Contacts of the strand formed by residues 79 - 84 (chain F) in PDB entry 5M73


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 79 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20F  PRO*     4.0     3.2    -      -       -      +
     45F  THR*     5.3     0.3    -      -       -      -
     46F  ALA*     3.9    10.7    +      -       -      +
     64F  LYS      3.9    18.7    +      -       -      +
     65F  ASN*     5.2    14.0    +      -       -      +
     66F  LYS      4.2     2.9    -      -       -      +
     67F  MET*     3.2    53.8    -      -       +      +
     74F  ARG*     4.6    16.4    +      -       -      +
     75F  ASP      3.3    10.3    +      -       -      -
     76F  VAL*     3.0    50.6    -      -       +      +
     77F  GLN      4.0     4.3    -      -       -      +
     78F  TYR*     1.3    82.3    -      -       -      +
     80F  GLY*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 80 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19F  TYR*     3.9     7.4    -      -       -      -
     20F  PRO*     3.2    20.1    -      -       -      +
     46F  ALA*     3.5    18.6    -      -       -      -
     63F  GLU      3.5     8.7    -      -       -      -
     64F  LYS*     4.1     6.0    +      -       -      -
     66F  LYS      2.8    21.4    +      -       -      +
     67F  MET*     4.6     1.1    -      -       -      +
     68F  TYR      5.2     0.5    +      -       -      -
     78F  TYR      3.9     0.7    +      -       -      +
     79F  ARG*     1.3    75.9    -      -       -      +
     81F  ARG*     1.3    60.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 81 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149E    A      4.2     4.4    +      -       -      -
    197E    G      2.7    33.7    +      -       -      -
    198E    G      2.8    18.9    +      -       -      -
     17F  CYS*     4.1    17.8    -      -       +      -
     18F  ILE      3.7    11.2    -      -       -      +
     19F  TYR*     3.6    35.5    +      -       +      -
     46F  ALA*     4.1     1.8    -      -       -      +
     61F  PHE      4.2     0.2    -      -       -      +
     62F  LEU*     3.5     3.6    -      -       -      +
     63F  GLU*     2.4    78.9    +      -       +      +
     66F  LYS*     3.9    16.6    -      -       +      +
     80F  GLY*     1.3    75.9    -      -       -      +
     82F  VAL*     1.3    74.4    +      -       -      +
     83F  ARG*     4.0    12.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16F  ILE      3.4     0.5    -      -       -      +
     17F  CYS*     3.3     6.1    -      -       -      -
     18F  ILE*     2.9    47.7    +      -       +      +
     46F  ALA*     4.2    20.0    -      -       +      +
     49F  ILE*     3.8    30.1    -      -       +      -
     50F  GLN*     4.7     3.4    -      -       +      +
     53F  CYS*     4.8     3.4    -      -       -      -
     60F  VAL*     3.5    28.5    -      -       +      -
     61F  PHE      3.8     4.3    -      -       -      +
     62F  LEU*     4.5     9.6    -      -       +      -
     81F  ARG*     1.3    80.5    -      -       -      +
     83F  ARG*     1.3    64.8    +      -       -      +
     84F  VAL*     4.1    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 83 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148E    G      3.8    11.0    +      -       -      -
    198E    G      5.4     0.6    +      -       -      -
     14F  ARG*     4.5     6.9    -      -       -      +
     15F  PHE*     3.1    44.1    +      -       +      +
     16F  ILE      2.9     9.6    -      -       -      -
     17F  CYS*     3.7    18.3    -      -       -      -
     60F  VAL*     2.8    26.7    -      -       -      +
     61F  PHE*     2.9    47.9    +      -       +      +
     63F  GLU*     2.8    49.4    +      -       +      +
     81F  ARG*     4.0    13.9    -      -       -      +
     82F  VAL*     1.3    73.9    -      -       -      +
     84F  VAL*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 84 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15F  PHE*     3.6     5.7    -      -       -      +
     16F  ILE*     2.9    56.0    +      -       +      +
     18F  ILE*     4.5    11.7    -      -       +      -
     53F  CYS*     6.0     1.3    -      -       +      -
     59F  ASN*     3.7     1.8    -      -       -      +
     60F  VAL*     3.5    29.8    -      -       +      -
     82F  VAL*     4.1    12.3    -      -       +      +
     83F  ARG*     1.3    78.6    -      -       -      +
     85F  GLN*     1.3    73.7    +      -       -      +
     86F  LEU*     3.6    20.7    +      -       +      -
    104F  VAL*     5.4     9.4    -      -       +      -
----------------------------------------------------------
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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