Contacts of the strand formed by residues 108 - 113 (chain C) in PDB entry 3DLX


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 ILE 108 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  GLY*     5.3     0.4    -      -       -      -
     85C  LEU*     3.7    15.3    -      -       +      +
     87C  ALA*     3.9    12.3    -      -       +      -
     99C  LEU*     3.8    31.6    -      -       +      -
    102C  LEU*     3.8    30.4    +      -       +      +
    103C  LEU*     3.8    22.0    -      -       +      +
    106C  LYS*     3.4     8.3    -      -       -      +
    107C  GLN*     1.3    83.2    -      -       -      +
    109C  LYS*     1.3    61.8    +      -       -      +
    110C  ARG      3.5    28.0    -      -       -      +
    111C  MET*     3.9     6.5    -      -       +      -
    125C  GLN*     4.7     5.9    -      -       -      +
    130C  GLU      5.0     3.6    -      -       -      +
    131C  LEU*     3.8    19.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 109 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  GLY*     3.9    26.5    -      -       -      +
     85C  LEU      2.9    10.7    +      -       -      +
     86C  THR*     5.9     1.6    -      -       -      +
    108C  ILE*     1.3    75.0    -      -       -      +
    110C  ARG*     1.3    61.3    +      -       +      +
    130C  GLU      4.8     4.3    -      -       -      +
    131C  LEU*     3.6     6.8    -      -       -      +
    132C  GLU*     3.0    52.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 110 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  LEU      3.3     3.0    +      -       -      -
     86C  THR*     3.2    26.6    -      -       +      +
     87C  ALA      2.7    32.2    +      -       -      -
    108C  ILE*     3.5     7.3    -      -       -      +
    109C  LYS*     1.3    83.4    -      -       +      +
    111C  MET*     1.3    64.9    +      -       -      +
    112C  VAL*     4.4     1.1    -      -       -      -
    132C  GLU*     3.0    44.3    +      -       -      +
    133C  VAL      4.5     0.7    -      -       -      +
    134C  GLU*     3.0    37.0    +      -       -      +
    172C  ILE*     3.9    20.8    -      -       -      +
    182C  ILE*     4.8    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 111 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  ALA*     3.3    17.9    -      -       -      +
     89C  SER*     4.3     2.7    -      -       -      -
     91C  ASN      3.7    13.2    -      -       -      +
     92C  ALA*     3.9    17.7    -      -       +      -
     99C  LEU*     2.9    38.4    -      -       +      -
    103C  LEU*     4.3     4.7    -      -       +      -
    108C  ILE*     3.9    14.1    -      -       +      -
    110C  ARG*     1.3    78.2    -      -       -      +
    112C  VAL*     1.3    61.9    +      -       -      +
    113C  SER*     3.1    29.2    -      -       -      +
    122C  PHE*     4.3     5.2    -      -       +      -
    131C  LEU*     4.1    19.7    -      -       +      -
    132C  GLU      2.9     9.8    +      -       -      +
    133C  VAL*     3.3    12.7    -      -       +      +
    134C  GLU      2.9    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 112 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86C  THR*     4.2    22.7    -      -       +      -
     87C  ALA      2.8     8.9    +      -       -      -
     88C  VAL*     3.6    19.2    -      -       +      +
     89C  SER      3.0    25.6    +      -       -      +
    110C  ARG*     4.4     1.8    -      -       -      -
    111C  MET*     1.3    77.1    -      -       -      +
    113C  SER*     1.3    58.1    +      -       -      +
    134C  GLU*     3.6    33.0    -      -       +      +
    136C  THR*     3.6    21.3    -      -       +      +
    141C  LEU*     3.9    20.4    -      -       +      +
    144C  ARG*     5.3     1.3    -      -       -      +
    203C  ILE*     4.4    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 113 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89C  SER      2.8    21.0    +      -       -      -
     90C  ASN      3.4     7.4    -      -       -      -
     91C  ASN      4.6     0.2    -      -       -      -
    111C  MET*     3.1    29.7    -      -       -      +
    112C  VAL*     1.3    74.8    -      -       -      +
    114C  SER*     1.3    60.7    +      -       -      +
    116C  VAL*     3.5    23.6    -      -       -      -
    133C  VAL*     4.9     1.8    -      -       -      -
    134C  GLU      3.2     9.2    +      -       -      +
    135C  LEU*     3.3     6.8    -      -       -      +
    136C  THR*     2.9    24.1    +      -       -      -
    141C  LEU*     4.2     5.4    -      -       -      -
----------------------------------------------------------
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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