Contacts of the strand formed by residues 329 - 334 (chain B) in PDB entry 3RT0


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 ALA 329 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  VAL      3.6     5.4    -      -       -      -
    242B  TYR*     3.5    22.2    -      -       +      -
    254B  CYS*     5.0     1.1    -      -       -      -
    258B  LEU*     5.6     2.7    -      -       +      -
    294B  PHE*     3.9    23.1    -      -       +      -
    328B  THR*     1.3    77.2    -      -       -      +
    330B  VAL*     1.3    60.0    +      -       -      +
    331B  VAL*     4.1     0.7    -      -       +      -
    342B  SER      3.8     1.6    -      -       -      +
    343B  ASN*     3.6     2.8    +      -       -      -
    344B  CYS*     2.8    38.8    +      -       -      +
    400B  ILE*     4.2    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  GLY*     3.3     2.4    -      -       -      -
    241B  VAL*     2.9    55.3    +      -       +      +
    329B  ALA*     1.3    74.2    -      -       -      +
    331B  VAL*     1.3    64.3    +      -       -      +
    341B  VAL*     4.4     3.8    -      -       +      -
    342B  SER      3.6     4.9    -      -       -      +
    343B  ASN*     3.4    25.8    -      -       +      +
    347B  SER*     3.9    19.2    -      -       -      -
    348B  ARG      4.0     4.7    -      -       -      +
    349B  ALA*     3.9    33.7    -      -       +      +
    361B  SER*     4.6     0.2    -      -       -      +
    429B  LEU*     3.7    16.3    -      -       +      +
    430B  ALA      4.7     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  PHE*     3.4    30.3    -      -       +      -
    239B  PHE      3.3     5.8    -      -       -      +
    240B  GLY*     4.3     0.4    -      -       -      -
    242B  TYR*     3.9    19.3    -      -       +      +
    258B  LEU*     3.8    24.7    -      -       +      -
    290B  PHE*     4.1    21.1    -      -       +      -
    294B  PHE*     4.2    12.1    -      -       +      -
    330B  VAL*     1.3    80.1    -      -       -      +
    332B  ALA*     1.3    67.0    +      -       -      +
    333B  LEU*     4.1     3.6    -      -       +      -
    340B  VAL      3.8     0.3    -      -       -      +
    341B  VAL*     3.3     6.0    -      -       -      +
    342B  SER*     2.8    40.7    +      -       -      +
    429B  LEU*     4.3     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 332 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237B  HIS      3.6     2.9    -      -       -      +
    239B  PHE*     2.8    43.5    +      -       +      +
    331B  VAL*     1.3    75.5    -      -       -      +
    333B  LEU*     1.3    65.2    +      -       -      +
    334B  VAL*     4.9     0.4    -      -       +      -
    339B  ILE*     4.6     2.7    -      -       +      -
    340B  VAL      3.3     4.3    -      -       -      +
    341B  VAL*     3.9    19.1    -      -       +      -
    427B  LEU*     4.1    13.9    -      -       +      -
    429B  LEU*     3.9    24.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 333 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  LEU*     3.8    25.8    -      -       +      -
    215B  LEU*     4.6     9.6    -      -       +      -
    236B  GLY*     5.7     0.4    -      -       -      -
    237B  HIS      3.2     8.5    -      -       -      +
    238B  PHE*     3.9    15.3    -      -       +      -
    262B  LEU*     3.7    23.3    -      -       +      -
    266B  ILE*     5.1     0.2    -      -       +      -
    286B  TRP*     3.5    37.7    -      -       +      -
    290B  PHE*     3.9    18.6    -      -       +      -
    331B  VAL*     4.1     0.7    -      -       +      -
    332B  ALA*     1.3    79.6    -      -       -      +
    334B  VAL*     1.3    62.8    +      -       -      +
    335B  CYS*     6.1     0.2    -      -       -      -
    338B  HIS      3.8     0.9    -      -       -      +
    339B  ILE*     3.4     5.5    -      -       -      +
    340B  VAL*     2.8    38.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 334 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  CYS*     4.4     6.5    -      -       -      -
    215B  LEU*     5.9     0.4    -      -       -      -
    236B  GLY*     3.6     1.4    -      -       -      -
    237B  HIS*     3.0    40.9    +      -       +      -
    239B  PHE*     3.8    28.7    -      -       +      -
    333B  LEU*     1.3    78.8    -      -       -      +
    335B  CYS*     1.3    72.7    +      -       -      +
    338B  HIS      3.7     4.3    -      -       -      +
    339B  ILE*     4.5     8.5    -      -       +      -
    420B  ARG*     4.0    13.7    -      -       -      +
    427B  LEU*     4.1    24.5    -      -       +      -
    499B  ILE*     4.6     7.4    -      -       +      -
    501B  LEU*     4.4    14.1    -      -       +      -
----------------------------------------------------------
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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