Contacts of the strand formed by residues 1061 - 1067 (chain A) in PDB entry 3PT6


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 GLY1061 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    937A  TYR*     3.4    16.6    -      -       -      -
    943A  VAL*     3.6     3.5    -      -       -      -
    944A  TYR*     2.8    35.6    +      -       -      +
   1059A  VAL*     3.6     5.2    -      -       -      +
   1060A  GLN*     1.3    80.7    -      -       -      +
   1062A  ARG*     1.3    61.7    +      -       -      -
   1359A  ARG*     6.0     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1062 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    935A  VAL*     4.7    10.2    -      -       +      +
    936A  VAL*     3.1    43.1    +      -       -      +
    937A  TYR*     3.5    23.9    +      -       +      -
    938A  ARG*     5.9     3.7    -      -       -      +
    941A  ASP*     4.0    21.9    +      -       +      -
    942A  SER      3.3    17.9    -      -       -      +
    944A  TYR*     3.9     9.0    -      -       -      -
   1061A  GLY*     1.3    74.7    -      -       -      -
   1063A  CYS*     1.3    73.8    +      -       -      +
   1064A  THR*     5.4     4.2    +      -       -      -
   1084A  ASP*     4.2     9.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS1063 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    941A  ASP*     5.3     0.9    -      -       -      +
    942A  SER*     3.1    48.0    +      -       -      +
    943A  VAL      4.2     1.1    -      -       -      -
    944A  TYR*     3.5    38.8    -      -       +      +
    997A  ILE*     3.9    17.3    -      -       -      -
   1061A  GLY      4.0     0.2    +      -       -      -
   1062A  ARG*     1.3    84.4    -      -       -      +
   1064A  THR*     1.3    64.1    +      -       -      +
   1065A  VAL*     4.2     7.2    -      -       -      -
   1084A  ASP*     3.3    17.7    -      -       +      +
   1086A  PHE*     4.4     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1064 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1062A  ARG*     5.4     4.5    +      -       -      -
   1063A  CYS*     1.3    78.0    +      -       -      +
   1065A  VAL*     1.3    62.4    +      -       -      +
   1066A  GLU*     3.6    22.0    -      -       +      +
   1078A  TYR*     3.2    22.7    -      -       +      +
   1083A  PRO      5.5     1.2    +      -       -      -
   1084A  ASP*     3.0    10.3    +      -       -      +
   1085A  ARG*     4.5     9.0    -      -       +      +
   1086A  PHE*     2.7    33.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1065 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    942A  SER*     3.8    27.5    +      -       -      +
    997A  ILE*     4.2    10.1    -      -       +      -
    999A  ARG*     4.5    15.0    +      -       -      +
   1024A  PHE*     3.4    29.8    -      -       +      -
   1045A  LEU*     4.0    17.0    -      -       +      -
   1063A  CYS*     4.1     4.6    +      -       -      -
   1064A  THR*     1.3    80.5    -      -       -      +
   1066A  GLU*     1.3    72.3    +      -       -      +
   1086A  PHE*     3.5    24.0    -      -       +      +
   1087A  TYR*     4.5     1.3    -      -       -      -
   1088A  PHE*     3.5    19.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1066 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    999A  ARG*     5.6     1.7    +      -       -      -
   1064A  THR*     3.6    16.8    -      -       +      +
   1065A  VAL*     1.3    90.0    +      -       -      +
   1067A  TYR*     1.3    72.1    +      -       -      +
   1068A  GLY      3.3     0.2    +      -       -      -
   1070A  ASP*     4.8     9.9    -      -       +      +
   1071A  LEU*     5.5     7.6    -      -       +      +
   1078A  TYR*     3.5    33.2    -      -       +      +
   1086A  PHE      3.3     6.3    +      -       -      -
   1087A  TYR*     3.2     7.4    -      -       +      +
   1088A  PHE*     3.2    23.6    +      -       -      -
   1108A  SER*     5.2     4.9    +      -       -      -
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Residues in contact with TYR1067 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1066A  GLU*     1.3    74.2    +      -       -      +
   1068A  GLY*     1.3    76.3    +      -       -      +
   1069A  GLU*     3.3    35.0    -      -       +      +
   1070A  ASP*     3.2    44.2    +      -       +      +
   1071A  LEU*     3.5     7.4    +      -       -      +
   1088A  PHE*     3.2    39.2    -      +       +      -
   1089A  LEU*     3.6    12.8    +      -       -      -
   1101A  ASP*     5.0     3.6    -      -       -      +
   1102A  PRO*     3.3    31.2    +      -       +      +
   1106A  ALA      5.1     0.8    +      -       -      +
   1107A  ARG*     4.4    27.8    -      -       +      -
   1114A  LYS*     3.9    19.2    +      -       -      -
----------------------------------------------------------
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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