Contacts of the strand formed by residues 103 - 107 (chain D) in PDB entry 1XDM


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 VAL 103 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  ILE*     4.1     9.6    -      -       +      -
     21D  SER*     4.1    23.8    -      -       -      +
     22D  ILE*     4.3     6.3    -      -       +      -
     74D  GLY      3.2    20.1    +      -       -      +
     75D  GLY*     2.9     5.1    -      -       -      -
     76D  VAL      2.7    32.2    +      -       -      -
    101D  GLY      4.7     5.6    -      -       -      +
    102D  ILE*     1.3    74.0    -      -       -      +
    104D  VAL*     1.3    56.2    +      -       -      +
    143D  ASP*     3.2    42.4    -      -       +      +
    144D  PHE*     4.3     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 104 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76D  VAL      3.4     5.2    -      -       -      +
     78D  LEU*     3.6    29.2    -      -       +      -
     83D  LEU*     4.7    11.9    -      -       +      -
     94D  ARG*     3.7    15.5    -      -       +      +
     97D  LEU*     3.7    34.1    -      -       +      -
     98D  LYS*     4.7     4.3    -      -       +      +
    102D  ILE      4.0     2.2    -      -       -      +
    103D  VAL*     1.3    79.4    -      -       -      +
    105D  GLY*     1.3    66.1    +      -       -      +
    141D  GLY      4.0    15.3    -      -       -      +
    142D  VAL*     3.3     4.9    -      -       +      +
    143D  ASP*     3.0    28.9    +      -       -      -
    144D  PHE*     3.4     7.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 105 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76D  VAL      2.4    22.1    +      -       -      +
     77D  ILE*     3.5     6.7    -      -       -      -
     78D  LEU*     2.8    22.5    +      -       -      +
    104D  VAL*     1.3    76.4    -      -       -      +
    106D  ILE*     1.3    61.5    +      -       -      +
    142D  VAL*     3.8     2.9    -      -       -      -
    144D  PHE*     3.0    32.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 106 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77D  ILE*     3.5     7.5    -      -       -      +
     78D  LEU*     2.9    33.4    -      -       +      +
     79D  PHE      3.7    17.3    -      -       -      +
     80D  HIS      3.9     2.5    -      -       -      +
     83D  LEU*     4.1    15.7    -      -       +      -
    105D  GLY*     1.3    76.4    -      -       -      +
    107D  LYS*     1.3    63.2    +      -       -      +
    108D  LEU*     2.9    28.6    +      -       +      +
    137D  TYR*     3.1    48.0    -      -       +      +
    142D  VAL*     3.8    16.8    -      -       +      -
    144D  PHE      3.0    13.2    +      -       -      +
    145D  GLY*     4.8     1.3    -      -       -      -
    146D  LYS      3.4    13.5    +      -       -      -
    182D  LEU*     5.3     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 107 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  ASP*     3.4    39.1    +      -       +      +
     34D  GLU*     5.1     0.8    -      -       -      +
     35D  SER*     4.5    13.9    +      -       -      +
     77D  ILE*     3.8     3.0    -      -       -      +
     78D  LEU      3.0    18.4    +      -       -      +
     79D  PHE*     3.7    32.6    -      -       +      -
     80D  HIS*     5.0     2.6    +      -       -      +
    106D  ILE*     1.3    73.3    -      -       -      +
    108D  LEU*     1.3    59.0    +      -       -      +
    109D  ASP*     3.2    31.8    +      -       +      +
    133D  ARG*     4.5     6.1    +      -       -      -
    137D  TYR*     4.9     0.9    +      -       -      -
    146D  LYS*     4.2    16.2    -      -       +      +
    148D  ARG*     3.6    26.0    -      -       -      +
----------------------------------------------------------
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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