Contacts of the strand formed by residues 127 - 134 (chain D) in PDB entry 3K9S


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 GLY 127 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123D  ARG*     4.0     5.4    -      -       -      +
    125D  GLY      4.0     1.2    +      -       -      -
    126D  SER*     1.3    77.4    -      -       -      +
    128D  TRP*     1.3    61.1    +      -       -      -
    143D  THR      3.2    12.6    -      -       -      -
    145D  ASN      3.5    14.1    -      -       -      -
    168D  VAL*     2.8    38.1    +      -       -      +
    169D  TRP*     3.4    12.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 128 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80D  ASN*     3.5    44.3    -      -       +      +
     81D  HIS*     3.8    16.6    -      +       -      -
     83D  LEU*     6.4     0.4    -      -       +      -
     84D  PHE*     3.7    26.0    -      +       +      -
    123D  ARG*     4.5     1.9    +      -       -      +
    127D  GLY*     1.3    75.2    -      -       -      -
    129D  ALA*     1.3    60.2    +      -       -      +
    130D  TRP*     3.4    38.6    -      +       +      +
    142D  SER*     3.3     6.9    -      -       -      -
    143D  THR*     3.0    35.4    +      -       -      +
    145D  ASN      3.1    21.8    +      -       -      -
    146D  GLN*     2.8    20.8    +      -       -      -
    165D  GLY      4.5     1.8    -      -       -      -
    166D  LEU*     3.3    13.5    -      -       -      -
    167D  ASP*     3.3    53.2    -      -       +      -
    168D  VAL*     3.9     4.9    -      -       -      +
    169D  TRP*     4.1     0.2    -      -       -      +
    208D  PEO      4.1     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 129 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116D  PHE*     3.7    16.4    -      -       +      -
    119D  ALA*     4.2    11.9    -      -       +      +
    120D  ALA*     3.8    39.9    -      -       +      +
    128D  TRP*     1.3    76.0    -      -       -      +
    130D  TRP*     1.3    63.0    +      -       -      +
    141D  VAL      3.7     3.6    -      -       -      -
    142D  SER*     4.4     0.4    -      -       -      +
    165D  GLY*     3.2     4.7    -      -       -      -
    166D  LEU*     2.9    35.3    +      -       +      +
    168D  VAL*     4.8     1.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 130 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80D  ASN*     3.5    36.3    -      -       +      -
     83D  LEU*     4.2    17.3    -      -       +      -
    116D  PHE*     3.8     6.0    -      -       -      -
    128D  TRP*     3.4    37.4    -      +       +      +
    129D  ALA*     1.3    78.9    -      -       -      +
    131D  LEU*     1.3    58.9    +      -       -      +
    132D  VAL*     3.9    16.6    -      -       +      -
    140D  VAL*     3.3    10.7    -      -       -      +
    141D  VAL*     2.8    44.5    +      -       +      +
    142D  SER*     4.2     0.9    -      -       -      -
    143D  THR*     2.9    30.6    +      -       +      -
    147D  ASP      4.2     2.2    -      -       -      -
    148D  SER*     5.0     1.6    -      -       -      -
    149D  PRO*     3.5    30.9    -      -       +      +
    162D  PRO*     4.1    22.4    -      -       +      -
    164D  MET      3.5    19.5    -      -       -      -
    165D  GLY*     3.9    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 131 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98D  LEU*     4.8     4.3    -      -       +      -
    102D  ILE*     4.6    11.7    -      -       +      -
    106D  PHE*     4.2     6.3    -      -       +      -
    112D  PHE*     3.8    35.2    -      -       +      -
    116D  PHE*     4.0     2.1    -      -       +      -
    130D  TRP*     1.3    71.6    -      -       -      +
    132D  VAL*     1.3    54.6    +      -       -      +
    138D  LEU*     4.1    23.8    -      -       +      -
    139D  ALA      3.5    17.3    -      -       -      +
    140D  VAL*     4.7     0.7    -      -       +      +
    162D  PRO*     3.7     1.0    -      -       -      +
    163D  ILE*     2.6    58.6    +      -       +      +
    164D  MET*     3.0    34.3    +      -       +      +
    194D  TRP*     4.6     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 132 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130D  TRP*     3.9     4.9    -      -       +      -
    131D  LEU*     1.3    79.1    -      -       -      +
    133D  LEU*     1.3    61.6    +      -       -      +
    134D  LYS*     4.0     9.0    -      -       +      -
    138D  LEU*     3.3     8.3    -      -       -      +
    139D  ALA*     2.9    55.3    +      -       +      +
    141D  VAL*     3.7    26.7    -      -       +      -
    149D  PRO*     3.7    25.4    -      -       +      -
    159D  SER      3.4    19.1    -      -       -      +
    160D  GLY      4.0     1.6    -      -       -      -
    161D  PHE      3.2     9.4    -      -       -      +
    162D  PRO*     4.0     9.2    -      -       +      -
    163D  ILE*     4.1     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  VAL*     1.3    72.2    -      -       -      +
    134D  LYS*     1.3    60.6    +      -       -      +
    135D  GLY*     3.4    27.7    +      -       -      +
    136D  ASP      4.1     5.4    -      -       -      +
    137D  LYS      3.7    14.8    -      -       -      +
    138D  LEU*     3.5    19.7    -      -       +      +
    160D  GLY*     3.8     0.5    -      -       -      -
    161D  PHE*     2.6    40.5    +      -       +      +
    163D  ILE*     3.9    14.4    -      -       +      -
    201D  PHE*     3.7    28.7    -      -       +      +
    204D  LYS*     4.0    33.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  VAL*     4.0    17.0    -      -       +      -
    133D  LEU*     1.3    71.6    -      -       -      +
    135D  GLY*     1.3    66.1    +      -       -      +
    136D  ASP*     2.8     5.0    +      -       -      +
    137D  LYS*     2.8    30.5    +      -       +      +
    139D  ALA*     4.3    13.8    -      -       +      +
    141D  VAL*     4.3    14.5    -      -       -      +
    153D  GLU*     4.0     9.1    +      -       -      -
    159D  SER*     3.3    36.8    +      -       -      +
    160D  GLY*     4.1     9.0    -      -       -      -
----------------------------------------------------------
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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