Contacts of the strand formed by residues 1076 - 1082 (chain D) 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 PHE1076 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    986D  GLU*     3.5    34.8    -      -       +      -
    989D  ALA*     3.3    28.7    -      -       +      +
    990D  ALA*     3.7    18.6    -      -       +      +
   1012D  PHE*     4.6    13.2    -      +       -      -
   1029D  PHE*     4.1    14.4    -      -       +      -
   1030D  ILE      3.4     7.9    -      -       -      -
   1031D  LYS*     3.7    52.9    -      -       +      -
   1032D  LYS*     3.5    13.2    -      -       -      -
   1072D  GLU*     3.4     3.5    -      -       -      -
   1073D  ASN*     2.7    38.3    +      -       -      +
   1075D  GLY*     1.3    81.0    -      -       -      +
   1077D  PHE*     1.3    58.6    +      -       -      +
   1078D  GLN*     3.6    11.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE1077 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1044A  PRO*     5.0     1.3    -      -       +      -
   1029D  PHE*     3.3     5.2    -      -       -      -
   1030D  ILE*     2.7    52.8    +      -       +      +
   1032D  LYS*     3.8    15.9    -      -       +      -
   1035D  VAL*     5.2     0.7    -      -       +      -
   1040D  TRP*     3.7    23.6    -      +       -      -
   1048D  LYS      3.4    22.4    -      -       -      -
   1049D  VAL*     3.6    25.6    -      -       +      -
   1050D  THR*     4.3     9.4    -      -       +      -
   1053D  ILE*     3.6    28.0    -      -       +      -
   1070D  ILE*     4.9     2.7    -      -       +      -
   1071D  PHE      3.6    15.3    -      -       -      +
   1072D  GLU*     3.5    31.9    -      -       +      -
   1076D  PHE*     1.3    75.5    -      -       -      +
   1078D  GLN*     1.3    64.1    +      -       -      +
   1079D  LEU      4.0     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN1078 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    990D  ALA      2.8    28.9    -      -       -      +
    992D  GLU      5.0     1.6    +      -       -      -
    994D  GLU      5.9     0.2    -      -       -      +
    995D  TYR*     3.8    34.6    -      -       +      +
   1027D  VAL*     4.2     5.2    -      -       +      -
   1028D  LYS      3.6     3.8    -      -       -      -
   1029D  PHE*     3.7    14.8    -      -       +      -
   1069D  ASP      4.0     0.2    -      -       -      +
   1070D  ILE*     3.6     2.7    -      -       -      -
   1071D  PHE*     3.0    68.5    +      -       +      +
   1072D  GLU*     3.2     8.7    -      -       -      +
   1073D  ASN*     3.2    21.8    +      -       -      +
   1076D  PHE*     3.6     9.9    -      -       -      +
   1077D  PHE*     1.3    73.1    -      -       -      +
   1079D  LEU*     1.3    61.6    +      -       -      +
   1080D  VAL*     3.5     6.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU1079 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1026D  VAL      3.6     1.7    -      -       -      +
   1027D  VAL*     3.4     0.9    -      -       -      -
   1028D  LYS*     2.8    58.0    +      -       +      +
   1030D  ILE*     4.6     4.9    -      -       +      -
   1052D  GLU*     4.6    11.2    -      -       +      +
   1053D  ILE*     4.0    31.0    -      -       +      +
   1056D  LEU*     4.1    21.5    -      -       +      -
   1067D  VAL*     3.7    38.6    -      -       +      -
   1069D  ASP      4.1     2.9    -      -       -      +
   1070D  ILE*     4.8     6.7    -      -       +      +
   1077D  PHE*     4.0     1.2    -      -       -      +
   1078D  GLN*     1.3    69.3    -      -       -      +
   1080D  VAL*     1.3    62.9    +      -       -      +
   1081D  MET*     3.8    24.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1080 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    995D  TYR*     4.1    20.4    -      -       +      -
    999D  TYR*     3.6    41.7    -      -       +      +
   1025D  VAL*     3.7    26.2    -      -       +      -
   1026D  VAL      3.3     5.2    -      -       -      +
   1027D  VAL*     4.1     7.9    -      -       +      -
   1067D  VAL*     3.6     5.7    -      -       -      +
   1068D  LEU*     2.8    27.0    +      -       +      -
   1069D  ASP*     2.9    28.1    +      -       +      +
   1071D  PHE*     4.6     1.3    -      -       +      -
   1078D  GLN      4.1     7.9    -      -       -      +
   1079D  LEU*     1.3    73.7    -      -       -      +
   1081D  MET*     1.3    63.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET1081 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  ADP      4.0    18.6    -      -       +      +
   1013D  VAL*     5.6     0.2    -      -       +      -
   1025D  VAL*     3.6     0.7    -      -       -      +
   1026D  VAL*     2.7    50.5    +      -       +      +
   1028D  LYS*     3.8    32.8    -      -       +      -
   1056D  LEU*     4.6     2.7    -      -       -      -
   1065D  ILE*     3.8    25.6    -      -       +      -
   1066D  LYS      3.2    13.7    -      -       -      +
   1067D  VAL*     4.7     4.3    -      -       +      -
   1068D  LEU*     3.6    14.4    -      -       -      +
   1079D  LEU*     3.8    31.6    -      -       +      +
   1080D  VAL*     1.3    78.1    -      -       -      +
   1082D  GLU*     1.3    73.3    +      -       -      +
   1083D  LYS      3.6     0.2    +      -       -      -
   1145D  ILE*     5.5     2.7    -      -       -      -
   1146D  ASP      6.0     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU1082 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  ADP      2.9    25.1    +      -       -      -
   1023D  LYS*     6.1     2.2    -      -       -      +
   1024D  GLU      5.7     0.2    -      -       -      -
   1025D  VAL*     5.3     0.2    -      -       -      +
   1026D  VAL*     4.2     0.9    -      -       -      +
   1064D  ILE      4.3     0.3    -      -       -      +
   1065D  ILE*     3.7    14.3    -      -       +      +
   1066D  LYS*     2.7    51.9    +      -       +      +
   1068D  LEU*     3.6    21.2    -      -       +      +
   1081D  MET*     1.3    74.8    -      -       -      +
   1083D  LYS*     1.3    67.1    +      -       -      +
   1084D  HIS*     4.2     9.9    +      -       -      +
   1143D  LYS*     3.5    28.5    +      -       -      -
----------------------------------------------------------
 Back to top of page


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