Contacts of the strand formed by residues 26 - 35 (chain D) 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 GLN 26 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25D  SER*     1.3    91.5    +      -       -      +
     27D  CYS*     1.3    60.0    +      -       -      +
    115D  ASN*     5.7     1.2    -      -       -      +
    140D  VAL*     3.8    22.8    -      -       +      +
    141D  VAL      3.1    19.3    -      -       -      +
    142D  ASP*     3.9    13.2    -      -       -      +
    143D  VAL*     4.3     1.8    -      -       -      +
    149D  LYS*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 27 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  GLN*     1.3    74.8    -      -       -      +
     28D  SER*     1.3    63.5    +      -       -      +
    139D  PHE*     4.1     3.3    -      -       -      -
    140D  VAL*     3.3     2.5    -      -       -      +
    141D  VAL*     2.8    43.2    +      -       -      +
    143D  VAL*     4.1     5.7    -      -       +      +
    149D  LYS*     3.3    32.5    -      -       +      +
    152D  THR*     3.7    34.8    -      -       -      -
    153D  CYS*     3.7    19.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 28 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  CYS*     1.3    80.0    -      -       -      +
     29D  SER*     1.3    67.2    +      -       -      +
     30D  THR*     5.4     0.9    +      -       -      -
    138D  SER*     5.4     1.7    -      -       -      -
    139D  PHE*     2.6    28.6    +      -       -      -
    140D  VAL*     4.2     8.9    -      -       -      +
    149D  LYS*     5.3     4.1    -      -       -      +
    153D  CYS*     3.9     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 29 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  SER*     1.3    80.2    +      -       -      +
     30D  THR*     1.3    76.4    +      -       -      +
     31D  LEU*     4.8     0.2    -      -       -      -
    138D  SER*     3.5     2.9    -      -       -      -
    139D  PHE*     3.3    53.7    +      -       -      +
    153D  CYS*     4.3     4.9    -      -       -      -
    157D  GLU*     2.6    32.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 30 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  SER*     5.4     0.7    +      -       -      -
     29D  SER*     1.3    83.6    +      -       -      +
     31D  LEU*     1.3    72.6    +      -       -      +
     32D  VAL*     4.6     5.8    -      -       +      +
    136D  ILE*     3.6    29.2    -      -       +      -
    137D  GLU      3.5     8.3    -      -       -      +
    138D  SER*     3.7    12.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  THR*     1.3    84.8    -      -       -      +
     32D  VAL*     1.3    66.0    +      -       -      +
    135D  ALA      3.9     0.3    -      -       -      +
    136D  ILE*     3.4     4.3    -      -       -      +
    137D  GLU      2.8    38.6    +      -       -      +
    139D  PHE*     4.4     4.7    -      -       +      -
    157D  GLU*     3.4    50.0    -      -       +      +
    160D  ILE*     3.9    24.7    -      -       +      -
    161D  GLN*     3.5    33.2    -      -       +      +
    164D  LEU*     4.0    16.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 32 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  THR*     4.6     5.4    -      -       +      -
     31D  LEU*     1.3    82.5    -      -       -      +
     33D  LYS*     1.3    62.5    +      -       -      +
     34D  HIS*     4.1    15.3    -      -       +      +
    134D  LEU*     3.1    35.7    -      -       +      -
    135D  ALA      3.3     3.4    -      -       -      +
    136D  ILE*     4.0    21.8    -      -       +      -
    161D  GLN*     4.0    11.9    +      -       -      +
    164D  LEU*     4.4     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 33 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  VAL*     1.3    79.2    -      -       -      +
     34D  HIS*     1.3    76.6    +      -       -      +
     35D  ILE*     3.7    11.7    +      -       +      +
    134D  LEU*     3.7     1.7    -      -       -      -
    135D  ALA*     2.8    42.4    +      -       +      +
    161D  GLN*     5.1     3.1    -      -       -      +
    164D  LEU*     3.7    36.8    -      -       +      +
    165D  ASN*     3.5    28.9    +      -       -      +
    168D  ALA*     3.5    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 34 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  VAL*     4.1    16.0    -      -       +      +
     33D  LYS*     1.3    92.9    +      -       -      +
     35D  ILE*     1.3    61.7    +      -       -      +
     36D  LYS*     4.3     1.7    +      -       -      +
    125D  GLU*     2.7    37.1    +      -       -      +
    127D  ILE*     4.0    12.3    -      -       +      +
    133D  THR      3.7     4.3    -      -       -      -
    134D  LEU*     3.9    12.9    -      -       +      +
    172D  GLU*     4.5     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 35 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  LYS*     4.0    13.2    -      -       +      +
     34D  HIS*     1.3    79.2    -      -       -      +
     36D  LYS*     1.3    64.4    +      -       -      +
     37D  ALA*     3.1    14.6    +      -       +      +
     42D  VAL*     4.0    16.6    -      -       +      -
    125D  GLU*     5.2     1.2    -      -       -      +
    132D  GLY*     3.7     3.8    -      -       -      -
    133D  THR*     2.7    46.0    +      -       +      +
    135D  ALA*     4.4     9.2    -      -       +      -
    167D  LEU*     3.8    35.4    -      -       +      -
    168D  ALA*     3.8    18.2    -      -       +      +
    171D  THR*     3.1    22.4    -      -       -      +
    172D  GLU*     3.6    10.3    -      -       -      +
----------------------------------------------------------
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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