Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 1DGD


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 104 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  LEU      4.0     0.2    -      -       -      -
    103A  ASP*     1.3    82.3    -      -       -      +
    105A  ALA*     1.3    59.3    +      -       -      +
    283A  ILE*     3.7     0.9    -      -       -      +
    284A  VAL*     3.2     4.4    -      -       -      +
    285A  THR*     2.8    46.9    +      -       +      +
    287A  ALA*     3.3    35.2    +      -       -      +
    290A  GLU*     2.8    47.5    +      -       +      +
    291A  GLU*     2.8    32.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ALA*     4.2    34.6    +      -       +      +
     94A  LEU*     4.2    23.3    -      -       +      -
    103A  ASP      4.3     0.8    +      -       -      -
    104A  ARG*     1.3    74.8    -      -       -      +
    106A  LEU*     1.3    61.6    +      -       -      +
    107A  LEU*     4.4     6.0    +      -       +      +
    282A  ALA*     5.3     0.2    -      -       +      -
    283A  ILE*     3.1    10.5    -      -       -      +
    284A  VAL*     4.4     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  ALA*     1.3    74.7    -      -       -      +
    107A  LEU*     1.3    61.2    +      -       -      +
    108A  LEU*     3.7    30.9    +      -       +      +
    117A  ALA*     4.0    17.0    -      -       +      -
    121A  MET*     5.7     1.3    -      -       +      -
    282A  ALA*     3.0    26.3    -      -       -      +
    283A  ILE*     3.0    24.6    +      -       +      +
    298A  TYR*     4.2    16.8    -      -       +      +
    300A  PHE*     4.4    13.9    -      -       +      +
    305A  VAL*     3.9    23.3    -      -       +      -
    306A  SER*     5.6     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  VAL*     3.7    46.2    -      -       +      +
     90A  LEU*     4.1    33.2    -      -       +      -
     91A  ALA*     4.6     5.2    -      -       +      +
     94A  LEU*     4.3     8.3    -      -       +      -
    105A  ALA*     4.5     9.0    -      -       +      +
    106A  LEU*     1.3    82.5    -      -       -      +
    108A  LEU*     1.3    59.6    +      -       -      +
    274A  LEU*     5.6     0.2    -      -       +      -
    280A  LEU*     4.6     8.3    -      -       +      -
    281A  ALA      3.6     3.6    -      -       -      +
    282A  ALA*     3.9    15.7    -      -       +      -
    304A  HIS      4.1     0.6    -      -       -      +
    305A  VAL*     3.3     8.9    -      -       -      +
    306A  SER*     3.0    32.8    +      -       -      +
    307A  ASP      5.7     0.2    -      -       -      +
    311A  ALA*     4.3     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     3.7    19.0    +      -       +      +
    107A  LEU*     1.3    78.3    -      -       -      +
    109A  SER*     1.3    67.6    +      -       -      +
    110A  THR      4.6     0.7    -      -       -      +
    113A  GLU*     3.4    20.9    -      -       +      +
    114A  SER*     4.0    12.6    -      -       -      -
    117A  ALA*     3.9    27.1    -      -       +      -
    279A  PRO      4.2     1.2    -      -       -      +
    280A  LEU*     3.5    12.1    -      -       -      +
    281A  ALA*     2.9    31.8    +      -       +      +
    282A  ALA*     5.1     0.4    -      -       -      -
    283A  ILE*     4.7     3.1    -      -       +      -
    300A  PHE*     3.9     9.9    -      -       +      -
    302A  THR*     3.6    32.5    -      -       +      +
    304A  HIS      4.8     4.1    -      -       -      +
    305A  VAL*     4.0    17.3    -      -       +      +
    310A  PRO*     5.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  LEU*     1.3    77.8    +      -       -      +
    110A  THR*     1.3    68.8    +      -       -      +
    113A  GLU*     2.6    22.6    +      -       -      -
    279A  PRO*     3.3    39.0    +      -       -      +
    280A  LEU      3.3     4.7    +      -       -      +
    281A  ALA*     3.9     4.0    -      -       -      -
    302A  THR*     5.1     0.5    +      -       -      -
    304A  HIS*     3.6    33.0    +      -       -      +
----------------------------------------------------------
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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