Contacts of the strand formed by residues 769 - 775 (chain B) in PDB entry 5M64


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 PHE 769 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    744B  LEU*     5.1     4.7    -      -       +      -
    746B  THR*     3.4    28.9    -      -       -      +
    748B  GLN*     3.6    17.3    -      -       +      -
    768B  GLY*     1.3    82.4    -      -       -      +
    770B  ASN*     1.3    75.1    +      -       -      +
    771B  ALA*     4.6     3.1    -      -       +      -
    796B  ARG*     5.6     5.8    -      -       -      +
    798B  PHE*     3.4    48.5    -      +       -      -
    799B  GLY*     3.5    28.7    -      -       -      -
    917B  PHE*     5.0     6.5    -      +       -      -
   1032B  TYR*     3.2    16.9    -      -       -      -
   1033B  TYR*     3.2    33.4    +      -       +      +
   1034B  GLN      5.9     0.4    -      -       -      -
   1035B  ARG*     5.2    10.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 770 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    748B  GLN*     4.3     3.4    -      -       -      +
    749B  THR      3.1    27.7    +      -       -      -
    750B  PRO*     3.5     6.4    -      -       -      +
    751B  ILE*     3.3    22.8    +      -       +      +
    769B  PHE*     1.3    83.8    -      -       -      +
    771B  ALA*     1.3    61.6    +      -       -      +
   1030B  VAL*     5.6     4.5    -      -       +      -
   1031B  VAL      4.4     3.1    -      -       -      +
   1032B  TYR*     3.2    33.7    +      -       -      +
      8J  PHE*     4.6     6.9    -      -       -      -
     48J  ARG*     3.7    22.5    +      -       -      +
     49J  MET*     5.9     1.0    -      -       -      +
     52J  THR*     3.3    18.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 771 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    769B  PHE*     4.4     4.9    +      -       +      -
    770B  ASN*     1.3    75.0    -      -       -      +
    772B  VAL*     1.3    64.2    +      -       -      +
    773B  VAL*     3.4     5.4    +      -       -      +
    798B  PHE*     3.9    18.6    -      -       +      -
    946B  ASP*     3.3    25.8    -      -       -      +
    947B  ILE*     4.7     5.8    -      -       +      -
   1030B  VAL*     3.5    16.3    -      -       -      +
   1031B  VAL      3.5    12.5    +      -       -      +
   1033B  TYR*     4.7     8.0    -      -       +      +
      8J  PHE*     4.5     2.5    -      -       +      -
     48J  ARG*     3.4    11.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 772 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    771B  ALA*     1.3    70.6    -      -       -      +
    773B  VAL*     1.3    63.5    +      -       -      +
    943B  ILE*     5.3    13.9    -      -       +      -
    944B  GLN      4.2     9.4    -      -       -      +
    945B  PRO*     4.2     8.4    -      -       +      +
    946B  ASP*     2.9    42.2    +      -       -      +
    947B  ILE*     3.3    11.6    +      -       -      +
    970B  LYS*     6.2     0.4    -      -       -      -
   1028B  VAL*     3.8    22.4    -      -       +      -
   1029B  GLY      3.3    12.6    -      -       -      +
   1030B  VAL*     3.7     9.4    -      -       +      -
      8J  PHE*     4.6     2.2    -      -       +      -
      9J  SER*     5.0     3.1    -      -       -      +
     44J  TYR*     5.4     7.0    -      -       +      -
     45J  CYS*     5.8     1.6    -      -       +      -
     48J  ARG*     3.3    20.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 773 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    771B  ALA      3.8     5.6    -      -       -      +
    772B  VAL*     1.3    68.2    -      -       -      +
    774B  ALA*     1.3    61.7    +      -       -      +
    775B  VAL*     4.0    10.3    +      -       +      +
    947B  ILE*     4.2     4.9    -      -       +      -
    949B  ILE*     4.0    22.2    -      -       +      +
    962B  MET*     4.4     9.6    -      -       +      -
    966B  SER*     4.9     2.0    -      -       -      +
   1028B  VAL*     3.3     4.8    -      -       -      +
   1029B  GLY*     2.4    55.6    +      -       -      +
   1031B  VAL*     3.5    32.3    -      -       +      +
   1033B  TYR*     3.3    41.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 774 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    772B  VAL      3.9     0.2    +      -       -      -
    773B  VAL*     1.3    74.1    -      -       -      +
    775B  VAL*     1.3    60.9    +      -       -      +
    776B  ILE*     3.0    21.0    +      -       +      +
    937B  PRO*     6.4     0.4    -      -       +      -
    945B  PRO*     3.6    33.9    -      -       +      -
    947B  ILE      3.5    12.1    +      -       -      +
    948B  ILE*     3.5     7.6    -      -       +      -
    949B  ILE      3.4    16.8    +      -       -      -
   1026B  ILE*     4.8     6.1    -      -       +      -
   1027B  TYR      3.8     6.7    -      -       -      +
   1028B  VAL*     4.2     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 775 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    827A  THR*     2.9    21.7    +      -       -      -
    828A  CYS      4.7     4.0    -      -       -      +
    773B  VAL*     3.9    10.7    -      -       +      +
    774B  ALA*     1.3    68.0    -      -       -      +
    776B  ILE*     1.3    60.0    +      -       -      +
    949B  ILE*     3.5    21.5    -      -       +      +
    951B  PRO*     3.6    20.9    -      -       +      -
    954B  PHE*     3.6    34.5    -      -       +      -
    962B  MET*     5.1     5.2    -      -       +      -
    963B  PHE*     4.5     8.1    -      -       +      -
    966B  SER*     5.6     0.9    -      -       -      +
   1027B  TYR*     3.0    46.0    +      -       +      +
----------------------------------------------------------
 Back to top of page


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