Contacts of the strand formed by residues 44 - 51 (chain F) in PDB entry 43C9


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 GLY 44 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87E  PHE*     6.4     1.6    -      -       -      -
     38F  ARG      3.7     1.6    -      -       -      +
     39F  GLN*     3.6     8.1    -      -       -      -
     40F  SER      2.7    37.7    +      -       -      -
     41F  PRO*     4.2     3.2    +      -       -      -
     42F  GLY      3.5     2.8    +      -       -      -
     43F  LYS*     1.3    80.0    -      -       -      +
     45F  LEU*     1.3    60.7    +      -       -      -
     46F  GLU*     4.4     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 45 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  PRO*     4.5     6.1    -      -       +      -
     87E  PHE*     3.5    50.5    -      -       +      -
     98E  PHE*     3.3    56.8    +      -       +      +
     99E  GLY      5.2     2.8    +      -       -      +
     37F  VAL*     4.3     9.4    -      -       +      -
     38F  ARG      3.8     1.1    -      -       -      -
     39F  GLN*     3.8    32.5    -      -       +      +
     43F  LYS      4.1     1.2    -      -       -      +
     44F  GLY*     1.3    72.5    -      -       -      -
     46F  GLU*     1.3    63.3    +      -       -      +
     91F  TYR*     5.7     0.7    -      -       +      -
    103F  TRP*     4.3    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 46 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98E  PHE*     4.0     1.9    -      -       -      -
     37F  VAL*     3.2     7.7    -      -       -      +
     38F  ARG*     2.7    83.2    +      -       +      +
     43F  LYS*     3.5    43.2    -      -       -      +
     44F  GLY      4.4     2.0    -      -       -      +
     45F  LEU*     1.3    78.3    -      -       -      +
     47F  TRP*     1.3    63.4    +      -       -      +
     48F  LEU*     3.6     3.6    +      -       +      +
     60F  ASN*     5.8     2.5    -      -       -      +
     63F  LEU*     6.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 47 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89E  GLN*     3.5    21.5    -      -       -      -
     94E  ALA*     4.2     9.9    -      -       +      -
     95E  PRO*     3.4    31.0    -      -       +      -
     96E  ARG*     3.4    36.6    -      -       +      +
     97E  THR*     4.6     2.5    -      -       +      +
     98E  PHE*     3.9     7.7    -      -       +      -
     35F  HIS*     3.1    25.9    +      -       -      -
     36F  TRP      4.3     1.1    -      -       -      -
     37F  VAL*     4.1    12.6    -      -       +      -
     46F  GLU*     1.3    72.1    -      -       -      +
     48F  LEU*     1.3    58.0    +      -       -      +
     49F  GLY*     3.4    38.6    +      -       -      -
     50F  MET*     3.8    18.6    -      -       +      -
     58F  GLU*     3.9    19.7    -      -       +      -
     59F  TYR      3.9     3.8    -      -       -      -
     60F  ASN*     2.7    49.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 48 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36F  TRP*     2.9    26.9    +      -       +      +
     37F  VAL*     4.4     5.6    -      -       -      +
     38F  ARG*     4.1    16.6    -      -       +      +
     46F  GLU*     4.3     7.4    -      -       +      +
     47F  TRP*     1.3    78.0    -      -       -      +
     49F  GLY*     1.3    56.8    +      -       -      +
     59F  TYR*     3.5     0.7    -      -       -      -
     60F  ASN*     2.7    32.5    +      -       -      +
     63F  LEU*     3.3    28.9    -      -       +      -
     67F  LEU*     3.4    17.8    -      -       +      +
     69F  ILE*     5.0     0.2    -      -       -      -
     80F  LEU*     3.7    32.1    -      -       +      -
     82F  MET*     3.9    14.8    -      -       +      -
     90F  TYR*     3.9    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 49 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35F  HIS*     3.5     1.7    -      -       -      -
     36F  TRP*     2.8    27.3    +      -       -      +
     47F  TRP*     3.4    18.6    -      -       -      -
     48F  LEU*     1.3    83.5    -      -       -      +
     50F  MET*     1.3    59.7    +      -       -      +
     58F  GLU      2.9    15.5    -      -       -      -
     69F  ILE*     3.8    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 50 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96E  ARG*     3.3    29.2    -      -       -      +
     33F  ASN*     3.8    17.0    -      -       +      -
     34F  VAL      3.3    14.4    -      -       -      +
     35F  HIS*     3.1    37.7    -      -       +      +
     36F  TRP*     4.5     0.9    -      -       -      +
     47F  TRP*     4.0     9.6    -      -       +      -
     49F  GLY*     1.3    75.7    -      -       -      +
     51F  ILE*     1.3    63.3    +      -       -      +
     52F  TRP*     3.5    45.3    -      -       +      +
     57F  ILE*     3.5     8.7    -      -       -      +
     58F  GLU*     2.8    43.3    +      -       +      -
     69F  ILE*     3.7     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32F  TYR      4.4     0.7    -      -       -      +
     33F  ASN*     3.7     0.6    -      -       -      -
     34F  VAL*     3.0    37.5    +      -       +      +
     50F  MET*     1.3    80.8    -      -       -      +
     52F  TRP*     1.3    72.5    +      -       -      +
     55F  GLY*     4.1    10.3    -      -       -      +
     56F  SER      3.1    11.9    -      -       -      +
     57F  ILE*     4.3    16.4    -      -       +      -
     69F  ILE*     4.1    11.2    -      -       +      -
     70F  SER*     4.2     4.3    -      -       -      -
     71F  LYS*     3.2    50.4    +      -       +      +
     78F  ILE*     3.9    24.7    -      -       +      -
----------------------------------------------------------
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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