Contacts of the strand formed by residues 1040 - 1043 (chain A) in PDB entry 3DLS


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 TRP1040 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1032A  LYS*     3.6    49.1    -      -       +      -
   1035A  VAL*     3.8    14.5    -      -       +      +
   1036A  LEU      3.2    24.3    +      -       -      -
   1037A  GLU*     3.7    20.7    +      -       -      +
   1038A  ASP      3.6     2.6    -      -       -      +
   1039A  CYS*     1.3    79.0    +      -       -      +
   1041A  ILE*     1.3    70.0    +      -       -      +
   1048A  LYS*     3.2    40.6    -      -       +      +
   1049A  VAL      3.4    16.8    -      -       -      -
   1050A  THR*     4.5     2.7    -      -       +      -
   1072A  GLU*     5.9     0.2    -      -       -      -
   1077A  PHE*     3.7    28.0    -      +       -      -
   1155E  ARG*     3.4    42.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1041 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1038A  ASP      5.9     1.3    -      -       -      +
   1039A  CYS      4.1     0.9    -      -       -      +
   1040A  TRP*     1.3    84.3    -      -       -      +
   1042A  GLU*     1.3    63.3    +      -       -      +
   1043A  ASP*     3.4    12.4    +      -       +      +
   1047A  GLY      3.2     2.8    -      -       -      +
   1048A  LYS*     3.6     5.2    +      -       -      -
   1049A  VAL*     2.7    39.1    +      -       +      +
   1050A  THR      4.5     0.7    -      -       -      -
   1051A  LEU*     3.7    43.5    -      -       +      -
   1054A  ALA*     4.1    21.5    -      -       +      -
   1058A  ARG*     4.5     3.4    -      -       -      +
   1044D  PRO      4.9     0.7    -      -       -      +
   1045D  LYS*     3.4    44.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU1042 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1041A  ILE*     1.3    73.2    -      -       -      +
   1043A  ASP*     1.3    62.5    +      -       -      +
   1044A  PRO*     3.8     0.5    -      -       -      +
   1047A  GLY*     3.8     3.8    -      -       -      -
   1048A  LYS*     3.3    40.4    +      -       +      +
   1045D  LYS*     3.6    12.6    +      -       -      +
   1046D  LEU*     3.7    20.2    -      -       +      +
   1068D  LEU      5.8     0.2    -      -       -      +
   1069D  ASP*     4.1    17.8    -      -       -      +
   1070D  ILE*     5.3     5.6    -      -       +      +
   1071D  PHE*     5.5     3.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP1043 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1041A  ILE*     3.4     9.2    +      -       +      +
   1042A  GLU*     1.3    72.9    -      -       -      +
   1044A  PRO*     1.3    72.7    -      -       -      +
   1045A  LYS*     3.6    10.4    +      -       -      +
   1046A  LEU*     3.2    33.9    +      -       -      +
   1047A  GLY*     2.8    42.4    +      -       -      +
   1049A  VAL*     4.2    16.6    -      -       +      -
   1054A  ALA*     4.7     4.9    -      -       +      -
   1057A  SER*     5.6     1.1    -      -       -      -
   1058A  ARG*     2.7    38.0    +      -       -      +
   1046D  LEU      4.2     0.9    -      -       -      +
   1070D  ILE      4.7     1.0    -      -       -      +
   1071D  PHE*     5.0     1.4    -      -       -      -
----------------------------------------------------------
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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