Contacts of the strand formed by residues 333 - 339 (chain B) in PDB entry 5T4S


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 333 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  TYR*     3.3    56.2    +      -       +      +
    193B  ILE      3.3    11.7    -      -       -      +
    194B  ASN*     3.4    25.0    -      -       -      +
    195B  LEU*     4.1     3.7    -      -       -      +
    201B  TRP*     3.5     6.9    -      -       -      -
    328B  ASP*     2.9    52.4    +      -       +      +
    331B  ASN*     3.6    32.6    -      -       +      +
    332B  ASN*     1.3    77.3    -      -       -      +
    334B  ILE*     1.3    64.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 334 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  HIS      3.7     1.0    -      -       -      +
    192B  TYR*     3.3     4.2    -      -       -      -
    193B  ILE*     2.8    43.0    +      -       -      +
    195B  LEU*     3.7    21.1    -      -       +      -
    201B  TRP*     3.6    25.8    -      -       +      +
    203B  ILE*     4.0    10.3    -      -       +      -
    225B  VAL*     3.6    29.2    -      -       +      -
    325B  THR*     3.5    31.2    -      -       +      -
    326B  GLU      3.3     3.8    -      -       -      +
    327B  PHE*     3.9     7.9    -      -       +      -
    333B  ARG*     1.3    78.8    -      -       -      +
    335B  GLY*     1.3    62.7    +      -       -      +
    336B  PHE*     3.7    20.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 335 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  PHE*     3.8     9.6    -      -       -      -
    191B  HIS      3.4     5.2    -      -       -      -
    192B  TYR*     3.4    28.8    -      -       -      -
    324B  TYR      3.7     0.3    -      -       -      +
    325B  THR*     3.3     6.4    -      -       -      +
    326B  GLU*     2.8    40.0    +      -       -      +
    334B  ILE*     1.3    72.1    -      -       -      +
    336B  PHE*     1.3    62.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 336 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  ASN      4.2     0.9    -      -       -      +
    190B  PHE*     3.4     3.2    -      -       -      -
    191B  HIS*     2.9    29.5    +      -       -      +
    193B  ILE*     3.6    31.9    -      -       +      -
    203B  ILE*     4.2     5.4    -      -       +      -
    225B  VAL*     3.9    20.9    -      -       +      -
    272B  LEU*     4.0    15.9    -      -       +      -
    277B  TYR*     3.5    32.3    +      +       +      +
    315B  LEU*     4.8     0.2    -      -       +      -
    319B  PHE*     3.5    28.9    -      +       -      -
    323B  PHE*     3.9    10.8    -      -       +      -
    324B  TYR      3.4     1.8    -      -       -      -
    325B  THR*     3.3    34.3    -      -       +      -
    334B  ILE*     3.7    17.9    -      -       +      -
    335B  GLY*     1.3    77.2    -      -       -      -
    337B  ALA*     1.3    61.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 337 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  TYR*     4.0    15.9    -      -       +      -
    187B  GLU      3.8    15.9    -      -       -      +
    189B  ASN      3.9    13.0    -      -       -      +
    190B  PHE*     3.7    18.8    -      -       +      -
    277B  TYR*     5.8     0.4    -      -       -      -
    323B  PHE*     3.4     8.5    -      -       -      -
    324B  TYR*     2.8    32.9    +      -       -      +
    336B  PHE*     1.3    76.1    -      -       -      +
    338B  LEU*     1.3    62.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 338 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  ARG*     5.9     1.1    -      -       -      +
    186B  TYR*     3.3     2.6    -      -       -      -
    187B  GLU*     2.8    59.2    +      -       +      +
    322B  LYS*     3.7    42.4    -      -       +      +
    323B  PHE*     4.1    16.4    -      -       +      -
    337B  ALA*     1.3    70.5    -      -       -      +
    339B  ALA*     1.3    69.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 339 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  TYR*     4.2    13.5    -      -       +      -
    164B  ARG*     4.9    10.7    +      -       -      +
    185B  HIS      3.4     9.9    -      -       -      +
    187B  GLU*     5.0     2.3    -      -       -      +
    320B  ILE      4.3     1.6    -      -       -      +
    321B  ARG      3.4    18.8    -      -       -      +
    322B  LYS      2.8    20.6    +      -       -      +
    323B  PHE      4.3     0.2    -      -       -      -
    324B  TYR*     3.6    19.1    -      -       +      +
    337B  ALA      3.2     2.4    +      -       -      -
    338B  LEU*     1.3    82.9    -      -       -      +
    340B  ARG*     1.3    63.9    +      -       -      +
----------------------------------------------------------
 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