Contacts of the strand formed by residues 96 - 104 (chain K) 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 THR 96 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94K  LEU*     4.0     9.9    -      -       -      +
     95K  GLN*     1.3    80.5    -      -       +      +
     97K  VAL*     1.3    70.9    +      -       -      +
     98K  THR*     4.8     2.6    +      -       -      -
    143K  ARG*     3.6    30.6    +      -       -      +
    144K  VAL      3.4     6.4    +      -       -      -
    145K  ASP*     3.3    21.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 97 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89K  PHE*     3.5    28.0    -      -       +      -
     94K  LEU*     3.5    26.5    -      -       +      -
     96K  THR*     1.3    82.0    +      -       -      +
     98K  THR*     1.3    69.6    +      -       -      +
     99K  LEU*     3.5    23.3    +      -       +      +
    117K  VAL*     4.5    16.2    -      -       +      -
    120K  VAL*     3.7    17.7    -      -       +      -
    142K  VAL      3.6     0.9    -      -       -      +
    143K  ARG*     4.7     0.2    -      -       -      -
    144K  VAL*     2.9    35.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 98 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96K  THR*     4.9     3.6    +      -       -      -
     97K  VAL*     1.3    77.5    -      -       -      +
     99K  LEU*     1.3    65.3    +      -       -      +
    100K  LEU*     3.7    16.5    +      -       +      +
    117K  VAL*     4.6     7.1    -      -       -      +
    141K  GLU*     4.1    28.5    -      -       +      +
    142K  VAL      3.4    12.1    -      -       -      +
    143K  ARG*     4.5     4.3    -      -       -      +
    160K  ASP*     4.2    17.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 99 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85K  LEU*     4.6     6.3    -      -       +      -
     87K  VAL*     4.4    10.8    -      -       +      -
     97K  VAL*     3.5    33.9    -      -       +      +
     98K  THR*     1.3    72.6    -      -       -      +
    100K  LEU*     1.3    62.4    +      -       -      +
    114K  PHE*     3.4    39.2    -      -       +      -
    115K  LEU      5.3     2.0    -      -       -      +
    117K  VAL*     5.0     9.6    -      -       +      -
    120K  VAL*     4.6     9.9    -      -       +      -
    122K  ILE*     3.7    31.0    -      -       +      -
    140K  MET      3.9     0.3    -      -       -      +
    141K  GLU*     3.5     4.7    -      -       -      -
    142K  VAL*     2.9    35.9    +      -       +      +
    144K  VAL*     4.2    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 100 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98K  THR*     3.7    17.7    +      -       +      +
     99K  LEU*     1.3    77.2    -      -       -      +
    101K  LEU*     1.3    60.8    +      -       -      +
    102K  LYS*     5.7     9.9    -      -       -      +
    114K  PHE*     3.3     5.5    -      -       -      -
    115K  LEU*     2.8    61.0    +      -       +      +
    117K  VAL*     5.5     1.7    -      -       +      +
    139K  ASN*     6.2     0.2    -      -       -      +
    140K  MET      3.6     2.9    -      -       -      +
    141K  GLU*     3.8    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 101 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100K  LEU*     1.3    76.0    -      -       -      +
    102K  LYS*     1.3    68.1    +      -       -      +
    103K  ALA*     3.8    18.6    -      -       +      +
    109K  VAL*     3.7    31.4    -      -       +      -
    110K  LYS      4.3     1.6    -      -       -      +
    113K  ASP*     3.8    19.3    -      -       +      +
    114K  PHE*     3.7    43.1    -      -       +      +
    115K  LEU*     5.3     1.1    -      -       -      -
    129K  ILE*     4.2     4.0    -      -       +      -
    138K  LEU*     3.8     5.8    -      -       +      +
    139K  ASN*     3.2     6.5    +      -       -      +
    140K  MET*     2.9    60.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 102 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100K  LEU*     5.7    11.5    -      -       -      +
    101K  LEU*     1.3    75.1    -      -       -      +
    103K  ALA*     1.3    61.7    +      -       -      +
    107K  LYS*     5.6     0.5    +      -       -      -
    113K  ASP      4.9     4.3    +      -       -      +
    115K  LEU*     5.6    12.4    -      -       +      +
    138K  LEU      3.5     2.0    -      -       -      +
    139K  ASN*     3.4    42.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 103 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101K  LEU*     3.8    13.7    -      -       +      +
    102K  LYS*     1.3    76.4    -      -       -      +
    104K  GLU*     1.3    67.0    +      -       -      +
    107K  LYS*     3.8    27.8    -      -       +      +
    109K  VAL*     3.8    19.7    -      -       +      -
    113K  ASP*     5.4     0.9    -      -       +      -
    132K  LEU*     4.1     2.2    -      -       +      -
    137K  ARG*     3.7     1.2    -      -       -      +
    138K  LEU*     2.9    33.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 104 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103K  ALA*     1.3    79.5    -      -       -      +
    105K  GLY*     1.3    70.9    +      -       -      +
    107K  LYS*     3.3    17.2    -      -       -      +
    132K  LEU*     3.8     3.6    -      -       -      -
    136K  GLY      3.4     7.0    -      -       -      -
    137K  ARG*     3.2    42.6    +      -       +      +
----------------------------------------------------------
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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