Contacts of the strand formed by residues 137 - 147 (chain K) in PDB entry 5D4C


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 ARG 137 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59K  GLU*     4.7    17.8    +      -       -      -
     60K  ASP*     4.8    10.7    +      -       -      -
     68K  ILE*     3.9    21.0    -      -       -      +
     69K  PRO      4.1     4.4    +      -       -      -
     71K  VAL*     4.5     0.9    -      -       -      +
    103K  ALA      3.7     4.7    -      -       -      +
    104K  GLU*     3.6    31.8    +      -       +      +
    132K  LEU*     3.6     2.9    -      -       -      +
    135K  GLY*     3.4    13.6    +      -       -      +
    136K  GLY*     1.3    75.3    -      -       -      -
    138K  LEU*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58K  ILE*     3.8    17.9    -      -       +      -
     68K  ILE*     4.0    15.5    -      -       +      -
     71K  VAL*     5.2     2.7    -      -       +      -
     78K  ILE*     5.0     4.3    -      -       +      -
    101K  LEU*     3.5    15.5    -      -       +      +
    102K  LYS*     3.5     2.0    -      -       -      +
    103K  ALA*     2.9    41.6    +      -       +      +
    109K  VAL*     4.8     3.4    -      -       +      -
    129K  ILE*     4.9     2.9    -      -       +      -
    130K  ALA*     4.1    15.9    -      -       +      -
    132K  LEU*     3.5    30.5    -      -       +      +
    137K  ARG*     1.3    75.6    -      -       -      +
    139K  ASN*     1.3    61.2    +      -       -      +
    140K  MET*     3.6    46.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 139 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57K  TYR*     3.8     5.6    -      -       -      +
     58K  ILE*     3.3     6.7    -      -       -      +
     59K  GLU*     3.0    58.3    +      -       +      +
    100K  LEU*     6.0     1.0    -      -       -      +
    101K  LEU      3.3     6.3    +      -       -      +
    102K  LYS*     3.2    40.1    -      -       +      +
    138K  LEU*     1.3    76.9    -      -       -      +
    140K  MET*     1.3    68.9    +      -       -      +
    141K  GLU*     5.2     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 140 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56K  VAL*     5.0     0.4    -      -       +      -
     57K  TYR      3.1     6.7    -      -       -      +
     58K  ILE*     3.8    19.5    -      -       +      -
     78K  ILE*     4.2     7.9    -      -       -      -
     82K  LEU*     4.2    21.8    -      -       +      -
     99K  LEU      3.6     0.7    -      -       -      +
    100K  LEU*     3.5     4.3    -      -       -      -
    101K  LEU*     2.9    67.4    +      -       +      +
    114K  PHE*     4.1    12.7    -      -       +      -
    129K  ILE*     4.1    11.7    -      -       +      -
    138K  LEU*     3.6    37.0    -      -       +      -
    139K  ASN*     1.3    81.7    +      -       -      +
    141K  GLU*     1.3    64.9    +      -       -      +
    142K  VAL*     4.0     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 141 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55K  SER      4.6     0.2    -      -       -      -
     56K  VAL*     3.7     1.2    -      -       -      -
     57K  TYR*     2.9    48.7    +      -       +      +
     98K  THR*     4.0    18.4    -      -       +      +
     99K  LEU      3.4     5.2    -      -       -      -
    100K  LEU*     3.8    20.2    -      -       +      +
    139K  ASN*     5.2     7.8    +      -       -      +
    140K  MET*     1.3    76.3    -      -       -      +
    142K  VAL*     1.3    62.3    +      -       -      +
    143K  ARG      3.9     1.4    +      -       -      -
    160K  ASP*     5.6     4.0    -      -       -      +
    161K  ARG*     3.6    35.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53K  VAL*     3.9    12.6    -      -       +      -
     55K  SER      3.3     7.9    -      -       -      +
     56K  VAL*     3.7    14.6    -      -       +      -
     82K  LEU*     3.7    29.8    -      -       +      -
     85K  LEU*     4.9     4.3    -      -       +      -
     97K  VAL      3.5     1.4    -      -       -      +
     98K  THR*     3.4     3.2    -      -       -      -
     99K  LEU*     2.9    50.6    +      -       +      +
    114K  PHE*     3.5    32.5    -      -       +      -
    140K  MET*     4.5    11.4    -      -       +      -
    141K  GLU*     1.3    75.3    -      -       -      +
    143K  ARG*     1.3    59.9    +      -       -      +
    144K  VAL*     3.6     6.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 143 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53K  VAL*     3.5     1.6    -      -       -      +
     54K  THR*     2.7    33.1    +      -       -      +
     55K  SER*     2.9    25.3    +      -       -      -
     96K  THR*     3.9    19.2    +      -       -      +
     97K  VAL      3.7     3.8    -      -       -      +
     98K  THR*     4.5     6.3    -      -       +      +
    141K  GLU      3.9     2.0    +      -       -      -
    142K  VAL*     1.3    70.3    -      -       -      +
    144K  VAL*     1.3    54.9    +      -       -      +
    145K  ASP*     2.7    36.6    +      -       -      +
    158K  ILE*     3.6    32.0    -      -       -      +
    159K  LYS      5.4     1.6    +      -       -      -
    160K  ASP*     3.0    39.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51K  THR*     4.2     8.3    -      -       -      -
     52K  ALA      3.5    15.7    -      -       -      +
     53K  VAL*     3.8    26.0    -      -       +      -
     85K  LEU*     4.7     0.9    -      -       +      -
     87K  VAL*     4.0    26.0    -      -       +      -
     89K  PHE*     3.8    19.6    -      -       +      -
     96K  THR*     3.3     4.5    +      -       -      -
     97K  VAL      2.9    36.9    +      -       -      +
     99K  LEU*     3.9    22.0    -      -       +      -
    142K  VAL*     4.2     7.0    -      -       +      +
    143K  ARG*     1.3    76.1    -      -       -      +
    145K  ASP*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 145 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51K  THR*     3.3     9.8    -      -       -      -
     52K  ALA      3.1    30.2    +      -       -      +
     54K  THR*     2.8    30.0    +      -       +      +
     89K  PHE*     4.5     0.9    -      -       -      -
     95K  GLN*     3.4     7.3    -      -       -      +
     96K  THR*     3.3    17.4    -      -       -      +
    143K  ARG*     2.7    45.5    +      -       -      +
    144K  VAL*     1.3    74.2    -      -       -      +
    146K  ARG*     1.3    70.1    +      -       -      +
    158K  ILE*     4.9     4.3    -      -       +      -
    171K  PHE*     3.7     4.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 146 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49K  PRO*     5.9     4.4    -      -       -      +
     50K  GLY*     3.5    11.2    +      -       -      +
     51K  THR*     4.0     9.0    -      -       +      +
     89K  PHE*     3.5    34.3    +      -       +      +
     91K  ASN      3.1    23.6    +      -       -      -
     92K  PRO*     3.7    17.3    +      -       -      +
     94K  LEU      2.9    28.4    +      -       -      +
     95K  GLN*     2.9    42.5    +      -       -      +
    145K  ASP*     1.3    81.1    -      -       -      +
    147K  GLY*     1.3    59.4    +      -       -      +
    171K  PHE*     4.0     2.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 147 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49K  PRO*     3.4     6.2    -      -       -      +
     50K  GLY      3.0    32.5    +      -       -      +
    146K  ARG*     1.3    75.9    -      -       -      +
    148K  VAL*     1.3    61.5    +      -       -      -
    171K  PHE*     3.3    24.7    -      -       -      +
----------------------------------------------------------
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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