Contacts of the strand formed by residues 138 - 142 (chain C) in PDB entry 5D4D


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 SER 138 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  ILE*     3.6    21.7    -      -       -      +
     22C  GLN*     4.2    10.8    +      -       -      +
    136C  ILE      3.7     1.4    +      -       -      -
    137C  VAL*     1.3    80.9    -      -       -      +
    139C  GLN*     1.3    61.7    +      -       -      +
    140C  ILE      4.2     0.2    -      -       -      -
    333C  ILE*     3.6    24.0    -      -       -      -
    334C  ARG      3.4     9.9    -      -       -      -
    335C  THR*     4.0    10.9    -      -       -      +
    336C  VAL      5.0     0.3    +      -       -      -
    339C  LEU*     4.8     0.7    -      -       -      -
    407C  LYS      4.7     0.5    +      -       -      -
    409C  ARG      3.4    12.8    +      -       -      -
    410C  ILE*     4.5     4.0    -      -       -      -
    411C  SER*     2.9    25.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 139 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137C  VAL      3.8     0.2    +      -       -      -
    138C  SER*     1.3    76.1    -      -       -      +
    140C  ILE*     1.3    69.8    +      -       -      +
    141C  HIS*     5.2     1.1    -      -       -      -
    332C  ARG      3.5     0.5    -      -       -      +
    333C  ILE*     4.4     2.5    -      -       -      -
    334C  ARG*     2.8    74.7    +      -       +      +
    339C  LEU*     3.9     2.3    -      -       +      +
    391C  LEU*     3.6    23.2    -      -       +      +
    411C  SER      3.2    13.7    -      -       -      +
    412C  ALA      4.8     0.2    +      -       -      -
    413C  LEU      2.9    22.3    +      -       -      +
    414C  GLY      3.8     1.2    +      -       -      -
    415C  PRO      3.2    23.4    +      -       -      +
    416C  GLY      3.6     4.0    -      -       -      -
    417C  GLY*     3.6    20.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 140 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  GLN*     1.3    80.2    +      -       -      +
    141C  HIS*     1.3    67.5    +      -       -      +
    328C  LEU*     4.0    20.9    -      -       +      -
    331C  ARG*     3.3    54.2    +      -       +      +
    332C  ARG      3.4    10.3    -      -       -      +
    333C  ILE*     3.8    11.4    -      -       +      -
    410C  ILE*     3.7    21.6    -      -       +      +
    411C  SER      3.0    11.1    +      -       -      +
    412C  ALA*     3.6    28.3    -      -       +      +
    438C  ILE*     4.1    15.7    -      -       +      -
    453C  THR*     5.7     0.7    -      -       -      +
    467C  ILE*     5.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 141 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  GLN*     4.8     3.4    -      -       +      +
    140C  ILE*     1.3    78.6    -      -       -      +
    142C  ARG*     1.3    74.7    +      -       -      +
    144C  PRO*     4.4     5.4    -      -       +      -
    166C  PRO*     3.7    34.1    -      -       +      +
    331C  ARG*     3.1    13.9    -      -       -      +
    332C  ARG*     2.9    79.1    +      -       +      +
    334C  ARG*     3.3    30.5    -      -       +      -
    416C  GLY      4.7    12.2    +      -       -      +
    417C  GLY*     5.7     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 142 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141C  HIS*     1.3    90.6    +      -       -      +
    143C  SER*     1.3    69.3    +      -       -      +
    144C  PRO*     3.4     2.6    -      -       -      +
    147C  TYR*     3.7    32.9    -      -       -      +
    149C  THR*     5.3     2.2    -      -       -      +
    161C  SER*     5.7     2.8    -      -       -      -
    163C  ILE*     3.4    31.9    -      -       +      +
    164C  PRO      5.6     0.2    -      -       -      +
    171C  TRP*     3.7    26.7    -      -       +      -
    325C  ILE*     3.4    53.2    +      -       +      +
    330C  ASN*     3.7     7.0    +      -       -      +
    331C  ARG*     4.6     4.0    -      -       +      +
----------------------------------------------------------
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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