Contacts of the strand formed by residues 1048 - 1052 (chain B) in PDB entry 7CN9


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 HIS1048 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    909B  ILE*     3.1    29.3    -      -       -      +
   1032B  CYS*     3.4    18.4    -      -       +      -
   1036B  GLN*     6.0     0.4    -      -       -      -
   1037B  SER*     4.4    27.3    +      -       -      +
   1038B  LYS*     6.0     3.8    -      -       -      +
   1039B  ARG      5.4     2.8    +      -       -      -
   1040B  VAL*     5.7     6.2    -      -       +      +
   1043B  CYS*     2.7    50.7    +      -       +      +
   1044B  GLY*     4.0     7.4    -      -       -      +
   1046B  GLY      2.8    10.6    +      -       -      +
   1047B  TYR*     1.3    70.6    -      -       -      +
   1049B  LEU*     1.3    84.5    +      -       -      +
   1050B  MET*     3.1    35.0    +      -       -      -
   1065B  VAL      4.1     4.7    -      -       -      -
   1066B  THR*     4.5     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1049 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    720B  ILE*     5.2     9.6    -      -       +      -
    902B  MET*     4.2    15.9    -      -       -      -
    905B  ARG*     3.5    17.7    -      -       +      -
    906B  PHE*     3.4    38.6    -      -       +      -
    909B  ILE*     4.1     7.0    -      -       +      -
   1036B  GLN*     3.0    53.7    +      -       -      +
   1047B  TYR      3.9     1.2    +      -       -      -
   1048B  HIS*     1.3    80.0    +      -       -      +
   1050B  MET*     1.3    64.2    +      -       +      +
   1065B  VAL*     3.0    34.3    +      -       +      +
   1067B  TYR*     4.7    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET1050 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    881B  THR*     5.0     3.8    -      -       +      +
    882B  ILE*     4.7    10.5    -      -       +      -
    902B  MET*     3.9    24.2    -      -       +      -
    905B  ARG*     4.0    29.6    -      -       -      +
   1032B  CYS      4.3     4.0    -      -       -      +
   1033B  VAL*     4.8    11.4    -      -       +      +
   1035B  GLY      5.2     4.9    -      -       -      +
   1048B  HIS*     3.1    15.0    +      -       -      -
   1049B  LEU*     1.3    81.8    -      -       -      +
   1051B  SER*     1.3    90.1    +      -       -      +
   1052B  PHE*     3.4    28.7    -      -       +      -
   1064B  HIS*     3.4     2.1    -      -       -      -
   1065B  VAL*     2.9    41.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER1051 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1032B  CYS*     3.4    23.1    +      -       -      -
   1033B  VAL*     3.3    22.8    -      -       -      +
   1048B  HIS*     4.6     2.7    -      -       -      -
   1050B  MET*     1.3    96.1    -      -       -      +
   1052B  PHE*     1.3    69.4    +      -       -      +
   1053B  PRO*     4.2     0.3    -      -       -      +
   1062B  PHE*     3.8     2.9    -      -       -      +
   1063B  LEU      2.1    28.1    +      -       -      -
   1064B  HIS*     2.2    28.4    +      -       -      +
   1065B  VAL*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE1052 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    802B  PHE*     3.4    38.4    -      +       -      -
    805B  ILE*     5.1    17.7    -      -       +      -
    806B  LEU*     6.3     0.2    -      -       +      -
    882B  ILE*     3.9    26.0    -      -       +      -
    898B  PHE*     4.5     6.5    -      +       -      -
    902B  MET*     6.0     0.2    -      -       +      -
    927B  PHE*     4.3    18.4    -      +       -      -
    931B  ILE*     6.5     0.7    -      -       +      -
   1033B  VAL*     5.0     1.6    -      -       -      -
   1050B  MET*     3.4    31.2    -      -       +      -
   1051B  SER*     1.3    80.3    -      -       -      +
   1053B  PRO*     1.3    74.4    -      -       +      +
   1062B  PHE*     3.3     8.6    -      -       -      +
   1063B  LEU*     2.9    43.6    +      -       +      +
   1065B  VAL*     6.0     3.6    -      -       +      -
----------------------------------------------------------
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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