Contacts of the strand formed by residues 40 - 46 (chain A) in PDB entry 1D0N


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 GLY 40 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  GLU      3.3     4.0    +      -       -      -
     39A  PRO*     1.3    75.6    -      -       -      +
     41A  LEU*     1.3    60.4    +      -       -      -
     42A  GLN*     5.5     2.5    -      -       -      -
     71A  LEU      3.9     0.9    -      -       -      +
     72A  LYS*     3.6    14.8    -      -       -      +
     73A  THR*     2.9    35.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLY*     1.3    75.2    -      -       -      +
     42A  GLN*     1.3    66.4    +      -       -      +
     43A  ILE*     4.3     3.6    -      -       +      -
     59A  TYR*     3.5    40.3    +      -       +      -
     70A  ILE*     3.7    30.3    -      -       +      -
     71A  LEU      3.8     5.8    -      -       -      +
     72A  LYS*     4.4    17.7    -      -       +      +
    133A  TYR*     4.1    36.8    -      -       +      +
    134A  PHE*     4.2    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LYS*     2.9    33.9    +      -       -      +
     35A  ALA*     3.6     2.0    -      -       -      +
     36A  GLY*     3.0    24.3    +      -       -      -
     37A  LYS      5.6     0.4    -      -       -      -
     38A  GLU      5.7     1.2    -      -       -      +
     40A  GLY      5.5     1.1    -      -       -      -
     41A  LEU*     1.3    79.2    -      -       -      +
     43A  ILE*     1.3    69.5    +      -       -      +
     44A  TRP*     3.8    28.4    -      -       +      -
     59A  TYR*     3.8     5.4    -      -       -      +
     69A  VAL      4.1     0.2    -      -       -      +
     70A  ILE*     3.5     2.1    -      -       -      +
     71A  LEU*     3.0    44.6    +      -       -      +
     73A  THR*     4.9     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  LEU*     4.3     4.3    -      -       +      -
     42A  GLN*     1.3    82.9    -      -       -      +
     44A  TRP*     1.3    72.6    +      -       -      +
     53A  PRO*     3.8     3.8    -      -       -      +
     54A  VAL*     3.0    42.7    +      -       +      +
     59A  TYR*     3.5    47.5    +      -       +      -
     60A  GLY      4.8     0.2    -      -       -      +
     62A  PHE*     4.5     8.7    -      -       +      -
     68A  TYR*     4.1    10.1    -      -       +      -
     69A  VAL      3.6     3.1    -      -       -      -
     70A  ILE*     3.9    27.1    -      -       +      -
    134A  PHE*     3.9    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  GLU*     2.8    54.2    +      -       +      +
     34A  LYS*     5.3     1.6    -      -       +      -
     35A  ALA*     3.8    22.2    -      -       +      -
     42A  GLN*     3.8    35.7    -      -       +      -
     43A  ILE*     1.3    77.7    -      -       -      +
     45A  ARG*     1.3    61.0    +      -       -      +
     51A  LEU*     4.0    29.6    -      -       +      -
     52A  VAL      3.4     7.0    -      -       -      +
     53A  PRO*     3.6    28.0    -      -       +      +
     54A  VAL*     4.2     0.9    -      -       -      +
     68A  TYR*     3.3     9.9    -      -       -      +
     69A  VAL*     2.9    61.3    +      -       +      +
     71A  LEU*     3.9    22.4    -      -       +      -
    108A  LEU*     4.6     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  TRP*     1.3    75.2    -      -       -      +
     46A  VAL*     1.3    71.3    +      -       -      +
     47A  GLU*     2.7    41.3    +      -       -      +
     50A  ASP      3.4     1.0    -      -       -      +
     51A  LEU*     3.8     1.1    -      -       -      -
     52A  VAL      2.9    33.1    +      -       -      +
     54A  VAL*     4.1     4.9    -      -       +      +
     63A  PHE*     3.9    14.4    -      -       -      -
     66A  ASP*     2.7    30.5    +      -       +      +
     67A  ALA      3.8     5.2    -      -       -      +
     68A  TYR*     3.6    29.8    -      -       +      -
    144A  GLY      3.5     1.8    -      -       -      -
    145A  VAL*     3.3    21.7    -      -       -      +
    149A  PHE      2.5    31.9    +      -       -      -
    150A  LYS*     3.7    16.7    -      -       -      +
    151A  HIS*     4.1    14.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ARG*     1.3    77.4    -      -       -      +
     47A  GLU*     1.3    63.3    +      -       -      +
     48A  LYS      4.1     0.2    -      -       -      -
     49A  PHE      4.3     1.3    -      -       -      +
     50A  ASP      3.3    13.9    -      -       -      +
     51A  LEU*     4.2     8.3    -      -       +      -
     66A  ASP*     4.9     1.2    -      -       -      +
     67A  ALA*     2.9    25.7    +      -       +      +
     68A  TYR*     4.6     0.2    -      -       -      -
     69A  VAL*     4.1    19.1    -      -       +      -
     97A  GLU*     3.8    22.2    -      -       -      +
    100A  ALA*     3.5    30.1    -      -       +      -
    101A  ALA*     4.1    25.4    -      -       +      -
    104A  PHE*     4.2     7.6    -      -       +      -
    145A  VAL*     4.1     7.6    -      -       -      +
----------------------------------------------------------
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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