Contacts of the strand formed by residues 74 - 79 (chain b) in PDB entry 3J7Y


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 ARG 74 (chain b).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2284A    C      2.6    31.9    +      -       -      -
   2285A    U      5.4     1.0    +      -       -      -
     30b  SER      3.4     1.6    -      -       -      +
     32b  SER*     2.6    49.2    +      -       -      +
     70b  CYS*     5.5     2.2    -      -       -      -
     72b  VAL*     3.5    36.6    +      -       -      +
     73b  PRO*     1.3    75.6    -      -       -      +
     75b  VAL*     1.3    62.0    +      -       -      +
     76b  VAL*     4.1     5.2    -      -       +      -
     86b  GLU*     4.6    24.7    -      -       +      -
     87b  GLU      3.4    14.1    -      -       -      +
     88b  SER*     4.2    12.6    -      -       -      -
     89b  ILE*     3.7     6.2    -      -       -      +
     43c  LYS*     3.7    17.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 75 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29b  LEU*     4.2    18.2    -      -       +      -
     30b  SER      3.2     2.9    -      -       -      +
     31b  PHE*     3.4    42.0    -      -       +      -
     74b  ARG*     1.3    72.5    -      -       -      +
     76b  VAL*     1.3    62.7    +      -       -      +
     77b  ALA      3.6     2.4    +      -       -      -
     85b  ARG      3.9     1.2    -      -       -      +
     87b  GLU*     2.8    40.3    +      -       +      +
     89b  ILE*     3.7    20.8    -      -       +      +
     97b  ILE*     6.6     0.2    -      -       +      -
    100b  LEU*     5.1     8.7    -      -       +      -
    101b  VAL*     5.0     4.9    -      -       +      -
    104b  LEU*     4.0    19.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 76 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28b  ARG      3.2     6.4    -      -       -      +
     29b  LEU*     3.3     1.5    -      -       -      -
     30b  SER*     2.8    57.2    +      -       -      +
     32b  SER*     5.9     1.3    -      -       -      +
     74b  ARG*     5.0     5.8    -      -       +      -
     75b  VAL*     1.3    74.3    -      -       -      +
     77b  ALA*     1.3    57.8    +      -       -      +
     78b  GLU*     3.8    13.8    +      -       +      +
     84b  VAL*     3.3    32.3    -      -       +      -
     85b  ARG      4.0     1.8    -      -       -      -
     86b  GLU*     3.2    34.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 77 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26b  LEU*     4.1     8.3    -      -       +      -
     28b  ARG      3.3     6.1    -      -       -      -
     29b  LEU*     3.7    17.0    -      -       +      -
     75b  VAL      3.6     1.2    +      -       -      -
     76b  VAL*     1.3    71.1    -      -       -      +
     78b  GLU*     1.3    61.7    +      -       -      +
     79b  TYR*     4.1     6.8    +      -       +      +
     83b  ALA      4.1     0.2    -      -       -      +
     84b  VAL*     3.5     2.8    -      -       -      -
     85b  ARG*     2.8    50.2    +      -       +      +
    104b  LEU*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 78 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26b  LEU*     3.3     3.1    -      -       -      +
     27b  GLN*     2.8    32.3    +      -       -      +
     28b  ARG*     2.8    55.3    +      -       +      +
     30b  SER*     4.6     4.1    +      -       -      +
     76b  VAL*     4.3    15.1    -      -       +      +
     77b  ALA*     1.3    75.5    -      -       -      +
     79b  TYR*     1.3    56.3    +      -       -      +
     82b  GLY      6.0     0.2    -      -       -      +
     83b  ALA      3.9     3.8    -      -       -      -
     84b  VAL*     4.0    27.7    -      -       +      +
     60c  ARG*     2.8    40.3    +      -       -      -
     65c  ASN*     4.8     0.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 79 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25b  GLN*     3.3    16.6    -      -       +      +
     26b  LEU*     3.7    20.0    -      -       +      -
     27b  GLN*     3.0    16.3    -      -       -      +
     77b  ALA*     4.2    10.3    -      -       +      -
     78b  GLU*     1.3    74.9    -      -       -      +
     80b  LEU*     1.3    64.7    +      -       -      +
     81b  ASN      3.3     2.2    -      -       -      +
     82b  GLY*     3.3    14.1    +      -       -      -
     83b  ALA      3.0    23.0    +      -       -      +
     85b  ARG*     3.8    34.8    -      -       +      -
    104b  LEU*     2.7    44.8    +      -       -      +
    107b  GLN*     3.2    25.1    -      -       +      +
    108b  SER      3.8     8.1    -      -       -      -
    109b  GLY*     3.6    32.5    -      -       -      -
    177c  GLN*     4.9     0.2    +      -       -      -
----------------------------------------------------------
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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