Contacts of the strand formed by residues 144 - 150 (chain A) in PDB entry 3F9C


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 TYR 144 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  TYR*     4.7     3.4    -      +       -      -
     86A  PRO*     3.8    18.4    -      -       +      -
    138A  LEU*     3.9    17.9    -      -       +      -
    139A  ARG*     2.5    55.6    +      -       -      +
    140A  PRO      3.8     2.1    +      -       -      -
    142A  GLU*     3.6    43.1    -      -       +      -
    143A  LYS*     1.3    71.8    -      -       -      +
    145A  PRO*     1.3    71.1    -      -       -      +
    146A  LEU      3.8     0.3    +      -       -      -
    171A  GLY*     3.1    26.2    -      -       -      +
    173A  ILE*     3.6    34.1    -      -       +      -
    261A  SER*     2.9    10.9    +      -       -      +
    262A  ILE*     3.6     9.7    -      -       -      +
    263A  ASP*     2.8    24.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLU*     5.4     2.7    -      -       -      +
    143A  LYS      4.0     5.8    -      -       -      +
    144A  TYR*     1.3    88.5    -      -       +      +
    146A  LEU*     1.3    60.5    +      -       -      +
    171A  GLY      3.6    13.5    -      -       -      +
    172A  PHE*     3.6    35.7    -      -       +      -
    173A  ILE*     3.2    20.4    +      -       -      -
    263A  ASP*     4.1     5.1    -      -       +      +
    266A  LYS*     3.4    29.8    -      -       +      +
    396A  LEU*     4.7     1.1    -      -       +      -
    398A  LEU*     4.0    22.0    -      -       +      -
    400A  LYS*     6.5     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  PRO*     1.3    76.3    -      -       -      +
    147A  VAL*     1.4    74.7    +      -       -      +
    148A  VAL*     4.8     3.4    -      -       +      +
    172A  PHE*     4.7     0.2    -      -       -      -
    173A  ILE*     3.4    35.2    -      -       +      +
    175A  ALA*     4.5    12.6    -      -       +      +
    233A  LEU*     3.7    29.8    -      -       +      -
    236A  ILE*     3.8    31.4    -      -       +      -
    237A  LEU*     5.2     0.7    -      -       +      -
    262A  ILE*     4.3    24.5    -      -       +      -
    263A  ASP      4.8     0.2    +      -       -      -
    266A  LYS      2.8     9.6    +      -       -      +
    267A  ILE*     3.4    10.6    -      -       +      +
    268A  ALA*     3.0    24.6    +      -       -      +
    396A  LEU*     5.4     0.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  LEU*     1.4    79.8    -      -       -      +
    148A  VAL*     1.3    75.7    +      -       -      +
    149A  PHE*     4.3     2.9    -      -       +      +
    167A  LEU*     4.4     8.7    -      -       +      -
    172A  PHE*     3.8    24.7    -      -       +      -
    173A  ILE      2.9    11.5    +      -       -      +
    174A  VAL*     3.5    20.5    -      -       +      -
    175A  ALA      2.9    26.2    +      -       -      -
    268A  ALA*     3.3    20.0    -      -       +      +
    270A  ILE*     3.8    33.4    -      -       +      -
    392A  LEU*     4.4     4.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  LEU*     4.2     6.5    +      -       +      -
    147A  VAL*     1.3    73.4    -      -       -      +
    149A  PHE*     1.3    63.0    +      -       -      +
    175A  ALA*     3.5    14.6    -      -       +      +
    177A  VAL*     4.0    20.6    -      -       +      -
    229A  CYS*     3.9    38.4    -      -       +      +
    232A  ALA*     5.0     1.3    -      -       +      -
    233A  LEU*     4.4    19.7    -      -       +      +
    236A  ILE*     5.3     0.2    -      -       +      -
    267A  ILE*     5.5     0.4    -      -       +      -
    268A  ALA      2.8    10.3    +      -       -      -
    269A  VAL*     3.4     4.9    -      -       +      +
    270A  ILE      2.8    28.4    +      -       -      +
    289A  PHE*     3.7    27.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  VAL*     4.0     4.2    -      -       +      -
    148A  VAL*     1.3    76.7    -      -       -      +
    150A  SER*     1.3    76.5    +      -       -      +
    151A  HIS*     4.1     2.3    +      -       +      -
    160A  TYR*     3.4    52.0    -      +       +      -
    163A  ILE*     3.8    28.9    -      -       +      -
    164A  GLY      6.0     0.2    -      -       -      -
    174A  VAL*     4.2    14.8    -      -       +      -
    175A  ALA      2.8    14.4    +      -       -      +
    176A  ALA*     3.6    18.5    -      -       +      +
    177A  VAL*     3.0    32.8    +      -       -      +
    270A  ILE*     3.2    36.1    -      -       +      -
    271A  GLY*     4.1     8.7    -      -       -      -
    272A  HIS      4.1     4.5    -      -       -      -
    295A  LEU*     4.1     5.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  PHE*     1.3    77.9    -      -       -      +
    151A  HIS*     1.3    57.7    +      -       -      +
    179A  HIS*     2.7    29.5    +      -       -      -
    225A  ARG*     3.1    15.2    +      -       -      -
    229A  CYS*     4.1     9.0    -      -       -      -
    269A  VAL*     5.5     0.9    -      -       -      -
    270A  ILE      2.9    14.3    +      -       -      -
    271A  GLY*     3.1    19.1    -      -       -      -
    272A  HIS      3.1     8.5    +      -       -      -
    275A  GLY*     3.4    10.3    -      -       -      -
    278A  THR*     3.4    20.3    -      -       -      +
    279A  VAL      5.3     0.9    -      -       -      -
----------------------------------------------------------
 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