Contacts of the strand formed by residues 127 - 133 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  ARG*     4.0     4.9    -      -       -      +
    125B  GLY      3.9     1.0    +      -       -      -
    126B  SER*     1.3    77.1    -      -       -      +
    128B  TRP*     1.3    65.6    +      -       -      -
    143B  THR      3.2    12.3    -      -       -      -
    145B  ASN      3.5    15.0    -      -       -      -
    168B  VAL*     3.0    30.1    +      -       -      +
    169B  TRP*     3.3    14.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  ASN*     3.5    42.1    -      -       +      +
     81B  HIS*     3.7    16.2    -      +       -      -
     83B  LEU*     6.0     0.4    -      -       +      -
     84B  PHE*     3.8    26.9    -      +       +      -
    123B  ARG*     4.4     1.4    +      -       -      +
    127B  GLY*     1.3    80.2    -      -       -      -
    129B  ALA*     1.3    59.3    +      -       -      +
    130B  TRP*     3.4    39.7    -      +       +      +
    142B  SER*     3.1     8.6    -      -       -      -
    143B  THR*     3.0    34.6    +      -       -      +
    145B  ASN      3.2    23.6    +      -       -      -
    146B  GLN*     2.9    22.0    +      -       -      +
    165B  GLY*     4.4     3.8    -      -       -      -
    166B  LEU      3.3    13.0    -      -       -      -
    167B  ASP*     3.5    53.0    +      -       +      -
    168B  VAL*     3.9     5.5    -      -       -      +
    169B  TRP*     4.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  PHE*     3.8    22.3    -      -       +      +
    119B  ALA*     4.4     6.5    -      -       +      +
    120B  ALA*     3.8    36.6    -      -       +      +
    128B  TRP*     1.3    74.4    -      -       -      +
    130B  TRP*     1.3    63.0    -      -       -      +
    141B  VAL      3.6     6.7    -      -       -      +
    142B  SER*     4.3     0.9    -      -       -      -
    165B  GLY*     3.2     4.9    -      -       -      -
    166B  LEU*     2.8    35.0    +      -       +      +
    168B  VAL*     4.7     1.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  ASN*     3.4    36.1    -      -       +      -
     83B  LEU*     4.5    16.2    -      -       +      -
    116B  PHE*     3.8     6.1    -      -       -      -
    128B  TRP*     3.4    37.8    -      +       +      +
    129B  ALA*     1.3    77.3    -      -       -      +
    131B  LEU*     1.3    58.8    +      -       -      +
    132B  VAL*     3.9    17.2    +      -       +      -
    139B  ALA      3.7     0.3    -      -       -      +
    140B  VAL*     3.2    10.0    -      -       -      +
    141B  VAL*     2.7    45.1    +      -       +      +
    142B  SER*     4.1     0.9    -      -       -      -
    143B  THR*     2.9    31.2    +      -       +      +
    147B  ASP      4.0     7.0    -      -       -      -
    148B  SER*     4.8     1.6    -      -       -      -
    149B  PRO*     3.6    24.7    -      -       +      +
    162B  PRO*     3.9    23.1    -      -       +      -
    164B  MET      3.6    18.4    -      -       -      +
    165B  GLY*     3.9    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  LEU*     4.6    13.2    -      -       +      -
    106B  PHE*     4.0    19.1    -      -       +      -
    112B  PHE*     3.9    26.7    -      -       +      -
    116B  PHE*     4.0     2.9    -      -       +      -
    130B  TRP*     1.3    71.0    -      -       -      +
    132B  VAL*     1.3    54.7    +      -       -      +
    138B  LEU*     4.1    15.7    -      -       +      -
    139B  ALA      3.5    11.9    -      -       -      +
    140B  VAL*     4.7     0.9    -      -       +      +
    162B  PRO*     3.7     1.4    -      -       -      +
    163B  ILE*     2.7    58.9    +      -       +      +
    164B  MET*     3.1    40.0    +      -       +      +
    194B  TRP*     4.7     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  TRP*     3.9    12.8    -      -       +      -
    131B  LEU*     1.3    78.6    -      -       -      +
    133B  LEU*     1.3    59.4    +      -       -      +
    134B  LYS*     4.1     7.4    -      -       +      -
    138B  LEU*     3.2    12.8    -      -       -      +
    139B  ALA*     2.8    55.9    +      -       +      +
    141B  VAL*     4.3    11.2    -      -       +      -
    149B  PRO*     3.8    30.7    -      -       +      -
    159B  SER      3.6    21.5    -      -       -      +
    160B  GLY*     4.1     4.3    -      -       -      -
    161B  PHE      3.2    10.3    -      -       -      +
    162B  PRO*     4.2     4.9    -      -       +      -
    163B  ILE*     4.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  ALA*     4.6     3.4    -      -       +      -
    132B  VAL*     1.3    71.8    -      -       -      +
    134B  LYS*     1.3    60.9    +      -       -      +
    135B  GLY      3.5    24.4    +      -       -      +
    137B  LYS      3.6    22.0    -      -       -      +
    138B  LEU*     3.7    18.2    -      -       +      +
    160B  GLY*     3.7     1.0    -      -       -      -
    161B  PHE*     2.8    39.5    +      -       +      +
    163B  ILE*     4.1    13.2    -      -       +      +
    201B  PHE*     4.0    17.9    -      -       +      -
    204B  LYS*     4.3    45.8    -      -       +      +
----------------------------------------------------------
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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