Contacts of the strand formed by residues 153 - 158 (chain B) in PDB entry 3S3O


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 THR 153 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  VAL*     4.4     0.4    -      -       +      -
    145B  VAL      3.2     9.9    -      -       -      +
    146B  VAL*     3.8     4.6    -      -       +      +
    151B  GLY      3.5    12.0    +      -       -      -
    152B  PHE*     1.3    79.0    -      -       -      +
    154B  TRP*     1.3    65.2    +      -       -      +
    155B  LEU*     3.6    31.0    -      -       +      -
    223B  LYS*     3.6    21.7    -      -       -      +
    227B  ILE*     4.0    15.3    -      -       +      +
    250B  GLN*     3.3     9.2    -      -       +      +
    253B  LEU*     4.3    14.4    -      -       +      +
    254B  ASN*     2.7    34.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  ILE*     3.5    36.1    -      -       +      +
    270A  PHE*     5.9     2.2    -      +       -      -
    122B  PHE*     4.9    10.3    -      +       -      -
    125B  PHE*     3.8    34.8    -      +       -      -
    143B  LEU      3.9     0.9    -      -       -      +
    144B  VAL*     3.7     0.2    -      -       -      -
    145B  VAL*     2.8    53.0    +      -       +      +
    147B  ASP*     4.1     9.2    -      -       +      -
    152B  PHE*     3.8    40.5    -      +       +      -
    153B  THR*     1.3    76.7    -      -       -      +
    155B  LEU*     1.3    64.3    +      -       -      +
    156B  TYR*     3.8    25.4    -      -       +      -
    173B  LEU*     3.5    25.7    -      -       +      +
    176B  ILE*     5.6     9.7    -      -       +      +
    177B  ALA*     5.5     3.8    -      -       +      -
    250B  GLN*     3.2     5.2    -      -       -      -
    269B  LEU*     4.3    15.3    -      -       +      -
    394B  HEZ      4.0     2.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  VAL*     3.9    13.0    -      -       +      -
    143B  LEU      3.5     1.8    -      -       -      -
    144B  VAL*     4.0    26.2    -      -       +      -
    153B  THR*     3.6    21.5    -      -       +      -
    154B  TRP*     1.3    74.8    -      -       -      +
    156B  TYR*     1.3    64.7    +      -       -      +
    157B  PRO*     4.3     1.1    -      -       -      +
    227B  ILE*     4.6    11.4    -      -       +      -
    231B  LEU*     5.7     2.0    -      -       +      -
    246B  LEU*     4.0    26.0    -      -       +      +
    249B  VAL*     3.8    30.3    -      -       +      -
    250B  GLN*     3.3    29.0    +      -       +      +
    253B  LEU*     4.4     3.6    -      -       +      -
    394B  HEZ      2.8    34.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 156 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  VAL*     6.3     0.4    -      -       +      -
    142B  VAL*     3.4     4.9    -      -       -      +
    143B  LEU*     2.7    47.2    +      -       +      +
    145B  VAL*     4.4    14.1    -      -       +      -
    154B  TRP*     3.8    21.8    -      -       +      -
    155B  LEU*     1.3    77.8    -      -       -      +
    157B  PRO*     1.3    70.9    -      -       +      +
    158B  THR*     3.6     0.9    +      -       -      +
    169B  SER*     3.6    37.9    -      -       -      +
    170B  LEU*     5.3     0.4    -      -       +      -
    172B  VAL*     4.2    22.4    -      -       +      +
    173B  LEU*     3.3    45.5    +      -       +      +
    176B  ILE*     5.7     2.3    -      -       -      +
    394B  HEZ      3.3    31.6    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  TYR*     3.7    33.6    -      -       +      -
    141B  TYR      3.3     8.7    -      -       -      +
    142B  VAL*     4.5     0.7    -      -       -      -
    156B  TYR*     1.3    87.0    -      -       +      +
    158B  THR*     1.3    61.8    -      -       -      +
    169B  SER*     4.4     3.8    +      -       -      -
    242B  TRP*     4.3     3.4    -      -       +      -
    243B  TYR*     3.7    25.8    -      -       +      -
    246B  LEU*     3.9    27.1    -      -       +      -
    394B  HEZ      4.1    16.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  TYR*     3.5    23.7    -      -       +      +
    139B  TYR*     3.6    10.8    -      -       -      -
    140B  LEU      3.0    22.5    +      -       -      -
    141B  TYR*     2.9    32.3    +      -       -      +
    143B  LEU*     4.5     1.8    -      -       +      -
    156B  TYR      3.9     7.2    -      -       -      +
    157B  PRO*     1.3    79.8    -      -       -      +
    159B  LYS*     1.3    60.3    +      -       -      +
    160B  ALA      3.0    20.5    +      -       -      -
    165B  ALA*     3.8    13.0    -      -       +      +
    169B  SER*     3.6    20.4    -      -       -      +
----------------------------------------------------------
 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