Contacts of the strand formed by residues 326 - 332 (chain B) in PDB entry 6DBU


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 THR 326 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264B  SER*     3.9     2.6    +      -       -      -
    321B  SER      3.9     0.2    -      -       -      -
    322B  LEU*     3.0    16.5    +      -       -      +
    323B  GLY      2.3    55.4    +      -       -      -
    324B  LYS*     2.9    10.4    +      -       -      +
    325B  GLY*     1.3    76.6    -      -       -      +
    327B  ALA*     1.3    61.7    +      -       -      +
    347B  GLN*     3.8    22.7    -      -       -      +
    348B  VAL      3.7     4.0    -      -       -      -
    349B  SER*     4.2    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  ILE*     4.6     8.3    -      -       +      -
    264B  SER*     4.8     4.9    -      -       -      -
    274B  PHE*     4.5    13.7    -      -       +      -
    320B  GLY      3.6     9.9    -      -       -      +
    321B  SER*     4.0     8.7    -      -       -      -
    322B  LEU*     3.4    11.8    -      -       -      +
    325B  GLY      4.6     1.8    -      -       -      +
    326B  THR*     1.3    76.9    -      -       -      +
    328B  LEU*     1.3    62.6    +      -       -      +
    329B  VAL*     5.4     0.9    -      -       +      -
    347B  GLN*     3.5     6.3    -      -       -      +
    348B  VAL*     2.9    46.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     4.8     9.9    -      -       +      -
     19B  PHE*     5.1    10.1    -      -       +      -
     21B  LEU*     4.7    15.7    -      -       +      -
     30B  LEU*     6.3     2.2    -      -       +      -
     48B  VAL*     5.9     2.5    -      -       +      -
     50B  ILE*     5.5     1.6    -      -       +      -
     55B  LEU*     4.2    20.2    -      -       +      -
    319B  GLY*     3.3     1.4    -      -       -      -
    320B  GLY      2.8    41.9    +      -       -      +
    322B  LEU*     4.1    18.4    -      -       +      +
    327B  ALA*     1.3    73.2    -      -       -      +
    329B  VAL*     1.3    76.5    +      -       -      +
    345B  PHE*     3.5    42.2    -      -       +      -
    346B  TYR      3.3    19.5    -      -       -      +
    347B  GLN*     4.6     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  ILE*     3.9    20.0    -      -       +      -
    274B  PHE*     4.9    11.7    -      -       +      -
    307B  TRP*     5.1     4.0    -      -       +      -
    311B  ILE*     4.7    10.5    -      -       +      -
    317B  TRP*     5.3    11.4    -      -       +      -
    318B  PHE      3.2     9.0    -      -       -      +
    319B  GLY*     4.1     0.4    -      -       -      -
    320B  GLY      5.4     0.2    -      -       -      +
    327B  ALA*     5.3     2.0    -      -       +      -
    328B  LEU*     1.3    83.5    -      -       -      +
    330B  ALA*     1.3    63.6    +      -       -      +
    331B  ILE*     5.0     2.0    -      -       +      -
    345B  PHE*     3.4     4.0    -      -       -      -
    346B  TYR*     2.9    60.5    +      -       +      +
    348B  VAL*     4.0    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  PHE*     6.1     0.2    -      -       +      -
    317B  TRP*     3.2     5.9    -      -       -      +
    318B  PHE*     2.9    56.4    +      -       +      -
    319B  GLY*     5.5     1.1    -      -       -      -
    328B  LEU*     5.6     0.4    -      -       +      -
    329B  VAL*     1.3    77.6    -      -       -      +
    331B  ILE*     1.3    66.0    +      -       -      +
    332B  PRO*     4.8     0.2    -      -       -      -
    343B  TYR*     4.7     4.9    -      -       +      -
    344B  HIS      3.1    13.0    -      -       -      +
    345B  PHE*     3.5    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310B  GLU*     4.9     2.7    -      -       +      +
    311B  ILE*     3.4    37.0    -      -       +      -
    314B  SER*     3.3    36.8    -      -       -      +
    316B  THR      3.4    10.3    -      -       -      +
    317B  TRP*     3.4    21.3    -      -       +      -
    329B  VAL*     5.0     2.7    -      -       +      -
    330B  ALA*     1.3    79.9    -      -       -      +
    332B  PRO*     1.3    70.2    -      -       -      +
    333B  SER*     3.1     1.1    +      -       -      -
    343B  TYR*     3.3     5.6    -      -       -      -
    344B  HIS*     2.9    35.4    +      -       +      +
    346B  TYR*     3.9    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 332 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314B  SER*     4.5     7.5    +      -       -      +
    316B  THR*     3.3    43.1    -      -       +      +
    317B  TRP*     4.4     2.7    -      -       -      -
    318B  PHE*     4.8     3.4    -      -       +      -
    330B  ALA      4.5     0.4    -      -       -      +
    331B  ILE*     1.3    88.1    -      -       +      +
    333B  SER*     1.3    64.0    +      -       -      +
    334B  GLU*     3.0    15.7    +      -       -      +
    342B  ALA*     3.0    10.8    -      -       +      +
    343B  TYR*     3.9    24.4    -      -       +      +
----------------------------------------------------------
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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