108D  PHE      3.4     6.3    -      -       -      -
    109D  ARG*     4.3    13.8    +      -       -      -
    292D  THR*     1.3    75.9    -      -       -      +
    294D  VAL*     1.3    60.0    +      -       -      +
    295D  LEU      4.1     0.4    +      -       -      -
    304D  GLU      4.0     0.9    -      -       -      +
    305D  ALA*     3.7     0.5    -      -       -      -
    306D  GLU*     2.9    60.1    +      -       -      +
    308D  ALA*     4.2    14.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 294 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  VAL*     4.4     1.3    -      -       -      -
    108D  PHE*     2.9    33.8    +      -       +      +
    110D  GLU*     6.5     0.7    -      -       +      -
    199D  MET*     5.2     8.3    -      -       +      -
    292D  THR*     4.6     9.9    -      -       -      +
    293D  SER*     1.3    81.0    +      -       -      +
    295D  LEU*     1.3    65.9    +      -       -      +
    296D  VAL*     3.3    15.5    +      -       +      +
    303D  VAL*     3.5    32.3    -      -       +      -
    304D  GLU      3.3     7.9    -      -       -      +
    305D  ALA*     3.9    16.8    -      -       +      +
    338D  ARG*     4.3    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 295 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99D  ILE*     4.8     0.7    -      -       +      -
    100D  ARG*     3.9    32.1    -      -       +      +
    103D  LEU*     4.2    19.5    -      -       +      -
    104D  GLY      3.6    27.1    -      -       -      +
    105D  GLY      3.7    22.0    -      -       -      +
    106D  THR      3.7     3.6    -      -       -      +
    107D  VAL*     3.7    27.0    -      -       +      +
    293D  SER*     4.1     1.0    +      -       -      -
    294D  VAL*     1.3    70.6    -      -       -      +
    296D  VAL*     1.3    58.9    +      -       -      +
    297D  CYS*     4.0     3.5    +      -       -      -
    303D  VAL*     3.5     7.3    -      -       -      -
    304D  GLU*     2.7    54.3    +      -       +      +
    306D  GLU*     5.5     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 296 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105D  GLY*     4.1     1.1    -      -       -      -
    106D  THR      2.8    37.4    +      -       -      +
    108D  PHE*     3.6    11.0    -      -       +      -
    195D  SER*     2.9    33.8    +      -       -      +
    198D  GLN*     4.9     4.9    -      -       +      -
    199D  MET*     3.5    35.7    -      -       +      +
    294D  VAL*     3.4    22.4    -      -       +      +
    295D  LEU*     1.3    72.7    -      -       -      +
    297D  CYS*     1.3    69.0    +      -       -      +
    300D  GLY*     5.9     1.6    -      -       -      -
    302D  THR      4.4     2.7    -      -       -      +
    303D  VAL*     4.8    12.1    -      -       +      -
----------------------------------------------------------
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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