Contacts of the strand formed by residues 71 - 76 (chain C) in PDB entry 3SPD


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 HIS 71 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  ARG*     3.9     1.7    -      -       -      +
     63C  ASP*     2.9    49.8    +      -       +      +
     66C  PRO*     3.5    25.0    -      -       +      +
     67C  LYS*     2.9    29.2    +      -       +      +
     68C  SER      4.1     2.4    +      -       -      +
     69C  LYS      4.2     0.4    +      -       -      -
     70C  MET*     1.3    77.7    -      -       -      +
     72C  LEU*     1.3    77.3    +      -       -      +
     73C  LEU*     3.9     0.2    -      -       -      +
    115C  GLU*     5.5     0.6    +      -       -      -
    149C  HIS*     2.9    30.4    +      +       +      -
    150C  ILE      3.7     2.7    -      -       -      -
    151C  MET*     3.8    21.4    -      -       +      +
    169C  PHE*     3.7    19.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 72 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  ILE*     4.0    22.2    -      -       +      -
     60C  LEU*     4.0    15.0    -      -       +      -
     61C  VAL      3.5     5.6    -      -       -      +
     62C  ARG*     4.0    18.4    -      -       +      -
     70C  MET*     4.1    22.7    -      -       +      -
     71C  HIS*     1.3    81.7    -      -       -      +
     73C  LEU*     1.3    71.1    +      -       -      +
    112C  ILE*     4.0    26.9    -      -       +      -
    115C  GLU*     3.8    31.2    -      -       +      +
    149C  HIS*     3.5     0.7    -      -       -      -
    150C  ILE*     2.7    41.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  LEU*     4.2    35.0    -      -       +      -
     41C  TYR*     6.1     0.2    -      -       +      -
     59C  VAL      3.4     2.4    -      -       -      +
     60C  LEU*     3.3     6.8    -      -       -      -
     61C  VAL*     2.8    54.3    +      -       +      +
     62C  ARG      5.2     0.2    -      -       -      +
     63C  ASP*     3.6    34.1    -      -       +      +
     71C  HIS*     3.9     1.8    -      -       +      +
     72C  LEU*     1.3    84.8    -      -       -      +
     74C  LEU*     1.3    59.1    +      -       -      +
     75C  MET*     4.5     3.1    -      -       +      -
    147C  HIS*     4.1    17.3    -      -       +      -
    148C  LEU      3.4     2.5    -      -       -      +
    149C  HIS*     3.5    33.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 74 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58C  VAL*     4.0    19.3    -      -       +      -
     59C  VAL      3.5    18.2    -      -       -      +
     60C  LEU*     4.1     3.4    -      -       +      -
     73C  LEU*     1.3    71.9    -      -       -      +
     75C  MET*     1.3    60.6    +      -       -      +
     76C  THR      4.2     0.9    +      -       -      -
    100C  LEU*     3.8    49.1    -      -       +      +
    103C  TYR*     4.2     9.4    -      -       +      -
    104C  VAL*     3.9    16.6    -      -       +      -
    108C  LEU*     3.9    23.1    -      -       +      -
    137C  PHE*     5.5     0.2    -      -       -      -
    146C  LEU      4.2     0.5    -      -       -      +
    147C  HIS*     3.7     0.5    -      -       -      -
    148C  LEU*     2.8    45.1    +      -       +      +
    150C  ILE*     3.7    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 75 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  LEU*     3.6    42.4    -      -       +      +
     41C  TYR*     4.3     6.3    -      -       -      -
     42C  ILE*     3.6    24.6    -      -       +      +
     58C  VAL*     3.2     6.2    -      -       -      -
     59C  VAL*     2.8    43.7    +      -       +      +
     61C  VAL*     4.3    18.8    -      -       +      -
     73C  LEU*     4.5     6.7    -      -       +      +
     74C  LEU*     1.3    76.7    -      -       -      +
     76C  THR*     1.3    63.8    +      -       -      +
     82C  THR*     5.1     0.4    -      -       -      +
    100C  LEU*     5.3     0.2    -      -       -      -
    145C  ASN*     3.6    30.7    -      -       +      +
    146C  LEU      3.6    16.2    -      -       -      +
    147C  HIS*     3.9    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 76 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  ILE*     3.3    17.0    -      -       -      +
     57C  ASP      3.5     9.5    +      -       -      -
     58C  VAL*     4.4     5.7    -      -       -      +
     74C  LEU      4.2     1.2    +      -       -      -
     75C  MET*     1.3    74.5    -      -       -      +
     77C  ARG*     1.3    62.9    +      -       -      +
     78C  ASP*     3.1    20.5    +      -       -      +
     81C  LEU*     4.1     5.9    -      -       +      +
     82C  THR*     3.9    32.8    +      -       -      +
     96C  LEU*     4.3    22.5    -      -       -      +
    100C  LEU*     4.9     5.8    -      -       -      +
    146C  LEU*     3.9    27.3    +      -       +      +
----------------------------------------------------------
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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