Contacts of the strand formed by residues 125 - 133 (chain B) in PDB entry 3K75


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 TRP 125 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  LEU*     3.8     6.8    -      -       +      +
     52B  GLU*     3.2     6.5    -      -       -      -
     53B  GLU      2.9    33.5    +      -       -      +
     55B  ILE*     4.5    13.5    -      -       +      -
     72B  VAL*     3.3    37.3    -      -       +      +
     73B  GLY*     3.2    46.9    -      -       -      +
     74B  SER*     4.1    10.3    -      -       -      -
     83B  ASP      5.4     4.7    -      -       -      -
     85B  GLU*     4.0    29.6    -      -       +      -
     87B  LEU*     5.2     1.5    -      -       +      +
    120B  ALA*     3.0    26.7    +      -       +      -
    121B  ALA*     5.8     0.2    -      -       -      -
    123B  LYS*     3.8    38.0    +      -       +      -
    124B  ARG*     1.3    83.5    -      -       -      +
    126B  ASP*     1.3    63.0    +      -       -      +
    127B  ARG      4.2     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  GLN*     3.5     2.2    -      -       -      +
     49B  LEU*     2.7    45.9    +      -       +      +
     51B  LYS*     4.2     3.1    -      -       -      -
     52B  GLU*     3.9    26.0    -      -       +      +
     73B  GLY      3.1     4.0    +      -       -      -
     74B  SER*     3.1    10.9    +      -       -      -
     75B  SER*     2.7    48.4    +      -       -      -
    125B  TRP*     1.3    75.0    -      -       -      +
    127B  ARG*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  VAL*     3.3    47.1    -      -       -      +
     46B  VAL*     3.9     4.7    -      -       +      -
     47B  LEU      3.3     9.2    -      -       -      -
     48B  GLN*     4.0     7.3    -      -       -      +
     49B  LEU*     4.3     1.0    -      -       -      +
     72B  VAL*     3.4     4.0    -      -       -      +
     73B  GLY      2.8    31.9    +      -       -      +
     74B  SER      3.7    10.1    +      -       -      +
     75B  SER*     4.0    26.7    +      -       -      +
     79B  ALA*     3.3    31.7    -      -       -      +
     84B  TYR*     3.6    16.5    +      -       +      +
    125B  TRP*     4.2     1.7    -      -       -      +
    126B  ASP*     1.3    94.5    -      -       -      +
    128B  VAL*     1.3    71.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     5.0     4.0    -      -       +      -
     45B  VAL      3.6     2.8    -      -       -      +
     46B  VAL*     4.4     2.2    -      -       -      +
     47B  LEU*     2.9    51.9    +      -       +      +
     49B  LEU*     5.1    13.5    -      -       +      -
     55B  ILE*     4.2     8.3    -      -       +      -
     70B  VAL*     4.8     1.1    -      -       +      -
     71B  LEU      3.4     7.4    -      -       -      +
     72B  VAL*     3.8    18.2    -      -       +      -
    125B  TRP*     5.9     0.2    -      -       +      -
    127B  ARG*     1.3    80.8    -      -       -      +
    129B  LYS*     1.3    62.3    +      -       -      +
    130B  ILE*     3.7     4.5    +      -       +      +
    149B  PHE*     3.7    44.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  SER*     3.6    22.2    -      -       -      +
     45B  VAL      3.3    12.1    -      -       -      +
     46B  VAL*     4.4    13.0    -      -       +      +
     69B  GLU      3.9     0.2    -      -       -      +
     70B  VAL*     3.4     3.3    -      -       -      +
     71B  LEU*     2.7    58.1    +      -       +      +
     80B  GLY      5.2     1.1    +      -       -      -
     81B  GLU*     3.8    32.7    +      -       -      +
     84B  TYR*     4.1    34.3    -      -       +      -
    128B  VAL*     1.3    71.3    -      -       -      +
    130B  ILE*     1.3    62.2    +      -       -      +
    131B  VAL*     4.2     7.6    -      -       +      -
    303D  VAL*     4.2    22.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  LEU*     5.0     1.8    -      -       +      -
     33B  TRP*     3.9     4.3    -      -       +      -
     43B  ILE      3.9     0.5    -      -       -      +
     44B  SER*     3.4     4.7    -      -       -      -
     45B  VAL*     3.0    48.4    +      -       +      +
     47B  LEU*     4.6     9.0    -      -       +      -
     60B  ILE*     5.6     0.9    -      -       +      -
     68B  VAL*     4.2    11.9    -      -       +      -
     69B  GLU      3.4     9.0    -      -       -      +
     70B  VAL*     4.4     9.2    -      -       +      -
    128B  VAL*     4.2     5.8    -      -       +      +
    129B  LYS*     1.3    79.2    -      -       -      +
    131B  VAL*     1.3    63.7    +      -       -      +
    132B  CYS*     4.5     3.8    -      -       -      -
    144B  LEU*     3.8    26.5    -      -       +      -
    147B  VAL*     4.1    22.9    -      -       +      -
    149B  PHE*     3.8    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  THR*     4.5    19.5    -      -       +      +
     43B  ILE      3.5    10.3    -      -       -      +
     44B  SER*     4.6     7.6    -      -       -      +
     67B  PHE      3.9     0.7    -      -       -      +
     68B  VAL*     3.4     4.5    -      -       -      +
     69B  GLU*     2.9    49.0    +      -       +      +
     71B  LEU*     3.9    25.4    -      -       +      -
    129B  LYS*     4.5    10.8    -      -       +      -
    130B  ILE*     1.3    73.9    -      -       -      +
    132B  CYS*     1.3    63.0    +      -       -      +
    133B  SER*     4.1     7.6    +      -       -      +
    303D  VAL*     4.1    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  TRP*     3.9    12.1    -      -       -      -
     42B  THR*     3.1     5.1    -      -       -      -
     43B  ILE*     2.8    53.6    +      -       +      -
     65B  SER*     3.4    21.3    -      -       -      +
     67B  PHE      3.6     3.4    -      -       -      -
     68B  VAL*     4.4     7.4    -      -       -      -
    130B  ILE*     4.0     1.3    +      -       -      -
    131B  VAL*     1.3    75.5    -      -       -      +
    133B  SER*     1.3    60.8    +      -       -      +
    142B  PHE*     3.7     4.0    -      -       +      -
    143B  GLY      4.3     2.0    -      -       -      -
    144B  LEU*     3.3    43.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  LYS      3.4     9.2    -      -       -      -
     42B  THR*     4.0    13.5    -      -       -      +
     65B  SER*     3.6     2.4    -      -       -      -
     66B  ALA      2.7    30.8    +      -       -      -
     67B  PHE*     3.0    37.6    +      -       -      +
     90B  THR*     5.5     2.4    -      -       -      +
    131B  VAL*     4.6     8.5    +      -       -      +
    132B  CYS*     1.3    75.3    +      -       -      +
    134B  GLN*     1.3    56.4    +      -       -      +
    135B  PRO*     4.1     4.0    -      -       -      -
    142B  PHE*     4.3     1.8    -      -       -      -
----------------------------------------------------------
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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