Contacts of the strand formed by residues 1024 - 1031 (chain F) 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 GLU1024 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1015F  THR*     3.9    17.0    -      -       +      +
   1016F  ALA      3.6     5.2    -      -       -      +
   1017F  VAL*     4.6     7.8    -      -       +      +
   1023F  LYS*     1.3    76.6    -      -       -      +
   1025F  VAL*     1.3    64.2    +      -       -      +
   1082F  GLU*     5.5     0.2    -      -       -      -
   1083F  LYS*     3.2    52.1    +      -       +      +
   1085F  GLY      4.9     3.5    -      -       -      +
   1086F  SER*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1025 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    999F  TYR*     3.8    29.6    -      -       +      -
   1015F  THR*     3.4     9.9    -      -       -      +
   1016F  ALA*     2.8    55.7    +      -       +      +
   1017F  VAL*     4.1     0.9    -      -       -      +
   1018F  ASP*     5.0     2.5    -      -       +      +
   1023F  LYS*     3.9     9.2    -      -       +      +
   1024F  GLU*     1.3    78.7    -      -       -      +
   1026F  VAL*     1.3    65.1    +      -       -      +
   1068F  LEU*     3.5    26.0    -      -       +      -
   1080F  VAL*     3.9    10.5    -      -       +      -
   1081F  MET      3.5     9.4    -      -       -      +
   1083F  LYS*     4.1     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1026 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  ADP      3.6    46.9    -      -       +      +
   1005F  LEU*     3.7    15.5    -      -       +      -
   1013F  VAL*     3.8    19.1    -      -       +      -
   1014F  TRP      3.5     4.0    -      -       -      +
   1025F  VAL*     1.3    75.0    -      -       -      +
   1027F  VAL*     1.3    63.8    +      -       -      +
   1079F  LEU      3.6     1.0    -      -       -      +
   1080F  VAL*     3.3     3.6    -      -       -      +
   1081F  MET*     2.7    43.6    +      -       +      +
   1082F  GLU      3.7    10.3    +      -       -      +
   1083F  LYS*     3.6    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1027 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    995F  TYR*     3.4    43.7    -      -       +      +
   1001F  THR*     4.5     0.4    -      -       +      -
   1012F  PHE      3.6     0.7    -      -       -      +
   1013F  VAL*     3.3     5.4    -      -       -      +
   1014F  TRP*     2.8    52.8    +      -       +      +
   1016F  ALA*     4.1     8.9    -      -       +      +
   1025F  VAL      4.2     0.6    -      -       -      -
   1026F  VAL*     1.3    75.8    -      -       -      +
   1028F  LYS*     1.3    68.5    +      -       -      +
   1029F  PHE*     3.7    32.3    -      -       +      -
   1078F  GLN*     4.4     4.9    -      -       +      -
   1079F  LEU      3.3    10.3    -      -       -      +
   1080F  VAL*     4.2     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1028 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  ADP      2.9    38.5    +      -       -      +
     18F   MG      4.1     0.4    -      -       -      -
   1012F  PHE*     3.3     6.3    -      -       +      +
   1013F  VAL*     3.8    15.0    -      -       +      -
   1027F  VAL*     1.3    74.5    -      -       -      +
   1029F  PHE*     1.3    68.8    +      -       -      +
   1030F  ILE*     3.8    12.0    +      -       +      +
   1052F  GLU*     2.9    33.5    +      -       -      +
   1077F  PHE      3.9     0.2    -      -       -      +
   1079F  LEU*     2.8    41.1    +      -       +      +
   1081F  MET*     3.4    24.9    -      -       +      +
   1146F  ASP*     2.7    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1029 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    990F  ALA*     3.2    42.4    -      -       +      -
    991F  CYS*     3.9     9.9    -      -       -      -
    995F  TYR*     4.0     7.9    -      +       -      -
   1001F  THR*     3.8    18.2    -      -       +      -
   1012F  PHE*     2.8    59.5    +      +       +      +
   1014F  TRP*     3.9    22.4    -      +       -      -
   1027F  VAL*     3.7    32.1    -      -       +      -
   1028F  LYS*     1.3    73.6    -      -       -      +
   1030F  ILE*     1.3    62.5    +      -       -      +
   1031F  LYS      4.0     1.4    +      -       -      -
   1076F  PHE*     4.1    10.3    -      -       +      -
   1077F  PHE      3.6     2.9    -      -       -      -
   1078F  GLN*     3.7    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1030 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1028F  LYS*     4.0    12.6    -      -       +      +
   1029F  PHE*     1.3    76.2    -      -       -      +
   1031F  LYS*     1.3    68.1    +      -       -      +
   1032F  LYS      3.6     0.9    +      -       -      -
   1050F  THR*     4.3    18.8    -      -       +      +
   1052F  GLU*     4.5    16.2    -      -       -      +
   1053F  ILE*     3.8    30.3    -      -       +      -
   1076F  PHE*     3.3     4.5    -      -       -      -
   1077F  PHE*     2.8    58.0    +      -       +      +
   1079F  LEU*     4.2    23.8    -      -       +      -
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Residues in contact with LYS1031 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1012F  PHE*     4.9    12.4    -      -       +      -
   1029F  PHE      4.0     1.6    +      -       -      -
   1030F  ILE*     1.3    79.3    -      -       -      +
   1032F  LYS*     1.3    54.7    +      -       -      +
   1033F  GLU*     2.7    29.2    +      -       +      -
   1034F  LYS*     3.4    13.9    +      -       +      +
   1035F  VAL*     4.6     2.4    +      -       -      +
   1075F  GLY      3.9     1.8    -      -       -      +
   1076F  PHE*     3.4    34.2    -      -       +      -
----------------------------------------------------------
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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