Contacts of the strand formed by residues 145 - 151 (chain A) in PDB entry 3SUP


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 145 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  HIS      3.7     1.7    -      -       -      +
    139A  TYR*     3.3     8.1    -      -       -      -
    140A  ASP      3.0    28.5    +      -       -      -
    143A  ASP*     3.3    26.6    +      -       +      +
    144A  ASP*     1.3    97.9    +      -       -      +
    146A  PHE*     1.3    59.7    +      -       -      +
    147A  TYR*     3.7    23.2    +      -       +      +
    184A  ASP      4.6     6.8    +      -       -      -
    185A  LYS*     3.3    37.2    -      -       -      +
    187A  ILE*     4.0    24.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  THR*     4.2    15.9    -      -       +      -
    138A  HIS      3.9     4.3    -      -       -      -
    139A  TYR*     3.8    24.0    -      +       +      -
    145A  ARG*     1.3    71.2    -      -       -      +
    147A  TYR*     1.3    62.0    +      -       -      +
    148A  VAL*     3.6     5.0    +      -       +      +
    182A  ILE*     3.7    32.8    -      -       +      -
    185A  LYS*     2.8    29.5    +      -       +      +
    186A  ILE*     3.5    14.4    -      -       +      -
    187A  ILE      2.9    27.6    +      -       -      +
    325A  ILE*     4.5     8.3    -      -       +      -
    328A  VAL*     4.0    18.4    -      -       +      -
    329A  TYR*     3.8    28.3    -      +       +      -
    332A  LEU*     3.7    31.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ILE      3.5     2.4    -      -       -      +
    137A  THR*     3.3     2.3    -      -       -      -
    138A  HIS      2.8    47.8    +      -       -      +
    140A  ASP*     4.0    11.4    -      -       +      -
    143A  ASP*     2.5    35.1    +      -       -      +
    145A  ARG*     3.8    23.4    -      -       +      +
    146A  PHE*     1.3    71.2    -      -       -      +
    148A  VAL*     1.3    59.5    +      -       -      +
    149A  PHE*     3.7    21.7    -      -       +      -
    187A  ILE*     3.5    40.5    -      -       +      +
    189A  MET*     3.9     9.4    -      -       +      -
    204A  PHE*     3.5    35.7    -      +       +      -
    208A  LYS*     3.6     8.8    +      -       -      -
----------------------------------------------------------
 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
----------------------------------------------------------
    135A  ALA*     6.1     0.2    -      -       +      -
    136A  ILE      3.3     3.6    -      -       -      +
    137A  THR*     3.9    15.9    -      -       +      +
    146A  PHE*     3.8     7.0    -      -       +      +
    147A  TYR*     1.3    74.8    -      -       -      +
    149A  PHE*     1.3    67.1    +      -       -      +
    150A  ASP*     4.8     0.9    -      -       +      -
    186A  ILE*     3.7    28.9    -      -       +      -
    187A  ILE      2.9     8.7    +      -       -      +
    188A  TYR*     4.0    16.6    -      -       +      -
    189A  MET*     2.9    35.0    +      -       -      +
    321A  ILE*     3.9    30.1    -      -       +      -
    324A  ASN*     5.2     1.3    -      -       -      +
    325A  ILE*     3.8    19.3    -      -       +      -
----------------------------------------------------------
 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
----------------------------------------------------------
    135A  ALA*     3.1     7.4    -      -       -      +
    136A  ILE*     2.6    54.6    +      -       +      +
    138A  HIS*     4.6     1.3    -      -       +      -
    147A  TYR*     3.7    17.9    -      -       +      -
    148A  VAL*     1.3    76.0    -      -       -      +
    150A  ASP*     1.3    58.5    +      -       -      +
    189A  MET*     3.5    32.8    -      -       +      -
    191A  PHE*     3.7    18.6    -      +       +      -
    197A  LEU*     4.1    22.0    -      -       +      +
    200A  GLU*     4.3     9.4    -      -       +      -
    201A  TYR*     3.6    55.9    -      +       +      -
    204A  PHE*     3.8    22.9    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  ASP      3.7     3.4    -      -       -      +
    148A  VAL*     4.8     2.0    -      -       +      -
    149A  PHE*     1.3    73.7    -      -       -      +
    151A  LEU*     1.3    68.9    +      -       -      +
    152A  LEU*     3.7     5.5    +      -       -      +
    188A  TYR*     2.7    43.0    +      -       +      +
    189A  MET      3.0     8.4    +      -       -      +
    190A  PRO*     3.3     1.1    -      -       +      +
    191A  PHE*     2.8    34.2    +      -       -      +
    197A  LEU*     3.9     3.1    -      -       -      -
    317A  HIS*     2.8    40.4    +      -       -      -
    321A  ILE*     3.3    20.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  PRO*     4.3     8.1    -      -       +      -
    133A  ILE      3.5    17.0    -      -       -      +
    134A  ASP*     3.2    27.4    +      -       +      -
    150A  ASP*     1.3    84.7    +      -       -      +
    152A  LEU*     1.3    60.3    +      -       -      +
    153A  ASN      3.3    27.8    -      -       -      +
    154A  SER*     4.1    15.0    -      -       -      -
    159A  VAL*     3.8     2.9    -      -       -      +
    191A  PHE      3.9     5.2    -      -       -      +
    193A  ASN*     3.3    12.8    -      -       -      +
    194A  GLU*     3.3    38.4    -      -       +      +
    197A  LEU*     3.8    11.3    -      -       +      +
    313A  ARG*     3.1    21.0    +      -       -      +
----------------------------------------------------------
 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