Contacts of the strand formed by residues 1062 - 1068 (chain D) in PDB entry 5ZX2


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 TYR1062 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1055D  LEU*     5.6     2.2    -      -       +      -
   1057D  ASP*     3.3    31.6    -      -       +      +
   1061D  PHE*     1.3    79.8    -      -       -      +
   1063D  LYS*     1.3    61.0    +      -       -      +
   1064D  ILE*     5.5     3.4    -      -       +      -
   1078D  ASP      3.9     5.4    -      -       -      +
   1079D  LYS*     4.3     0.5    -      -       -      -
   1080D  ILE*     3.0    56.1    +      -       +      +
   1081D  SER      3.3    20.0    -      -       -      -
   1082D  LYS*     3.6    43.7    +      -       +      +
   1084D  GLN      3.8    14.4    +      -       -      -
   1086D  LEU*     3.3    34.6    -      -       +      +
   1112D  MET*     4.2     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1063 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1054D  ARG      3.6     0.9    -      -       -      +
   1055D  LEU*     3.8     1.6    -      -       -      +
   1056D  GLU*     3.0    61.0    +      -       +      +
   1057D  ASP*     4.0     6.5    -      -       -      +
   1061D  PHE*     6.3     0.4    -      -       +      -
   1062D  TYR*     1.3    75.2    -      -       -      +
   1064D  ILE*     1.3    64.1    +      -       -      +
   1065D  THR      4.1     0.4    -      -       -      -
   1077D  TYR      4.2     7.6    -      -       -      +
   1078D  ASP      4.3     9.6    -      -       -      +
   1080D  ILE*     5.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1064 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1053D  VAL*     3.8    23.1    -      -       +      -
   1054D  ARG      3.5     2.7    -      -       -      +
   1055D  LEU*     5.1     9.0    -      -       +      -
   1062D  TYR*     5.3     3.1    -      -       +      -
   1063D  LYS*     1.3    79.6    -      -       -      +
   1065D  THR*     1.3    65.2    +      -       -      +
   1066D  ILE*     4.3     7.2    -      -       +      +
   1075D  VAL      3.9     0.7    -      -       -      +
   1076D  VAL*     3.4     1.3    -      -       -      -
   1077D  TYR*     2.7    43.5    +      -       +      +
   1080D  ILE*     3.8    25.4    -      -       +      -
   1086D  LEU*     6.2     0.2    -      -       +      -
   1099D  LEU*     4.1    18.2    -      -       +      -
   1111D  LEU*     3.6    43.5    -      -       +      -
   1112D  MET*     4.3     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR1065 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1053D  VAL*     3.4     6.9    -      -       -      +
   1054D  ARG*     2.8    59.9    +      -       +      +
   1056D  GLU*     4.1    15.6    +      -       -      -
   1063D  LYS*     4.1     0.7    -      -       -      +
   1064D  ILE*     1.3    74.5    +      -       -      +
   1066D  ILE*     1.3    67.8    +      -       -      +
   1067D  VAL      4.2     0.2    -      -       -      -
   1074D  GLU*     3.8    23.1    -      -       +      +
   1075D  VAL      3.3    11.7    -      -       -      +
   1076D  VAL*     4.2    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1066 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1047D  ALA*     4.0    29.8    -      -       +      -
   1048D  ASP*     4.9     2.9    -      -       -      +
   1049D  VAL*     3.9    20.9    -      -       +      +
   1051D  GLY*     4.7     6.7    -      -       -      +
   1052D  ARG      3.4     6.7    -      -       -      +
   1053D  VAL*     4.3     8.5    -      -       +      -
   1064D  ILE*     4.3     9.9    -      -       +      +
   1065D  THR*     1.3    80.5    -      -       -      +
   1067D  VAL*     1.3    68.9    +      -       -      +
   1068D  PRO*     3.4     7.0    -      -       +      +
   1074D  GLU*     3.2     5.4    -      -       -      -
   1075D  VAL*     2.7    44.2    +      -       +      +
   1105D  VAL*     4.6     8.7    -      -       +      -
   1111D  LEU*     4.2    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1067 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1051D  GLY*     3.2     0.8    -      -       -      -
   1052D  ARG*     2.8    59.0    +      -       -      +
   1054D  ARG*     3.4    48.5    -      -       +      +
   1065D  THR*     5.0     0.2    -      -       +      -
   1066D  ILE*     1.3    72.2    -      -       -      +
   1068D  PRO*     1.3    76.3    -      -       +      +
   1069D  ASP*     4.9     0.3    -      -       -      +
   1070D  ASP      5.4     1.1    -      -       -      +
   1072D  GLY      5.5     1.6    -      -       -      +
   1074D  GLU*     4.2     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO1068 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1049D  VAL*     4.6    15.0    -      -       +      +
   1050D  THR      3.4    11.7    -      -       -      +
   1051D  GLY*     4.0     0.9    -      -       -      -
   1066D  ILE*     3.4    14.1    -      -       +      +
   1067D  VAL*     1.3    98.5    -      -       +      +
   1069D  ASP*     1.3    61.5    +      -       -      +
   1070D  ASP*     2.8    32.4    -      -       -      +
   1072D  GLY*     3.3    34.1    -      -       -      +
   1073D  GLU      3.4    17.3    -      -       -      +
   1074D  GLU*     4.1     0.4    -      -       -      -
   1075D  VAL*     5.8     0.7    -      -       +      -
----------------------------------------------------------
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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